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Conserved domains on  [gi|116875838|ref|NP_073601|]
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methenyltetrahydrofolate synthase domain-containing protein isoform 3 [Homo sapiens]

Protein Classification

methenyltetrahydrofolate synthase domain-containing protein( domain architecture ID 10221107)

methenyltetrahydrofolate synthase domain-containing protein (MTHFSD) is a novel RNA-binding protein abnormally regulated in amyotrophic lateral sclerosis

Gene Symbol:  mthfsd
Gene Ontology:  GO:0003723
PubMed:  26525917

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM_MTHFSD cd12270
RNA recognition motif (RRM) found in vertebrate methenyltetrahydrofolate synthetase ...
306-377 2.95e-34

RNA recognition motif (RRM) found in vertebrate methenyltetrahydrofolate synthetase domain-containing proteins; This subfamily corresponds to methenyltetrahydrofolate synthetase domain (MTHFSD), a putative RNA-binding protein found in various vertebrate species. It contains an N-terminal 5-formyltetrahydrofolate cyclo-ligase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of MTHFSD remains unclear.


:

Pssm-ID: 409713 [Multi-domain]  Cd Length: 72  Bit Score: 121.27  E-value: 2.95e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116875838 306 DVYVGNLPGDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 377
Cdd:cd12270    1 TVYVGNIPRSVRVSDLKSALRERGINPLRITWQGARGKAFLHYSDMADADSAVSSLQGLRIGGNTLTVELAK 72
5-FTHF_cyc-lig super family cl00360
5-formyltetrahydrofolate cyclo-ligase family; 5-formyltetrahydrofolate cyclo-ligase or ...
9-206 1.90e-32

5-formyltetrahydrofolate cyclo-ligase family; 5-formyltetrahydrofolate cyclo-ligase or methenyl-THF synthetase EC:6.3.3.2 catalyzes the interchange of 5-formyltetrahydrofolate (5-FTHF) to 5-10-methenyltetrahydrofolate, this requires ATP and Mg2+. 5-FTHF is used in chemotherapy where it is clinically known as Leucovorin.


The actual alignment was detected with superfamily member pfam01812:

Pssm-ID: 444864 [Multi-domain]  Cd Length: 186  Bit Score: 120.49  E-value: 1.90e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116875838    9 KQDIREQI---WGYMESQNLADFPRPVHHRIPNFKGSylacQNIKDLDVFartqeVKVDPDKPLEGVRLLVLQSKKTLLV 85
Cdd:pfam01812   1 KQELRKQLlarRRALSEEERAAQSEALHQRLISLPEY----QKAKRVAAY-----VSVGGEIDTRELIDLLLEEGKRVLL 71
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116875838   86 PTPRLRTGLFN--KITPPPGATKDILRKCATSQGVRNYSVPIGLDsrvLVDLVVVGSVAVSEKGWRIGKGEGYADLEYAM 163
Cdd:pfam01812  72 PVPRPGSGHLDmvRFTPYYPEDSLPRGAWGLKEPVEEELRELALG---QLDLVLVPGVAFDRQGYRLGRGGGYYDRYLAR 148
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 116875838  164 MVSMGAvsKETPVVTIVHDCQVVDIPeelVEEHDITVDYILTP 206
Cdd:pfam01812 149 LQGHGA--KPYTVGLAFDEQLVERLP---VEPHDVPVDEVVTE 186
 
Name Accession Description Interval E-value
RRM_MTHFSD cd12270
RNA recognition motif (RRM) found in vertebrate methenyltetrahydrofolate synthetase ...
306-377 2.95e-34

RNA recognition motif (RRM) found in vertebrate methenyltetrahydrofolate synthetase domain-containing proteins; This subfamily corresponds to methenyltetrahydrofolate synthetase domain (MTHFSD), a putative RNA-binding protein found in various vertebrate species. It contains an N-terminal 5-formyltetrahydrofolate cyclo-ligase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of MTHFSD remains unclear.


Pssm-ID: 409713 [Multi-domain]  Cd Length: 72  Bit Score: 121.27  E-value: 2.95e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116875838 306 DVYVGNLPGDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 377
Cdd:cd12270    1 TVYVGNIPRSVRVSDLKSALRERGINPLRITWQGARGKAFLHYSDMADADSAVSSLQGLRIGGNTLTVELAK 72
5-FTHF_cyc-lig pfam01812
5-formyltetrahydrofolate cyclo-ligase family; 5-formyltetrahydrofolate cyclo-ligase or ...
9-206 1.90e-32

5-formyltetrahydrofolate cyclo-ligase family; 5-formyltetrahydrofolate cyclo-ligase or methenyl-THF synthetase EC:6.3.3.2 catalyzes the interchange of 5-formyltetrahydrofolate (5-FTHF) to 5-10-methenyltetrahydrofolate, this requires ATP and Mg2+. 5-FTHF is used in chemotherapy where it is clinically known as Leucovorin.


Pssm-ID: 396398 [Multi-domain]  Cd Length: 186  Bit Score: 120.49  E-value: 1.90e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116875838    9 KQDIREQI---WGYMESQNLADFPRPVHHRIPNFKGSylacQNIKDLDVFartqeVKVDPDKPLEGVRLLVLQSKKTLLV 85
Cdd:pfam01812   1 KQELRKQLlarRRALSEEERAAQSEALHQRLISLPEY----QKAKRVAAY-----VSVGGEIDTRELIDLLLEEGKRVLL 71
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116875838   86 PTPRLRTGLFN--KITPPPGATKDILRKCATSQGVRNYSVPIGLDsrvLVDLVVVGSVAVSEKGWRIGKGEGYADLEYAM 163
Cdd:pfam01812  72 PVPRPGSGHLDmvRFTPYYPEDSLPRGAWGLKEPVEEELRELALG---QLDLVLVPGVAFDRQGYRLGRGGGYYDRYLAR 148
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 116875838  164 MVSMGAvsKETPVVTIVHDCQVVDIPeelVEEHDITVDYILTP 206
Cdd:pfam01812 149 LQGHGA--KPYTVGLAFDEQLVERLP---VEPHDVPVDEVVTE 186
FAU1 COG0212
5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism];
133-209 2.92e-12

5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism];


Pssm-ID: 439982 [Multi-domain]  Cd Length: 186  Bit Score: 64.79  E-value: 2.92e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116875838 133 VDLVVVGSVAVSEKGWRIGKGEGYAD--LEyammvsmgAVSKETPVVTIVHDCQVVD-IPeelVEEHDITVDYILTPTRV 209
Cdd:COG0212  118 IDLVLVPLLAFDRRGYRLGYGGGYYDrtLA--------RLRPRPLTIGLAFDCQLVDeLP---VEPHDVPLDAIVTEKGV 186
MTHFS_bact TIGR02727
5,10-methenyltetrahydrofolate synthetase; This enzyme, 5,10-methenyltetrahydrofolate ...
77-206 2.29e-10

5,10-methenyltetrahydrofolate synthetase; This enzyme, 5,10-methenyltetrahydrofolate synthetase, is also called 5-formyltetrahydrofolate cycloligase. Function of bacterial proteins in this family was inferred originally from the known activity of eukaryotic homologs. Recently, activity was shown explicitly for the member from Mycoplasma pneumonia. Members of this family from alpha- and gamma-proteobacteria, designated ygfA, are often found in an operon with 6S structural RNA, and show a similar pattern of high expression during stationary phase. The function may be to deplete folate to slow 1-carbon biosynthetic metabolism. [Central intermediary metabolism, One-carbon metabolism]


Pssm-ID: 274270 [Multi-domain]  Cd Length: 179  Bit Score: 59.21  E-value: 2.29e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116875838   77 LQSKKTLLVP--TPRLRTGLFNKITPPpgatKDILRKcatsqGVRNYSVPIGLDSRVL----VDLVVVGSVAVSEKGWRI 150
Cdd:TIGR02727  63 LKEGKRVALPkvDPDGKEMLFFRIWSP----EQLLTK-----GPFGILEPVGDLEEPVppdeIDLIIVPGVAFDRRGYRL 133
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 116875838  151 GKGEGYADLEYAMMvsmgavskETPVVTIVHDCQVVD-IPeelVEEHDITVDYILTP 206
Cdd:TIGR02727 134 GYGGGYYDRFLARL--------KGITIGLAFDFQLVDeLP---REPHDVPVDAIITE 179
RRM smart00360
RNA recognition motif;
307-373 3.21e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 50.28  E-value: 3.21e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116875838   307 VYVGNLPGDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV 373
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVesvrlVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
307-372 4.16e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 44.15  E-value: 4.16e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 116875838  307 VYVGNLPGDARVSDLKRALRELGSV-----PLRLTWQgPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLR 372
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIksirlVRDETGR-SKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
PLN02812 PLN02812
5-formyltetrahydrofolate cyclo-ligase
133-210 2.73e-05

5-formyltetrahydrofolate cyclo-ligase


Pssm-ID: 178408  Cd Length: 211  Bit Score: 44.64  E-value: 2.73e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116875838 133 VDLVVVGSVAVSEKGWRIGKGEGYADleyAMMVSMGAVSKET-----PVVTIVHDCQVVDIPEELVEEHDITVDYILTPT 207
Cdd:PLN02812 132 LDLLLLPGLAFDRSGRRLGRGGGYYD---TFLSKYQELAKEKgwkqpLLVALSYSPQILDEGSVPVDETDVLVDALVTPS 208

                 ...
gi 116875838 208 RVI 210
Cdd:PLN02812 209 GVI 211
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
308-382 7.84e-05

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 40.85  E-value: 7.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116875838 308 YVGNLPGDARVSDLKRALRELGSV------PLRLTwQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD 381
Cdd:COG0724    5 YVGNLPYSVTEEDLRELFSEYGEVtsvkliTDRET-GRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPREE 83

                 .
gi 116875838 382 K 382
Cdd:COG0724   84 R 84
 
Name Accession Description Interval E-value
RRM_MTHFSD cd12270
RNA recognition motif (RRM) found in vertebrate methenyltetrahydrofolate synthetase ...
306-377 2.95e-34

RNA recognition motif (RRM) found in vertebrate methenyltetrahydrofolate synthetase domain-containing proteins; This subfamily corresponds to methenyltetrahydrofolate synthetase domain (MTHFSD), a putative RNA-binding protein found in various vertebrate species. It contains an N-terminal 5-formyltetrahydrofolate cyclo-ligase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of MTHFSD remains unclear.


Pssm-ID: 409713 [Multi-domain]  Cd Length: 72  Bit Score: 121.27  E-value: 2.95e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116875838 306 DVYVGNLPGDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 377
Cdd:cd12270    1 TVYVGNIPRSVRVSDLKSALRERGINPLRITWQGARGKAFLHYSDMADADSAVSSLQGLRIGGNTLTVELAK 72
5-FTHF_cyc-lig pfam01812
5-formyltetrahydrofolate cyclo-ligase family; 5-formyltetrahydrofolate cyclo-ligase or ...
9-206 1.90e-32

5-formyltetrahydrofolate cyclo-ligase family; 5-formyltetrahydrofolate cyclo-ligase or methenyl-THF synthetase EC:6.3.3.2 catalyzes the interchange of 5-formyltetrahydrofolate (5-FTHF) to 5-10-methenyltetrahydrofolate, this requires ATP and Mg2+. 5-FTHF is used in chemotherapy where it is clinically known as Leucovorin.


Pssm-ID: 396398 [Multi-domain]  Cd Length: 186  Bit Score: 120.49  E-value: 1.90e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116875838    9 KQDIREQI---WGYMESQNLADFPRPVHHRIPNFKGSylacQNIKDLDVFartqeVKVDPDKPLEGVRLLVLQSKKTLLV 85
Cdd:pfam01812   1 KQELRKQLlarRRALSEEERAAQSEALHQRLISLPEY----QKAKRVAAY-----VSVGGEIDTRELIDLLLEEGKRVLL 71
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116875838   86 PTPRLRTGLFN--KITPPPGATKDILRKCATSQGVRNYSVPIGLDsrvLVDLVVVGSVAVSEKGWRIGKGEGYADLEYAM 163
Cdd:pfam01812  72 PVPRPGSGHLDmvRFTPYYPEDSLPRGAWGLKEPVEEELRELALG---QLDLVLVPGVAFDRQGYRLGRGGGYYDRYLAR 148
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 116875838  164 MVSMGAvsKETPVVTIVHDCQVVDIPeelVEEHDITVDYILTP 206
Cdd:pfam01812 149 LQGHGA--KPYTVGLAFDEQLVERLP---VEPHDVPVDEVVTE 186
FAU1 COG0212
5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism];
133-209 2.92e-12

5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism];


Pssm-ID: 439982 [Multi-domain]  Cd Length: 186  Bit Score: 64.79  E-value: 2.92e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116875838 133 VDLVVVGSVAVSEKGWRIGKGEGYAD--LEyammvsmgAVSKETPVVTIVHDCQVVD-IPeelVEEHDITVDYILTPTRV 209
Cdd:COG0212  118 IDLVLVPLLAFDRRGYRLGYGGGYYDrtLA--------RLRPRPLTIGLAFDCQLVDeLP---VEPHDVPLDAIVTEKGV 186
MTHFS_bact TIGR02727
5,10-methenyltetrahydrofolate synthetase; This enzyme, 5,10-methenyltetrahydrofolate ...
77-206 2.29e-10

5,10-methenyltetrahydrofolate synthetase; This enzyme, 5,10-methenyltetrahydrofolate synthetase, is also called 5-formyltetrahydrofolate cycloligase. Function of bacterial proteins in this family was inferred originally from the known activity of eukaryotic homologs. Recently, activity was shown explicitly for the member from Mycoplasma pneumonia. Members of this family from alpha- and gamma-proteobacteria, designated ygfA, are often found in an operon with 6S structural RNA, and show a similar pattern of high expression during stationary phase. The function may be to deplete folate to slow 1-carbon biosynthetic metabolism. [Central intermediary metabolism, One-carbon metabolism]


Pssm-ID: 274270 [Multi-domain]  Cd Length: 179  Bit Score: 59.21  E-value: 2.29e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116875838   77 LQSKKTLLVP--TPRLRTGLFNKITPPpgatKDILRKcatsqGVRNYSVPIGLDSRVL----VDLVVVGSVAVSEKGWRI 150
Cdd:TIGR02727  63 LKEGKRVALPkvDPDGKEMLFFRIWSP----EQLLTK-----GPFGILEPVGDLEEPVppdeIDLIIVPGVAFDRRGYRL 133
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 116875838  151 GKGEGYADLEYAMMvsmgavskETPVVTIVHDCQVVD-IPeelVEEHDITVDYILTP 206
Cdd:TIGR02727 134 GYGGGYYDRFLARL--------KGITIGLAFDFQLVDeLP---REPHDVPVDAIITE 179
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
307-373 4.90e-09

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 52.29  E-value: 4.90e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 116875838 307 VYVGNLPGDARVSDLKRALRELGSV----PLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV 373
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVvsvrIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKV 71
RRM smart00360
RNA recognition motif;
307-373 3.21e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 50.28  E-value: 3.21e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116875838   307 VYVGNLPGDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV 373
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVesvrlVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
307-377 1.03e-06

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 45.70  E-value: 1.03e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 116875838 307 VYVGNLPGDARVSDLKRALRELGsvPLRLTW--QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 377
Cdd:cd12373    2 VYVGNLGPRVTKRELEDAFEKYG--PLRNVWvaRNPPGFAFVEFEDPRDAEDAVRALDGRRICGSRVRVELSR 72
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
307-372 4.16e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 44.15  E-value: 4.16e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 116875838  307 VYVGNLPGDARVSDLKRALRELGSV-----PLRLTWQgPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLR 372
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIksirlVRDETGR-SKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
307-376 8.99e-06

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 43.27  E-value: 8.99e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 116875838 307 VYVGNLPGDARVSDLKRALRELGSV-PLRL-----TWQgPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA 376
Cdd:cd12398    3 VFVGNIPYDATEEQLKEIFSEVGPVvSFRLvtdreTGK-PKGYGFCEFRDAETALSAVRNLNGYELNGRPLRVDFA 77
PLN02812 PLN02812
5-formyltetrahydrofolate cyclo-ligase
133-210 2.73e-05

5-formyltetrahydrofolate cyclo-ligase


Pssm-ID: 178408  Cd Length: 211  Bit Score: 44.64  E-value: 2.73e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116875838 133 VDLVVVGSVAVSEKGWRIGKGEGYADleyAMMVSMGAVSKET-----PVVTIVHDCQVVDIPEELVEEHDITVDYILTPT 207
Cdd:PLN02812 132 LDLLLLPGLAFDRSGRRLGRGGGYYD---TFLSKYQELAKEKgwkqpLLVALSYSPQILDEGSVPVDETDVLVDALVTPS 208

                 ...
gi 116875838 208 RVI 210
Cdd:PLN02812 209 GVI 211
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
308-382 7.84e-05

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 40.85  E-value: 7.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116875838 308 YVGNLPGDARVSDLKRALRELGSV------PLRLTwQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD 381
Cdd:COG0724    5 YVGNLPYSVTEEDLRELFSEYGEVtsvkliTDRET-GRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPREE 83

                 .
gi 116875838 382 K 382
Cdd:COG0724   84 R 84
RRM_SRSF3 cd12645
RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 3 (SRSF3); ...
302-380 1.21e-04

RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 3 (SRSF3); This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 241089 [Multi-domain]  Cd Length: 81  Bit Score: 40.41  E-value: 1.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116875838 302 PLAADVYVGNLPGDARVSDLKRALRELGsvPLRLTW--QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 379
Cdd:cd12645    2 PLDCKVYVGNLGNNGNKTELERAFGYYG--PLRSVWvaRNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE 79

                 .
gi 116875838 380 R 380
Cdd:cd12645   80 K 80
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
307-373 1.95e-04

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 39.43  E-value: 1.95e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116875838 307 VYVGNLPGDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV 373
Cdd:cd12399    1 LYVGNLPYSASEEQLKSLFGQFGAVfdvklPMDRETKRPRGFGFVELQEEESAEKAIAKLDGTDFMGRTIRV 72
RRM1_SRSF1_like cd12338
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
307-375 2.38e-04

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues.


Pssm-ID: 409775 [Multi-domain]  Cd Length: 72  Bit Score: 39.27  E-value: 2.38e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116875838 307 VYVGNLPGDARVSDLKRALRELGSVpLRLTWQGPRRR---AFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL 375
Cdd:cd12338    2 IYVGNLPGDIRERDIEDLFYKYGPI-LAIDLKNRRRGppfAFVEFEDPRDAEDAIRGRDGYDFDGYRLRVEF 72
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
307-377 2.44e-04

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.


Pssm-ID: 409673 [Multi-domain]  Cd Length: 77  Bit Score: 39.10  E-value: 2.44e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 116875838 307 VYVGNLPGDARVSDLKRALRELGSV-PLRL---TWQGPRRRAFLHY-PDSAAAQQAVSCLQGLRLGTDTLRVALAR 377
Cdd:cd12226    2 LFVGGLSPSITEDDLERRFSRFGTVsDVEIirkKDAPDRGFAYIDLrTSEAALQKCLSTLNGVKWKGSRLKIQLAK 77
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ...
307-373 3.00e-04

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64.


Pssm-ID: 410072 [Multi-domain]  Cd Length: 85  Bit Score: 39.42  E-value: 3.00e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116875838 307 VYVGNLPGDARVSDLKRALRELGSV-PLRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV 373
Cdd:cd12671    9 VFVGNIPYEATEEQLKDIFSEVGPVvSFRLVYDretgKPKGYGFCEYQDQETALSAMRNLNGYELNGRALRV 80
RRM_SRSF7 cd12646
RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 7 (SRSF7); ...
307-376 1.48e-03

RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 7 (SRSF7); This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 410050 [Multi-domain]  Cd Length: 77  Bit Score: 37.25  E-value: 1.48e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116875838 307 VYVGNLPGDARVSDLKRALRELGsvPLRLTW--QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA 376
Cdd:cd12646    2 VYVGNLGTGAGKGELERAFSYYG--PLRTVWiaRNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS 71
PRK10333 PRK10333
5-formyltetrahydrofolate cyclo-ligase family protein; Provisional
133-209 2.13e-03

5-formyltetrahydrofolate cyclo-ligase family protein; Provisional


Pssm-ID: 182385  Cd Length: 182  Bit Score: 38.76  E-value: 2.13e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 116875838 133 VDLVVVGSVAVSEKGWRIGKGEGYADLEYAMMVSMGAvskeTPVvTIVHDCQVVD-IPeelVEEHDITVDYILTPTRV 209
Cdd:PRK10333 110 LDVLITPLVAFDEYGQRLGMGGGFYDRTLQNWQHYKT----QPV-GYAHDCQLVEkLP---VEEWDIPLPAVVTPSKV 179
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
307-376 3.26e-03

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 35.99  E-value: 3.26e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 116875838 307 VYVGNLPGDARVSDLKRALRELG---SVPL---RLTwqGpRRR--AFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA 376
Cdd:cd21608    2 LYVGNLSWDTTEDDLRDLFSEFGeveSAKVitdRET--G-RSRgfGFVTFSTAEAAEAAIDALNGKELDGRSIVVNEA 76
RRM3_Spen cd12310
RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily ...
307-373 3.92e-03

RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409750 [Multi-domain]  Cd Length: 72  Bit Score: 35.72  E-value: 3.92e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 116875838 307 VYVGNLPGDARVSDLKRALRELGSvPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV 373
Cdd:cd12310    1 LWVGGLGPWTSLAELEREFDRFGA-IRKIDYRKGDDYAYILYESLDAAQAAVRALRGFPLGGPDRRL 66
RRM1_HuD cd12770
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup ...
344-377 4.69e-03

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410163 [Multi-domain]  Cd Length: 81  Bit Score: 35.85  E-value: 4.69e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 116875838 344 AFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 377
Cdd:cd12770   46 GFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR 79
RRM1_Hu cd12650
RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to ...
344-376 8.35e-03

RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410053 [Multi-domain]  Cd Length: 77  Bit Score: 35.07  E-value: 8.35e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 116875838 344 AFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA 376
Cdd:cd12650   45 GFVNYVDPSDAEKAINTLNGLRLQNKTIKVSYA 77
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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