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Conserved domains on  [gi|119628753|gb|EAX08348|]
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ring finger protein 17, isoform CRA_b [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Tudor_TDRD4_rpt1 cd20414
first Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins; ...
 465-541 6.05e-39

first Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins; TDRD4, also called RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis. It seems to be involved in the regulation of transcriptional activity of MYC. In vitro, TDRD4 inhibits the DNA-binding activity of Mad-MAX heterodimers. It can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. TDRD4 also acts as a potential cancer/testis antigen in liver cancer. TDRD4 contains a RING finger and five Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


:

Pssm-ID: 410485  Cd Length: 77  Bit Score: 138.11  E-value: 6.05e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 119628753 465 ELGARIFVSSIKNGMWCRGTITELIPIEGRNTRKPCSPTRLFVHEVALIQIFMVDFGNSEVLIVTGVVDTHVRPEHS 541
Cdd:cd20414    1 ELGERIAVKSKKNGMWCRGTITELIPLENKNKGKPCGPTRYKIHDVAVMQVFLLDYGHSEVFVVTGVGVLVVRPEDV 77
RING_Ubox super family cl17238
RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger ...
 47-74 3.69e-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 cd16564:

Pssm-ID: 473075 [Multi-domain]  Cd Length: 50  Bit Score: 35.84  E-value: 3.69e-03
                         10        20
                 ....*....|....*....|....*...
gi 119628753  47 CELQCGHAFCELCLLMTEECTTIICPDC 74
Cdd:cd16564   15 RILSCGHSFCEDCLVKQLVSMTISCPIC 42
Tudor_SF super family cl02573
Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally ...
 418-490 9.58e-03

Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally identified in the Tudor protein of Drosophila, that adopts a beta-barrel-like core structure containing four short beta-strands followed by an alpha-helical region. It binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Tudor domain-containing proteins may mediate protein-protein interactions required for various DNA-templated biological processes, such as RNA metabolism, as well as histone modification and the DNA damage response. Members of this superfamily contain one or more copies of the Tudor domain.


The actual alignment was detected with superfamily member cd20425:

Pssm-ID: 470623  Cd Length: 115  Bit Score: 36.67  E-value: 9.58e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 119628753 418 LVFVSHVIDPCHFYIRKYSQIKDAKVLEKKVNEFCNRSSHLDpSDILELGARIFVSSIKNGMWCRGTITELIP 490
Cdd:cd20425    3 EVYVSHVNSPSDFYVQLAQDEDELSMISEKLNASKANDEEVE-CESLQLGDLICAEYPEDGLWYRAVVKEKIP 74
 
Name Accession Description Interval E-value
Tudor_TDRD4_rpt1 cd20414
first Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins; ...
 465-541 6.05e-39

first Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins; TDRD4, also called RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis. It seems to be involved in the regulation of transcriptional activity of MYC. In vitro, TDRD4 inhibits the DNA-binding activity of Mad-MAX heterodimers. It can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. TDRD4 also acts as a potential cancer/testis antigen in liver cancer. TDRD4 contains a RING finger and five Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410485  Cd Length: 77  Bit Score: 138.11  E-value: 6.05e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 119628753 465 ELGARIFVSSIKNGMWCRGTITELIPIEGRNTRKPCSPTRLFVHEVALIQIFMVDFGNSEVLIVTGVVDTHVRPEHS 541
Cdd:cd20414    1 ELGERIAVKSKKNGMWCRGTITELIPLENKNKGKPCGPTRYKIHDVAVMQVFLLDYGHSEVFVVTGVGVLVVRPEDV 77
TUDOR pfam00567
Tudor domain;
419-526 3.97e-09

Tudor domain;


Pssm-ID: 425754 [Multi-domain]  Cd Length: 117  Bit Score: 54.67  E-value: 3.97e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119628753  419 VFVSHVIDPCHFYIRKYSQIKDAKVLEKKVNEFCNRSSHLDPSDILELGARIFVSSikNGMWCRGTITELIPIEgrntrk 498
Cdd:pfam00567   5 VVVSHIESPSTFYIQPKSDSKKLEKLTEELQEYYASKPPESLPPAVGDGCVAAFSE--DGKWYRAKITESLDDG------ 76

                          90       100
                  ....*....|....*....|....*...
gi 119628753  499 pcsptrlfvhevaLIQIFMVDFGNSEVL 526
Cdd:pfam00567  77 -------------LVEVLFIDYGNTETV 91
RING-HC_RNF222 cd16564
RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; ...
 47-74 3.69e-03

RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; RNF222 is an uncharacterized C3HC4-type RING-HC finger-containing protein. It may function as an E3 ubiquitin-protein ligase.


Pssm-ID: 438226 [Multi-domain]  Cd Length: 50  Bit Score: 35.84  E-value: 3.69e-03
                         10        20
                 ....*....|....*....|....*...
gi 119628753  47 CELQCGHAFCELCLLMTEECTTIICPDC 74
Cdd:cd16564   15 RILSCGHSFCEDCLVKQLVSMTISCPIC 42
Tudor_TDRD6_rpt6 cd20425
sixth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; ...
 418-490 9.58e-03

sixth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the sixth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410496  Cd Length: 115  Bit Score: 36.67  E-value: 9.58e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 119628753 418 LVFVSHVIDPCHFYIRKYSQIKDAKVLEKKVNEFCNRSSHLDpSDILELGARIFVSSIKNGMWCRGTITELIP 490
Cdd:cd20425    3 EVYVSHVNSPSDFYVQLAQDEDELSMISEKLNASKANDEEVE-CESLQLGDLICAEYPEDGLWYRAVVKEKIP 74
 
Name Accession Description Interval E-value
Tudor_TDRD4_rpt1 cd20414
first Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins; ...
 465-541 6.05e-39

first Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins; TDRD4, also called RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis. It seems to be involved in the regulation of transcriptional activity of MYC. In vitro, TDRD4 inhibits the DNA-binding activity of Mad-MAX heterodimers. It can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. TDRD4 also acts as a potential cancer/testis antigen in liver cancer. TDRD4 contains a RING finger and five Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410485  Cd Length: 77  Bit Score: 138.11  E-value: 6.05e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 119628753 465 ELGARIFVSSIKNGMWCRGTITELIPIEGRNTRKPCSPTRLFVHEVALIQIFMVDFGNSEVLIVTGVVDTHVRPEHS 541
Cdd:cd20414    1 ELGERIAVKSKKNGMWCRGTITELIPLENKNKGKPCGPTRYKIHDVAVMQVFLLDYGHSEVFVVTGVGVLVVRPEDV 77
TUDOR pfam00567
Tudor domain;
419-526 3.97e-09

Tudor domain;


Pssm-ID: 425754 [Multi-domain]  Cd Length: 117  Bit Score: 54.67  E-value: 3.97e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119628753  419 VFVSHVIDPCHFYIRKYSQIKDAKVLEKKVNEFCNRSSHLDPSDILELGARIFVSSikNGMWCRGTITELIPIEgrntrk 498
Cdd:pfam00567   5 VVVSHIESPSTFYIQPKSDSKKLEKLTEELQEYYASKPPESLPPAVGDGCVAAFSE--DGKWYRAKITESLDDG------ 76

                          90       100
                  ....*....|....*....|....*...
gi 119628753  499 pcsptrlfvhevaLIQIFMVDFGNSEVL 526
Cdd:pfam00567  77 -------------LVEVLFIDYGNTETV 91
Tudor_TDRD15_rpt5 cd20440
fifth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; ...
 415-538 5.98e-04

fifth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the fifth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410511  Cd Length: 127  Bit Score: 40.13  E-value: 5.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119628753 415 SAELVFVSHVIDPCHFYIRKYSQIKDAKVLEKKVNEFCN--RSSHLDPSDILELGARIFvssiKNGMWCRGTItelIPIE 492
Cdd:cd20440   10 SEEEVYITHVYSPAKFYCQLDRNTEILEALMEKIAEISKlfNSQILDNCKTRLCLAKYF----EDGQWYRALA---HPVE 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 119628753 493 grntrkpcSPTRLfvhevaliQIFMVDFGNSEVlivtgVVDTHVRP 538
Cdd:cd20440   83 --------SSSHL--------SVYFVDYGNKQI-----VEKNEVLP 107
RING-HC_RNF222 cd16564
RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; ...
 47-74 3.69e-03

RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; RNF222 is an uncharacterized C3HC4-type RING-HC finger-containing protein. It may function as an E3 ubiquitin-protein ligase.


Pssm-ID: 438226 [Multi-domain]  Cd Length: 50  Bit Score: 35.84  E-value: 3.69e-03
                         10        20
                 ....*....|....*....|....*...
gi 119628753  47 CELQCGHAFCELCLLMTEECTTIICPDC 74
Cdd:cd16564   15 RILSCGHSFCEDCLVKQLVSMTISCPIC 42
Tudor_TDRD6_rpt6 cd20425
sixth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; ...
 418-490 9.58e-03

sixth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the sixth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410496  Cd Length: 115  Bit Score: 36.67  E-value: 9.58e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 119628753 418 LVFVSHVIDPCHFYIRKYSQIKDAKVLEKKVNEFCNRSSHLDpSDILELGARIFVSSIKNGMWCRGTITELIP 490
Cdd:cd20425    3 EVYVSHVNSPSDFYVQLAQDEDELSMISEKLNASKANDEEVE-CESLQLGDLICAEYPEDGLWYRAVVKEKIP 74
RING-HC_RNF180 cd16554
RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins; ...
 45-74 9.77e-03

RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins; RNF180, also known as Rines, is a membrane-bound E3 ubiquitin-protein ligase well conserved among vertebrates. It is a critical regulator of the monoaminergic system, as well as emotional and social behavior. It interacts with brain monoamine oxidase A (MAO-A) and targets it for ubiquitination and degradation. It also functions as a novel tumor suppressor in gastric carcinogenesis. The hypermethylated CpG site count of the RNF180 DNA promoter can be used to predict survival of gastric cancer. RNF180 contains a novel conserved dual specificity protein phosphatase Rines conserved (DSPRC) domain, a basic coiled-coil domain, a C3HC4-type RING-HC finger, and a C-terminal hydrophobic region that is predicted to be a transmembrane domain.


Pssm-ID: 438216 [Multi-domain]  Cd Length: 59  Bit Score: 34.98  E-value: 9.77e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 119628753  45 HHCElQCGHAFCELCL--LMTEECTTIICPDC 74
Cdd:cd16554   16 YMCY-PCGHIFCEPCLrqLAKSSPKNTPCPLC 46
 
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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