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Conserved domains on  [gi|617644055|ref|XP_007532319|]
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DNA-directed RNA polymerase I subunit RPA43 [Erinaceus europaeus]

Protein Classification

DNA-directed RNA polymerase I subunit RPA43 family protein( domain architecture ID 14394049)

DNA-directed RNA polymerase subunit similar to Saccharomyces cerevisiae DNA-directed RNA polymerase I subunit Rpa43

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNAP_I_Rpa43_N cd04328
RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of ...
 36-122 1.75e-35

RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, involved in recruiting RNAP I to the pol I promoter.


:

Pssm-ID: 239820  Cd Length: 89  Bit Score: 123.88  E-value: 1.75e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 617644055  36 LVNNPYSCLVVGPHRRHIALSPRYLNRKRTGIREQLDAELLRYSESLLGVPIAYDNIKVV-GELGDIYDDQGHIHLNIEA 114
Cdd:cd04328    1 LGAGPYSCFETLTVSLYVSLAPKYLGNPLTGIKAQLLNPLLKYSPKLKGVVLAYSNIKLLeGELAKIVDDSPFIFVWISA 80


                 ....*...
gi 617644055 115 DFVIFCPE 122
Cdd:cd04328   81 DFLVFRPK 88
RPA43_OB super family cl39351
RPA43 OB domain in RNA Pol I; This is OB domain found in RPA43 proteins (DNA-directed RNA ...
 121-153 6.33e-10

RPA43 OB domain in RNA Pol I; This is OB domain found in RPA43 proteins (DNA-directed RNA polymerase I subunit RPA43, also known as A43) in yeast. Functional analysis of RNA polymerase I show that, subunits A14 and A43 form the heterodimer A14/43, which is distantly related to Rpb4/7 in Pol II and C17/25 in Pol III. Crystal structure analysis show that A43-A14 heterodimer forms the stalk that provides a platform for initiation factors and interacts with newly synthesized RNA.


The actual alignment was detected with superfamily member pfam17875:

Pssm-ID: 465545  Cd Length: 114  Bit Score: 55.84  E-value: 6.33e-10
                          10        20        30
                  ....*....|....*....|....*....|...
gi 617644055  121 PEPGQKLLGTVNKVSSSHIGCLVHRCFNASIPK 153
Cdd:pfam17875   1 PRVGMRLEGRINLQSPSHIGLLVYNTFNASIPA 33
 
Name Accession Description Interval E-value
RNAP_I_Rpa43_N cd04328
RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of ...
 36-122 1.75e-35

RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, involved in recruiting RNAP I to the pol I promoter.


Pssm-ID: 239820  Cd Length: 89  Bit Score: 123.88  E-value: 1.75e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 617644055  36 LVNNPYSCLVVGPHRRHIALSPRYLNRKRTGIREQLDAELLRYSESLLGVPIAYDNIKVV-GELGDIYDDQGHIHLNIEA 114
Cdd:cd04328    1 LGAGPYSCFETLTVSLYVSLAPKYLGNPLTGIKAQLLNPLLKYSPKLKGVVLAYSNIKLLeGELAKIVDDSPFIFVWISA 80


                 ....*...
gi 617644055 115 DFVIFCPE 122
Cdd:cd04328   81 DFLVFRPK 88
RPA43_OB pfam17875
RPA43 OB domain in RNA Pol I; This is OB domain found in RPA43 proteins (DNA-directed RNA ...
 121-153 6.33e-10

RPA43 OB domain in RNA Pol I; This is OB domain found in RPA43 proteins (DNA-directed RNA polymerase I subunit RPA43, also known as A43) in yeast. Functional analysis of RNA polymerase I show that, subunits A14 and A43 form the heterodimer A14/43, which is distantly related to Rpb4/7 in Pol II and C17/25 in Pol III. Crystal structure analysis show that A43-A14 heterodimer forms the stalk that provides a platform for initiation factors and interacts with newly synthesized RNA.


Pssm-ID: 465545  Cd Length: 114  Bit Score: 55.84  E-value: 6.33e-10
                          10        20        30
                  ....*....|....*....|....*....|...
gi 617644055  121 PEPGQKLLGTVNKVSSSHIGCLVHRCFNASIPK 153
Cdd:pfam17875   1 PRVGMRLEGRINLQSPSHIGLLVYNTFNASIPA 33
SHS2_Rpb7-N pfam03876
SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a ...
 50-106 5.72e-04

SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction.


Pssm-ID: 427560 [Multi-domain]  Cd Length: 57  Bit Score: 37.50  E-value: 5.72e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 617644055   50 RRHIALSPRYLNRKRTGIREqlDAELLRYSESL---LGVPIAYDNIKVVGElGDIYDDQG 106
Cdd:pfam03876   1 EDTVRLPPSYLGNPLKGAIE--DKLLEKYEGKVdkdLGVVIAVLDIKEIGE-GKILPGDG 57
 
Name Accession Description Interval E-value
RNAP_I_Rpa43_N cd04328
RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of ...
 36-122 1.75e-35

RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, involved in recruiting RNAP I to the pol I promoter.


Pssm-ID: 239820  Cd Length: 89  Bit Score: 123.88  E-value: 1.75e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 617644055  36 LVNNPYSCLVVGPHRRHIALSPRYLNRKRTGIREQLDAELLRYSESLLGVPIAYDNIKVV-GELGDIYDDQGHIHLNIEA 114
Cdd:cd04328    1 LGAGPYSCFETLTVSLYVSLAPKYLGNPLTGIKAQLLNPLLKYSPKLKGVVLAYSNIKLLeGELAKIVDDSPFIFVWISA 80


                 ....*...
gi 617644055 115 DFVIFCPE 122
Cdd:cd04328   81 DFLVFRPK 88
RPA43_OB pfam17875
RPA43 OB domain in RNA Pol I; This is OB domain found in RPA43 proteins (DNA-directed RNA ...
 121-153 6.33e-10

RPA43 OB domain in RNA Pol I; This is OB domain found in RPA43 proteins (DNA-directed RNA polymerase I subunit RPA43, also known as A43) in yeast. Functional analysis of RNA polymerase I show that, subunits A14 and A43 form the heterodimer A14/43, which is distantly related to Rpb4/7 in Pol II and C17/25 in Pol III. Crystal structure analysis show that A43-A14 heterodimer forms the stalk that provides a platform for initiation factors and interacts with newly synthesized RNA.


Pssm-ID: 465545  Cd Length: 114  Bit Score: 55.84  E-value: 6.33e-10
                          10        20        30
                  ....*....|....*....|....*....|...
gi 617644055  121 PEPGQKLLGTVNKVSSSHIGCLVHRCFNASIPK 153
Cdd:pfam17875   1 PRVGMRLEGRINLQSPSHIGLLVYNTFNASIPA 33
SHS2_Rpb7-N pfam03876
SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a ...
 50-106 5.72e-04

SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction.


Pssm-ID: 427560 [Multi-domain]  Cd Length: 57  Bit Score: 37.50  E-value: 5.72e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 617644055   50 RRHIALSPRYLNRKRTGIREqlDAELLRYSESL---LGVPIAYDNIKVVGElGDIYDDQG 106
Cdd:pfam03876   1 EDTVRLPPSYLGNPLKGAIE--DKLLEKYEGKVdkdLGVVIAVLDIKEIGE-GKILPGDG 57
 
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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