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Conserved domains on  [gi|1829010880|ref|NP_001366453|]
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transcription termination factor 2, mitochondrial precursor [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
mTERF super family cl47744
mTERF; This family contains one sequence of known function Human mitochondrial transcription ...
58-360 6.09e-12

mTERF; This family contains one sequence of known function Human mitochondrial transcription termination factor (mTERF) the rest of the family consists of hypothetical proteins none of which have any functional information. mTERF is a multizipper protein possessing three putative leucine zippers one of which is bipartite. The protein binds DNA as a monomer. The leucine zippers are not implicated in a dimerization role as in other leucine zippers.


The actual alignment was detected with superfamily member pfam02536:

Pssm-ID: 460581 [Multi-domain]  Cd Length: 313  Bit Score: 65.70  E-value: 6.09e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829010880  58 DIRKIRRLKGWVLLEE-ETYVEEIANILKELGANKTVIASILERCPEAIICS-PAAVNTKRKLWQMVCKNEAELVQLIEQ 135
Cdd:pfam02536  13 QISKILTRYPPVLHADvEKDLAPKLQFLLSLGASSSDLGKILSKYPRILGFKlEETMSTSVDFLKEIGVDKSSIGGALRS 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829010880 136 FPEsFFTVKNQENQKLNVQFFQELGLRNVVISRFLTTASSI--FHNPVENNKQMIGVLQESYLNLGGSEANakVWllKLL 213
Cdd:pfam02536  93 WPS-ILGMRVGNNIKNNVEYLRELGVPQKLLARLLISRPQLlaLDLVYLMKPKTFEEKVEFLKELGFSVED--VW--KII 167
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829010880 214 SQNPFIVLHSPRA-VGETLKCLQGQGFTDSEVLQLLSKLKGFLfQLQPGSIQNSISFTKTtFECTDYDLRQLVVKCPALL 292
Cdd:pfam02536 168 KKCPEILGLSIEKkLKKKIEFLKKCGLSEEELPRVIKKYPQIL-SLSERTILNRVEFLLG-LGFSKEEVAKMVKRFPQLL 245
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1829010880 293 CYPASVLEERIQALLKE-GISIAQIRESPMV----LELTpqiIQYRIRKLNSLGYgikDGHLAS-LNGTKKEFE 360
Cdd:pfam02536 246 GLSIEVLKPKLEFLVKEmKWPLKEVVEYPRVfgysLEKR---IKPRIKALVSKGL---ECSLSWmLACSDERFL 313
RING_Ubox super family cl17238
RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger ...
3-24 7.64e-03

RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type RING fingers are closely related to RING-HC fingers. In contrast, C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type RING fingers are more closely related to RING-H2 fingers. However, not all RING finger-containing proteins display regular RING finger features, and the RING finger family has turned out to be multifarious. The degenerate RING fingers of the Siz/PIAS RING (SP-RING) family proteins and sporulation protein RMD5, are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues. They bind only one Zn2+ ion. On the other hand, the RING fingers of the human APC11 and RBX1 proteins can bind a third Zn atom since they harbor four additional Zn ligands. U-box is a modified form of the RING finger domain that lacks metal chelating Cys and His residues. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. RING finger/U-box-containing proteins are a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enable efficient transfer of ubiquitin from E2 to the substrates.


The actual alignment was detected with superfamily member cd16537:

Pssm-ID: 473075  Cd Length: 52  Bit Score: 34.34  E-value: 7.64e-03
                          10        20
                  ....*....|....*....|..
gi 1829010880   3 WRLPTGHQLCRLCLLRKPRPAL 24
Cdd:cd16537    20 YRLPCGHLLCRPCLAEKQKSLA 41
 
Name Accession Description Interval E-value
mTERF pfam02536
mTERF; This family contains one sequence of known function Human mitochondrial transcription ...
58-360 6.09e-12

mTERF; This family contains one sequence of known function Human mitochondrial transcription termination factor (mTERF) the rest of the family consists of hypothetical proteins none of which have any functional information. mTERF is a multizipper protein possessing three putative leucine zippers one of which is bipartite. The protein binds DNA as a monomer. The leucine zippers are not implicated in a dimerization role as in other leucine zippers.


Pssm-ID: 460581 [Multi-domain]  Cd Length: 313  Bit Score: 65.70  E-value: 6.09e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829010880  58 DIRKIRRLKGWVLLEE-ETYVEEIANILKELGANKTVIASILERCPEAIICS-PAAVNTKRKLWQMVCKNEAELVQLIEQ 135
Cdd:pfam02536  13 QISKILTRYPPVLHADvEKDLAPKLQFLLSLGASSSDLGKILSKYPRILGFKlEETMSTSVDFLKEIGVDKSSIGGALRS 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829010880 136 FPEsFFTVKNQENQKLNVQFFQELGLRNVVISRFLTTASSI--FHNPVENNKQMIGVLQESYLNLGGSEANakVWllKLL 213
Cdd:pfam02536  93 WPS-ILGMRVGNNIKNNVEYLRELGVPQKLLARLLISRPQLlaLDLVYLMKPKTFEEKVEFLKELGFSVED--VW--KII 167
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829010880 214 SQNPFIVLHSPRA-VGETLKCLQGQGFTDSEVLQLLSKLKGFLfQLQPGSIQNSISFTKTtFECTDYDLRQLVVKCPALL 292
Cdd:pfam02536 168 KKCPEILGLSIEKkLKKKIEFLKKCGLSEEELPRVIKKYPQIL-SLSERTILNRVEFLLG-LGFSKEEVAKMVKRFPQLL 245
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1829010880 293 CYPASVLEERIQALLKE-GISIAQIRESPMV----LELTpqiIQYRIRKLNSLGYgikDGHLAS-LNGTKKEFE 360
Cdd:pfam02536 246 GLSIEVLKPKLEFLVKEmKWPLKEVVEYPRVfgysLEKR---IKPRIKALVSKGL---ECSLSWmLACSDERFL 313
RING-HC_RNF37 cd16537
RING finger, HC subclass, found in RING finger protein 37 (RNF37); RNF37, also known as ...
3-24 7.64e-03

RING finger, HC subclass, found in RING finger protein 37 (RNF37); RNF37, also known as KIAA0860, U-box domain-containing protein 5 (UBOX5), UbcM4-interacting protein 5 (UIP5), or ubiquitin-conjugating enzyme 7-interacting protein 5, is an E3 ubiquitin-protein ligase found exclusively in the nucleus as part of a nuclear dot-like structure. It interacts with the molecular chaperone VCP/p97 protein. RNF37 contains a U-box domain followed by a potential nuclear location signal (NLS) and a C-terminal C3HC4-type RING-HC finger. The U-box domain is a modified RING finger domain that lacks the hallmark metal-chelating cysteines and histidines of the latter, and is likely to adopt a RING finger-like conformation. The presence of the U-box, but not of the RING finger, is required for the E3 activity. The U-box domain can directly interact with several E2 enzymes, including UbcM2, UbcM3, UbcM4, UbcH5, and UbcH8, suggesting a similar function as the RING finger in the ubiquitination pathway. This model corresponds to the RING-HC finger.


Pssm-ID: 438199  Cd Length: 52  Bit Score: 34.34  E-value: 7.64e-03
                          10        20
                  ....*....|....*....|..
gi 1829010880   3 WRLPTGHQLCRLCLLRKPRPAL 24
Cdd:cd16537    20 YRLPCGHLLCRPCLAEKQKSLA 41
 
Name Accession Description Interval E-value
mTERF pfam02536
mTERF; This family contains one sequence of known function Human mitochondrial transcription ...
58-360 6.09e-12

mTERF; This family contains one sequence of known function Human mitochondrial transcription termination factor (mTERF) the rest of the family consists of hypothetical proteins none of which have any functional information. mTERF is a multizipper protein possessing three putative leucine zippers one of which is bipartite. The protein binds DNA as a monomer. The leucine zippers are not implicated in a dimerization role as in other leucine zippers.


Pssm-ID: 460581 [Multi-domain]  Cd Length: 313  Bit Score: 65.70  E-value: 6.09e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829010880  58 DIRKIRRLKGWVLLEE-ETYVEEIANILKELGANKTVIASILERCPEAIICS-PAAVNTKRKLWQMVCKNEAELVQLIEQ 135
Cdd:pfam02536  13 QISKILTRYPPVLHADvEKDLAPKLQFLLSLGASSSDLGKILSKYPRILGFKlEETMSTSVDFLKEIGVDKSSIGGALRS 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829010880 136 FPEsFFTVKNQENQKLNVQFFQELGLRNVVISRFLTTASSI--FHNPVENNKQMIGVLQESYLNLGGSEANakVWllKLL 213
Cdd:pfam02536  93 WPS-ILGMRVGNNIKNNVEYLRELGVPQKLLARLLISRPQLlaLDLVYLMKPKTFEEKVEFLKELGFSVED--VW--KII 167
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829010880 214 SQNPFIVLHSPRA-VGETLKCLQGQGFTDSEVLQLLSKLKGFLfQLQPGSIQNSISFTKTtFECTDYDLRQLVVKCPALL 292
Cdd:pfam02536 168 KKCPEILGLSIEKkLKKKIEFLKKCGLSEEELPRVIKKYPQIL-SLSERTILNRVEFLLG-LGFSKEEVAKMVKRFPQLL 245
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1829010880 293 CYPASVLEERIQALLKE-GISIAQIRESPMV----LELTpqiIQYRIRKLNSLGYgikDGHLAS-LNGTKKEFE 360
Cdd:pfam02536 246 GLSIEVLKPKLEFLVKEmKWPLKEVVEYPRVfgysLEKR---IKPRIKALVSKGL---ECSLSWmLACSDERFL 313
RING-HC_RNF37 cd16537
RING finger, HC subclass, found in RING finger protein 37 (RNF37); RNF37, also known as ...
3-24 7.64e-03

RING finger, HC subclass, found in RING finger protein 37 (RNF37); RNF37, also known as KIAA0860, U-box domain-containing protein 5 (UBOX5), UbcM4-interacting protein 5 (UIP5), or ubiquitin-conjugating enzyme 7-interacting protein 5, is an E3 ubiquitin-protein ligase found exclusively in the nucleus as part of a nuclear dot-like structure. It interacts with the molecular chaperone VCP/p97 protein. RNF37 contains a U-box domain followed by a potential nuclear location signal (NLS) and a C-terminal C3HC4-type RING-HC finger. The U-box domain is a modified RING finger domain that lacks the hallmark metal-chelating cysteines and histidines of the latter, and is likely to adopt a RING finger-like conformation. The presence of the U-box, but not of the RING finger, is required for the E3 activity. The U-box domain can directly interact with several E2 enzymes, including UbcM2, UbcM3, UbcM4, UbcH5, and UbcH8, suggesting a similar function as the RING finger in the ubiquitination pathway. This model corresponds to the RING-HC finger.


Pssm-ID: 438199  Cd Length: 52  Bit Score: 34.34  E-value: 7.64e-03
                          10        20
                  ....*....|....*....|..
gi 1829010880   3 WRLPTGHQLCRLCLLRKPRPAL 24
Cdd:cd16537    20 YRLPCGHLLCRPCLAEKQKSLA 41
 
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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