UniProtKB - Q9Y2W6 (TDRKH_HUMAN)
Protein
Tudor and KH domain-containing protein
Gene
TDRKH
Organism
Homo sapiens (Human)
Status
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
- RNA binding Source: UniProtKB-KW
GO - Biological processi
- cell differentiation Source: UniProtKB-KW
- DNA methylation involved in gamete generation Source: UniProtKB
- fertilization Source: UniProtKB
- gene silencing by RNA Source: UniProtKB-KW
- male meiotic nuclear division Source: UniProtKB
- piRNA metabolic process Source: UniProtKB
- spermatogenesis Source: UniProtKB
Keywordsi
Molecular function | RNA-binding |
Biological process | Differentiation, RNA-mediated gene silencing, Spermatogenesis |
Enzyme and pathway databases
PathwayCommonsi | Q9Y2W6 |
Reactomei | R-HSA-5601884, PIWI-interacting RNA (piRNA) biogenesis |
Names & Taxonomyi
Protein namesi | Recommended name: Tudor and KH domain-containing proteinAlternative name(s): Tudor domain-containing protein 2 |
Gene namesi | Name:TDRKH Synonyms:TDRD2 |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
HGNCi | HGNC:11713, TDRKH |
MIMi | 609501, gene |
neXtProti | NX_Q9Y2W6 |
VEuPathDBi | HostDB:ENSG00000182134.15 |
Subcellular locationi
Mitochondrion
- Mitochondrion By similarity
Other locations
- Cytoplasm 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
Mitochondrion
- mitochondrion Source: UniProtKB
Other locations
Keywords - Cellular componenti
Cytoplasm, MitochondrionPathology & Biotechi
Organism-specific databases
DisGeNETi | 11022 |
OpenTargetsi | ENSG00000182134 |
PharmGKBi | PA36431 |
Miscellaneous databases
Pharosi | Q9Y2W6, Tdark |
Genetic variation databases
BioMutai | TDRKH |
DMDMi | 332278122 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000050141 | 1 – 561 | Tudor and KH domain-containing proteinAdd BLAST | 561 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Cross-linki | 65 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication | ||
Cross-linki | 76 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication | ||
Cross-linki | 110 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication | ||
Cross-linki | 112 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication | ||
Cross-linki | 152 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication | ||
Cross-linki | 175 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication | ||
Cross-linki | 181 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication | ||
Cross-linki | 187 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication | ||
Cross-linki | 193 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication | ||
Cross-linki | 256 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication | ||
Cross-linki | 267 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication | ||
Modified residuei | 278 | PhosphoserineCombined sources | 1 | |
Cross-linki | 479 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication | ||
Cross-linki | 510 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication | ||
Cross-linki | 529 | Glycyl 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 conjugationProteomic databases
EPDi | Q9Y2W6 |
jPOSTi | Q9Y2W6 |
MassIVEi | Q9Y2W6 |
PaxDbi | Q9Y2W6 |
PeptideAtlasi | Q9Y2W6 |
PRIDEi | Q9Y2W6 |
ProteomicsDBi | 85917 [Q9Y2W6-2] 85918 [Q9Y2W6-3] |
PTM databases
iPTMneti | Q9Y2W6 |
PhosphoSitePlusi | Q9Y2W6 |
Expressioni
Gene expression databases
Bgeei | ENSG00000182134, Expressed in testis and 155 other tissues |
ExpressionAtlasi | Q9Y2W6, baseline and differential |
Genevisiblei | Q9Y2W6, HS |
Organism-specific databases
HPAi | ENSG00000182134, Tissue enhanced (parathyroid) |
Interactioni
Subunit structurei
Interacts with (symmetrically methylated) PIWIL1, PIWIL2 and PIWIL4.
By similarityBinary interactionsi
Hide detailsQ9Y2W6
Protein-protein interaction databases
BioGRIDi | 116212, 40 interactors |
DIPi | DIP-59459N |
IntActi | Q9Y2W6, 24 interactors |
STRINGi | 9606.ENSP00000357812 |
Miscellaneous databases
RNActi | Q9Y2W6, protein |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | Q9Y2W6 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q9Y2W6 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 52 – 115 | KH 1PROSITE-ProRule annotationAdd BLAST | 64 | |
Domaini | 124 – 190 | KH 2PROSITE-ProRule annotationAdd BLAST | 67 | |
Domaini | 353 – 412 | TudorPROSITE-ProRule annotationAdd BLAST | 60 |
Sequence similaritiesi
Belongs to the Tdrkh family.Curated
Keywords - Domaini
RepeatPhylogenomic databases
eggNOGi | KOG2279, Eukaryota |
GeneTreei | ENSGT00940000159364 |
InParanoidi | Q9Y2W6 |
OrthoDBi | 971207at2759 |
PhylomeDBi | Q9Y2W6 |
TreeFami | TF318292 |
Family and domain databases
Gene3Di | 2.40.50.90, 1 hit 3.30.1370.10, 2 hits |
InterProi | View protein in InterPro IPR004087, KH_dom IPR004088, KH_dom_type_1 IPR036612, KH_dom_type_1_sf IPR035437, SNase_OB-fold_sf IPR002999, Tudor |
Pfami | View protein in Pfam PF00013, KH_1, 2 hits PF00567, TUDOR, 1 hit |
SMARTi | View protein in SMART SM00322, KH, 2 hits SM00333, TUDOR, 1 hit |
SUPFAMi | SSF54791, SSF54791, 2 hits |
PROSITEi | View protein in PROSITE PS50084, KH_TYPE_1, 2 hits PS50304, TUDOR, 1 hit |
s (2+)i Sequence
Sequence statusi: Complete.
This entry describes 2 produced by isoformsialternative splicing. AlignAdd to basketThis 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 sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
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
Computationally mapped potential isoform sequencesi
There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basketF6TB26 | F6TB26_HUMAN | Tudor and KH domain-containing prot... | TDRKH | 605 | Annotation score: | ||
Q5SZR4 | Q5SZR4_HUMAN | Tudor and KH domain containing, iso... | TDRKH hCG_16924 | 557 | Annotation score: | ||
B7ZAG4 | B7ZAG4_HUMAN | Tudor and KH domain-containing prot... | TDRKH | 140 | Annotation score: | ||
E9PKN8 | E9PKN8_HUMAN | Tudor and KH domain-containing prot... | TDRKH | 131 | Annotation score: | ||
E9PQX4 | E9PQX4_HUMAN | Tudor and KH domain-containing prot... | TDRKH | 58 | Annotation score: |
Sequence cautioni
The sequence AAD30971 differs from that shown. Reason: Erroneous termination. Extended C-terminus.Curated
The sequence BC022467 differs from that shown. Reason: Erroneous termination. Truncated C-terminus.Curated
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 15 | Q → H in AAF36701 (PubMed:10767542).Curated | 1 | |
Sequence conflicti | 321 | F → S in AAF36701 (PubMed:10767542).Curated | 1 |
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_055980 | 257 | G → A. Corresponds to variant dbSNP:rs17853082Ensembl. | 1 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_040981 | 108 – 152 | Missing in isoform 2. CuratedAdd BLAST | 45 |
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. |
CCDSi | CCDS41394.1 [Q9Y2W6-2] CCDS41395.1 [Q9Y2W6-3] |
RefSeqi | NP_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] |
Genome annotation databases
Ensembli | ENST00000368822; ENSP00000357812; ENSG00000182134 [Q9Y2W6-2] ENST00000368824; ENSP00000357815; ENSG00000182134 [Q9Y2W6-2] ENST00000368825; ENSP00000357817; ENSG00000182134 [Q9Y2W6-3] ENST00000368827; ENSP00000357819; ENSG00000182134 [Q9Y2W6-2] ENST00000458431; ENSP00000395718; ENSG00000182134 [Q9Y2W6-2] |
GeneIDi | 11022 |
KEGGi | hsa:11022 |
UCSCi | uc001eza.6, human [Q9Y2W6-2] |
Keywords - Coding sequence diversityi
Alternative splicingSimilar 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. |
CCDSi | CCDS41394.1 [Q9Y2W6-2] CCDS41395.1 [Q9Y2W6-3] |
RefSeqi | NP_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] |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2DIQ | NMR | - | A | 329-425 | [»] | |
3FDR | X-ray | 1.75 | A | 327-420 | [»] | |
5J39 | X-ray | 1.95 | A/B | 309-498 | [»] | |
6B57 | X-ray | 1.93 | A/B | 309-497 | [»] | |
6PI7 | X-ray | 2.80 | A/D | 305-525 | [»] | |
SMRi | Q9Y2W6 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 116212, 40 interactors |
DIPi | DIP-59459N |
IntActi | Q9Y2W6, 24 interactors |
STRINGi | 9606.ENSP00000357812 |
PTM databases
iPTMneti | Q9Y2W6 |
PhosphoSitePlusi | Q9Y2W6 |
Genetic variation databases
BioMutai | TDRKH |
DMDMi | 332278122 |
Proteomic databases
EPDi | Q9Y2W6 |
jPOSTi | Q9Y2W6 |
MassIVEi | Q9Y2W6 |
PaxDbi | Q9Y2W6 |
PeptideAtlasi | Q9Y2W6 |
PRIDEi | Q9Y2W6 |
ProteomicsDBi | 85917 [Q9Y2W6-2] 85918 [Q9Y2W6-3] |
Protocols and materials databases
ABCDi | Q9Y2W6, 6 sequenced antibodies |
Antibodypediai | 10583, 69 antibodies |
DNASUi | 11022 |
Genome annotation databases
Ensembli | ENST00000368822; ENSP00000357812; ENSG00000182134 [Q9Y2W6-2] ENST00000368824; ENSP00000357815; ENSG00000182134 [Q9Y2W6-2] ENST00000368825; ENSP00000357817; ENSG00000182134 [Q9Y2W6-3] ENST00000368827; ENSP00000357819; ENSG00000182134 [Q9Y2W6-2] ENST00000458431; ENSP00000395718; ENSG00000182134 [Q9Y2W6-2] |
GeneIDi | 11022 |
KEGGi | hsa:11022 |
UCSCi | uc001eza.6, human [Q9Y2W6-2] |
Organism-specific databases
CTDi | 11022 |
DisGeNETi | 11022 |
GeneCardsi | TDRKH |
HGNCi | HGNC:11713, TDRKH |
HPAi | ENSG00000182134, Tissue enhanced (parathyroid) |
MIMi | 609501, gene |
neXtProti | NX_Q9Y2W6 |
OpenTargetsi | ENSG00000182134 |
PharmGKBi | PA36431 |
VEuPathDBi | HostDB:ENSG00000182134.15 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG2279, Eukaryota |
GeneTreei | ENSGT00940000159364 |
InParanoidi | Q9Y2W6 |
OrthoDBi | 971207at2759 |
PhylomeDBi | Q9Y2W6 |
TreeFami | TF318292 |
Enzyme and pathway databases
PathwayCommonsi | Q9Y2W6 |
Reactomei | R-HSA-5601884, PIWI-interacting RNA (piRNA) biogenesis |
Miscellaneous databases
BioGRID-ORCSi | 11022, 5 hits in 878 CRISPR screens |
EvolutionaryTracei | Q9Y2W6 |
GeneWikii | TDRKH |
GenomeRNAii | 11022 |
Pharosi | Q9Y2W6, Tdark |
PROi | PR:Q9Y2W6 |
RNActi | Q9Y2W6, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000182134, Expressed in testis and 155 other tissues |
ExpressionAtlasi | Q9Y2W6, baseline and differential |
Genevisiblei | Q9Y2W6, HS |
Family and domain databases
Gene3Di | 2.40.50.90, 1 hit 3.30.1370.10, 2 hits |
InterProi | View protein in InterPro IPR004087, KH_dom IPR004088, KH_dom_type_1 IPR036612, KH_dom_type_1_sf IPR035437, SNase_OB-fold_sf IPR002999, Tudor |
Pfami | View protein in Pfam PF00013, KH_1, 2 hits PF00567, TUDOR, 1 hit |
SMARTi | View protein in SMART SM00322, KH, 2 hits SM00333, TUDOR, 1 hit |
SUPFAMi | SSF54791, SSF54791, 2 hits |
PROSITEi | View protein in PROSITE PS50084, KH_TYPE_1, 2 hits PS50304, TUDOR, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | TDRKH_HUMAN | |
Accessioni | Q9Y2W6Primary (citable) accession number: Q9Y2W6 Secondary accession number(s): D3DV24 Q9NYV5 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | December 15, 2003 |
Last sequence update: | May 3, 2011 | |
Last modified: | February 10, 2021 | |
This is version 167 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any 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, Reference proteomeDocuments
- Human chromosome 1
Human chromosome 1: entries, gene names and cross-references to MIM - Human entries with genetic variants
List of human entries with genetic variants - Human variants curated from literature reports
Index of human variants curated from literature reports - MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families