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Protein

Tudor and KH domain-containing protein

Gene

TDRKH

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionRNA-binding
Biological processDifferentiation, RNA-mediated gene silencing, Spermatogenesis

Enzyme and pathway databases

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

EuPathDBiHostDB:ENSG00000182134.15
HGNCiHGNC:11713 TDRKH
MIMi609501 gene
neXtProtiNX_Q9Y2W6

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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 PRKN 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
ProteomicsDBi85917
85918 [Q9Y2W6-3]

PTM databases

iPTMnetiQ9Y2W6
PhosphoSitePlusiQ9Y2W6

Expressioni

Gene expression databases

BgeeiENSG00000182134 Expressed in 136 organ(s), highest expression level in testis
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, 23 interactors
DIPiDIP-59459N
IntActiQ9Y2W6, 13 interactors
STRINGi9606.ENSP00000357812

Structurei

Secondary structure

1561
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

Belongs to the Tdrkh family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG2279 Eukaryota
ENOG410Z0DP LUCA
GeneTreeiENSGT00730000110295
HOGENOMiHOG000037932
HOVERGENiHBG055309
InParanoidiQ9Y2W6
KOiK18406
PhylomeDBiQ9Y2W6
TreeFamiTF318292

Family and domain databases

Gene3Di2.40.50.90, 1 hit
3.30.1370.10, 2 hits
InterProiView protein in InterPro
IPR004087 KH_dom
IPR004088 KH_dom_type_1
IPR036612 KH_dom_type_1_sf
IPR035437 SNase_OB-fold_sf
IPR002999 Tudor
PfamiView protein in Pfam
PF00013 KH_1, 2 hits
PF00567 TUDOR, 1 hit
SMARTiView protein in SMART
SM00322 KH, 2 hits
SM00333 TUDOR, 1 hit
SUPFAMiSSF54791 SSF54791, 2 hits
PROSITEiView protein in PROSITE
PS50084 KH_TYPE_1, 2 hits
PS50304 TUDOR, 1 hit

Sequences (2+)i

Sequence statusi: Complete.

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

This entry has 2 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
Q5SZR4Q5SZR4_HUMAN
Tudor and KH domain containing, iso...
TDRKH hCG_16924
557Annotation score:
F6TB26F6TB26_HUMAN
Tudor and KH domain-containing prot...
TDRKH
605Annotation score:
E9PKN8E9PKN8_HUMAN
Tudor and KH domain-containing prot...
TDRKH
131Annotation score:
B7ZAG4B7ZAG4_HUMAN
cDNA, FLJ79178, highly similar to T...
TDRKH
140Annotation score:
E9PQX4E9PQX4_HUMAN
Tudor and KH domain-containing prot...
TDRKH
58Annotation score:

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 dbSNP:rs17853082Ensembl.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 No translation available.
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

Similar proteinsi

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 No translation available.
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[»]
6B57X-ray1.93A/B309-497[»]
ProteinModelPortaliQ9Y2W6
SMRiQ9Y2W6
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116212, 23 interactors
DIPiDIP-59459N
IntActiQ9Y2W6, 13 interactors
STRINGi9606.ENSP00000357812

PTM databases

iPTMnetiQ9Y2W6
PhosphoSitePlusiQ9Y2W6

Polymorphism and mutation databases

BioMutaiTDRKH
DMDMi332278122

Proteomic databases

EPDiQ9Y2W6
PaxDbiQ9Y2W6
PeptideAtlasiQ9Y2W6
PRIDEiQ9Y2W6
ProteomicsDBi85917
85918 [Q9Y2W6-3]

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
EuPathDBiHostDB:ENSG00000182134.15
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

ReactomeiR-HSA-5601884 PIWI-interacting RNA (piRNA) biogenesis

Miscellaneous databases

ChiTaRSiTDRKH human
EvolutionaryTraceiQ9Y2W6
GeneWikiiTDRKH
GenomeRNAii11022
PROiPR:Q9Y2W6
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000182134 Expressed in 136 organ(s), highest expression level in testis
CleanExiHS_TDRKH
ExpressionAtlasiQ9Y2W6 baseline and differential
GenevisibleiQ9Y2W6 HS

Family and domain databases

Gene3Di2.40.50.90, 1 hit
3.30.1370.10, 2 hits
InterProiView protein in InterPro
IPR004087 KH_dom
IPR004088 KH_dom_type_1
IPR036612 KH_dom_type_1_sf
IPR035437 SNase_OB-fold_sf
IPR002999 Tudor
PfamiView protein in Pfam
PF00013 KH_1, 2 hits
PF00567 TUDOR, 1 hit
SMARTiView protein in SMART
SM00322 KH, 2 hits
SM00333 TUDOR, 1 hit
SUPFAMiSSF54791 SSF54791, 2 hits
PROSITEiView protein in PROSITE
PS50084 KH_TYPE_1, 2 hits
PS50304 TUDOR, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiTDRKH_HUMAN
AccessioniPrimary (citable) accession number: Q9Y2W6
Secondary accession number(s): D3DV24
, Q5SZR3, Q5SZR5, Q8N582, Q9NYV5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: May 3, 2011
Last modified: November 7, 2018
This is version 151 of the entry and version 2 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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Main funding by: National Institutes of Health

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