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Protein

Tudor and KH domain-containing protein

Gene

TDRKH

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Participates in the primary piRNA biogenesis pathway and is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for the germline integrity. The piRNA metabolic process mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and govern the methylation and subsequent repression of transposons. Required for the final steps of primary piRNA biogenesis by participating in the processing of 31-37 nt intermediates into mature piRNAs. May act in pi-bodies and piP-bodies by transferring piRNA precursors or intermediates to or between these granules (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Differentiation, RNA-mediated gene silencing, Spermatogenesis

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciZFISH:G66-33155-MONOMER.
ReactomeiR-HSA-5601884. PIWI-interacting RNA (piRNA) biogenesis.

Names & Taxonomyi

Protein namesi
Recommended name:
Tudor and KH domain-containing protein
Alternative name(s):
Tudor domain-containing protein 2
Gene namesi
Name:TDRKH
Synonyms:TDRD2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:11713. TDRKH.

Subcellular locationi

  • Cytoplasm By similarity
  • Mitochondrion By similarity

  • Note: Probable component of the meiotic nuage, also named P granule, a germ-cell-specific organelle required to repress transposon activity during meiosis. Colocalizes with pi- and piP-bodies, a subset of the nuage which contains secondary piRNAs. Associated with mitochondria in the germline (By similarity).By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Mitochondrion

Pathology & Biotechi

Organism-specific databases

DisGeNETi11022.
OpenTargetsiENSG00000182134.
PharmGKBiPA36431.

Polymorphism and mutation databases

BioMutaiTDRKH.
DMDMi332278122.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000501411 – 561Tudor and KH domain-containing proteinAdd BLAST561

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki65Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki76Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki110Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki112Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki152Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki175Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki181Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki187Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki193Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki256Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki267Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Modified residuei278PhosphoserineCombined sources1
Cross-linki479Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki510Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki529Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

Post-translational modificationi

Ubiquitinated by PARK2 during mitophagy, leading to its degradation and enhancement of mitophagy. Deubiquitinated by USP30.1 Publication

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9Y2W6.
PaxDbiQ9Y2W6.
PeptideAtlasiQ9Y2W6.
PRIDEiQ9Y2W6.

PTM databases

iPTMnetiQ9Y2W6.
PhosphoSitePlusiQ9Y2W6.

Expressioni

Gene expression databases

BgeeiENSG00000182134.
CleanExiHS_TDRKH.
ExpressionAtlasiQ9Y2W6. baseline and differential.
GenevisibleiQ9Y2W6. HS.

Organism-specific databases

HPAiHPA016419.
HPA019625.

Interactioni

Subunit structurei

Interacts with (symmetrically methylated) PIWIL1, PIWIL2 and PIWIL4.By similarity

Protein-protein interaction databases

BioGridi116212. 2 interactors.
DIPiDIP-59459N.
STRINGi9606.ENSP00000357812.

Structurei

Secondary structure

1561
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi309 – 317Combined sources9
Beta strandi320 – 325Combined sources6
Helixi332 – 344Combined sources13
Beta strandi359 – 363Combined sources5
Turni365 – 367Combined sources3
Beta strandi370 – 378Combined sources9
Beta strandi380 – 382Combined sources3
Beta strandi384 – 388Combined sources5
Turni389 – 391Combined sources3
Beta strandi394 – 397Combined sources4
Helixi399 – 401Combined sources3
Helixi407 – 410Combined sources4
Beta strandi417 – 421Combined sources5
Beta strandi424 – 430Combined sources7
Helixi433 – 443Combined sources11
Turni444 – 448Combined sources5
Beta strandi451 – 461Combined sources11
Beta strandi464 – 473Combined sources10
Beta strandi475 – 477Combined sources3
Helixi482 – 488Combined sources7
Beta strandi491 – 494Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2DIQNMR-A329-425[»]
3FDRX-ray1.75A327-420[»]
5J39X-ray1.95A/B309-498[»]
ProteinModelPortaliQ9Y2W6.
SMRiQ9Y2W6.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Y2W6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini52 – 115KH 1PROSITE-ProRule annotationAdd BLAST64
Domaini124 – 190KH 2PROSITE-ProRule annotationAdd BLAST67
Domaini353 – 412TudorPROSITE-ProRule annotationAdd BLAST60

Sequence similaritiesi

Contains 2 KH domains.PROSITE-ProRule annotation
Contains 1 Tudor domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG2279. Eukaryota.
ENOG410Z0DP. LUCA.
GeneTreeiENSGT00730000110295.
HOGENOMiHOG000037932.
HOVERGENiHBG055309.
InParanoidiQ9Y2W6.
KOiK18406.
PhylomeDBiQ9Y2W6.
TreeFamiTF318292.

Family and domain databases

Gene3Di3.30.1370.10. 2 hits.
InterProiIPR004087. KH_dom.
IPR004088. KH_dom_type_1.
IPR002999. Tudor.
[Graphical view]
PfamiPF00013. KH_1. 2 hits.
PF00567. TUDOR. 1 hit.
[Graphical view]
SMARTiSM00322. KH. 2 hits.
SM00333. TUDOR. 1 hit.
[Graphical view]
SUPFAMiSSF54791. SSF54791. 2 hits.
PROSITEiPS50084. KH_TYPE_1. 2 hits.
PS50304. TUDOR. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9Y2W6-2) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSTERTSWTS LSTIQKIALG LGIPASATVA YILYRRYRES REERLTFVGE
60 70 80 90 100
DDIEIEMRVP QEAVKLIIGR QGANIKQLRK QTGARIDVDT EDVGDERVLL
110 120 130 140 150
ISGFPVQVCK AKAAIHQILT ENTPVSEQLS VPQRSVGRII GRGGETIRSI
160 170 180 190 200
CKASGAKITC DKESEGTLLL SRLIKISGTQ KEVAAAKHLI LEKVSEDEEL
210 220 230 240 250
RKRIAHSAET RVPRKQPISV RREDMTEPGG AGEPALWKNT SSSMEPTAPL
260 270 280 290 300
VTPPPKGGGD MAVVVSKEGS WEKPSDDSFQ KSEAQAIPEM PMFEIPSPDF
310 320 330 340 350
SFHADEYLEV YVSASEHPNH FWIQIVGSRS LQLDKLVNEM TQHYENSVPE
360 370 380 390 400
DLTVHVGDIV AAPLPTNGSW YRARVLGTLE NGNLDLYFVD FGDNGDCPLK
410 420 430 440 450
DLRALRSDFL SLPFQAIECS LARIAPSGDQ WEEEALDEFD RLTHCADWKP
460 470 480 490 500
LVAKISSYVQ TGISTWPKIY LYDTSNGKKL DIGLELVHKG YAIELPEDIE
510 520 530 540 550
ENRAVPDMLK DMATETDASL STLLTETKKS SGEITHTLSC LSLSEAASMS
560
GDDNLEDDYL L
Length:561
Mass (Da):62,046
Last modified:May 3, 2011 - v2
Checksum:iF89EBBDC48A8D420
GO
Isoform 2 (identifier: Q9Y2W6-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     108-152: Missing.

Show »
Length:516
Mass (Da):57,218
Checksum:i5D5972E323EF12BC
GO

Sequence cautioni

The sequence AAD30971 differs from that shown. Reason: Erroneous termination at position 562. Translated as stop.Curated
The sequence BC022467 differs from that shown. Reason: Erroneous termination at position 175. Translated as Lys.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti15Q → H in AAF36701 (PubMed:10767542).Curated1
Sequence conflicti321F → S in AAF36701 (PubMed:10767542).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_055980257G → A.Corresponds to variant rs17853082dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_040981108 – 152Missing in isoform 2. CuratedAdd BLAST45

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF119121 mRNA. Translation: AAD30971.1. Sequence problems.
AF227192 mRNA. Translation: AAF36701.1.
AL589765 Genomic DNA. Translation: CAI17175.1.
AL589765 Genomic DNA. Translation: CAI17177.1.
CH471121 Genomic DNA. Translation: EAW53411.1.
CH471121 Genomic DNA. Translation: EAW53409.1.
CH471121 Genomic DNA. Translation: EAW53410.1.
BC022467 mRNA. No translation available.
CCDSiCCDS41394.1. [Q9Y2W6-2]
CCDS41395.1. [Q9Y2W6-3]
RefSeqiNP_001077432.1. NM_001083963.1. [Q9Y2W6-2]
NP_001077433.1. NM_001083964.1. [Q9Y2W6-3]
NP_001077434.1. NM_001083965.1. [Q9Y2W6-2]
NP_006853.2. NM_006862.3. [Q9Y2W6-2]
XP_016855611.1. XM_017000122.1. [Q9Y2W6-2]
XP_016855612.1. XM_017000123.1. [Q9Y2W6-2]
XP_016855613.1. XM_017000124.1. [Q9Y2W6-2]
XP_016855614.1. XM_017000125.1. [Q9Y2W6-2]
XP_016855615.1. XM_017000126.1. [Q9Y2W6-2]
XP_016855616.1. XM_017000127.1. [Q9Y2W6-2]
UniGeneiHs.144439.

Genome annotation databases

EnsembliENST00000368822; ENSP00000357812; ENSG00000182134. [Q9Y2W6-2]
ENST00000368824; ENSP00000357815; ENSG00000182134. [Q9Y2W6-2]
ENST00000368825; ENSP00000357817; ENSG00000182134. [Q9Y2W6-3]
ENST00000368827; ENSP00000357819; ENSG00000182134. [Q9Y2W6-2]
ENST00000458431; ENSP00000395718; ENSG00000182134. [Q9Y2W6-2]
GeneIDi11022.
KEGGihsa:11022.
UCSCiuc001eza.6. human. [Q9Y2W6-2]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF119121 mRNA. Translation: AAD30971.1. Sequence problems.
AF227192 mRNA. Translation: AAF36701.1.
AL589765 Genomic DNA. Translation: CAI17175.1.
AL589765 Genomic DNA. Translation: CAI17177.1.
CH471121 Genomic DNA. Translation: EAW53411.1.
CH471121 Genomic DNA. Translation: EAW53409.1.
CH471121 Genomic DNA. Translation: EAW53410.1.
BC022467 mRNA. No translation available.
CCDSiCCDS41394.1. [Q9Y2W6-2]
CCDS41395.1. [Q9Y2W6-3]
RefSeqiNP_001077432.1. NM_001083963.1. [Q9Y2W6-2]
NP_001077433.1. NM_001083964.1. [Q9Y2W6-3]
NP_001077434.1. NM_001083965.1. [Q9Y2W6-2]
NP_006853.2. NM_006862.3. [Q9Y2W6-2]
XP_016855611.1. XM_017000122.1. [Q9Y2W6-2]
XP_016855612.1. XM_017000123.1. [Q9Y2W6-2]
XP_016855613.1. XM_017000124.1. [Q9Y2W6-2]
XP_016855614.1. XM_017000125.1. [Q9Y2W6-2]
XP_016855615.1. XM_017000126.1. [Q9Y2W6-2]
XP_016855616.1. XM_017000127.1. [Q9Y2W6-2]
UniGeneiHs.144439.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2DIQNMR-A329-425[»]
3FDRX-ray1.75A327-420[»]
5J39X-ray1.95A/B309-498[»]
ProteinModelPortaliQ9Y2W6.
SMRiQ9Y2W6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116212. 2 interactors.
DIPiDIP-59459N.
STRINGi9606.ENSP00000357812.

PTM databases

iPTMnetiQ9Y2W6.
PhosphoSitePlusiQ9Y2W6.

Polymorphism and mutation databases

BioMutaiTDRKH.
DMDMi332278122.

Proteomic databases

EPDiQ9Y2W6.
PaxDbiQ9Y2W6.
PeptideAtlasiQ9Y2W6.
PRIDEiQ9Y2W6.

Protocols and materials databases

DNASUi11022.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000368822; ENSP00000357812; ENSG00000182134. [Q9Y2W6-2]
ENST00000368824; ENSP00000357815; ENSG00000182134. [Q9Y2W6-2]
ENST00000368825; ENSP00000357817; ENSG00000182134. [Q9Y2W6-3]
ENST00000368827; ENSP00000357819; ENSG00000182134. [Q9Y2W6-2]
ENST00000458431; ENSP00000395718; ENSG00000182134. [Q9Y2W6-2]
GeneIDi11022.
KEGGihsa:11022.
UCSCiuc001eza.6. human. [Q9Y2W6-2]

Organism-specific databases

CTDi11022.
DisGeNETi11022.
GeneCardsiTDRKH.
HGNCiHGNC:11713. TDRKH.
HPAiHPA016419.
HPA019625.
MIMi609501. gene.
neXtProtiNX_Q9Y2W6.
OpenTargetsiENSG00000182134.
PharmGKBiPA36431.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2279. Eukaryota.
ENOG410Z0DP. LUCA.
GeneTreeiENSGT00730000110295.
HOGENOMiHOG000037932.
HOVERGENiHBG055309.
InParanoidiQ9Y2W6.
KOiK18406.
PhylomeDBiQ9Y2W6.
TreeFamiTF318292.

Enzyme and pathway databases

BioCyciZFISH:G66-33155-MONOMER.
ReactomeiR-HSA-5601884. PIWI-interacting RNA (piRNA) biogenesis.

Miscellaneous databases

EvolutionaryTraceiQ9Y2W6.
GeneWikiiTDRKH.
GenomeRNAii11022.
PROiQ9Y2W6.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000182134.
CleanExiHS_TDRKH.
ExpressionAtlasiQ9Y2W6. baseline and differential.
GenevisibleiQ9Y2W6. HS.

Family and domain databases

Gene3Di3.30.1370.10. 2 hits.
InterProiIPR004087. KH_dom.
IPR004088. KH_dom_type_1.
IPR002999. Tudor.
[Graphical view]
PfamiPF00013. KH_1. 2 hits.
PF00567. TUDOR. 1 hit.
[Graphical view]
SMARTiSM00322. KH. 2 hits.
SM00333. TUDOR. 1 hit.
[Graphical view]
SUPFAMiSSF54791. SSF54791. 2 hits.
PROSITEiPS50084. KH_TYPE_1. 2 hits.
PS50304. TUDOR. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTDRKH_HUMAN
AccessioniPrimary (citable) accession number: Q9Y2W6
Secondary accession number(s): D3DV24
, Q5SZR3, Q5SZR5, Q8N582, Q9NYV5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: May 3, 2011
Last modified: November 2, 2016
This is version 134 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.