Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Tudor and KH domain-containing protein

Gene

Tdrkh

Organism
Mus musculus (Mouse)
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.1 Publication

GO - Molecular functioni

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 meiosis Source: UniProtKB
  • piRNA metabolic process Source: UniProtKB
  • spermatogenesis Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

Differentiation, RNA-mediated gene silencing, Spermatogenesis

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-MMU-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
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 3

Organism-specific databases

MGIiMGI:1919884. Tdrkh.

Subcellular locationi

  • Cytoplasm
  • Mitochondrion

  • 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.

GO - Cellular componenti

  • cytoplasm Source: MGI
  • cytosol Source: Reactome
  • mitochondrion Source: UniProtKB
  • pi-body Source: UniProtKB
  • piP-body Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Mitochondrion

Pathology & Biotechi

Disruption phenotypei

Male mice are sterile due to defects in male meiosis, piRNA production defects, DNA demethylation of LINE-1 (L1) transposable elements and an increase in L1 expression in the adult testis. Mutants have severely reduced levels of mature piRNAs and accumulate 1'U-containing, 2'O-methylated 31-37 nt RNAs that complement the missing mature piRNAs.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 560560Tudor and KH domain-containing proteinPRO_0000050142Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki65 – 65Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki76 – 76Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki110 – 110Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki112 – 112Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki152 – 152Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki175 – 175Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki181 – 181Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki187 – 187Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki193 – 193Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki256 – 256Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki267 – 267Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki479 – 479Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki510 – 510Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki529 – 529Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity

Post-translational modificationi

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

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

EPDiQ80VL1.
MaxQBiQ80VL1.
PaxDbiQ80VL1.
PRIDEiQ80VL1.

PTM databases

iPTMnetiQ80VL1.
PhosphoSiteiQ80VL1.

Expressioni

Tissue specificityi

Highly expressed in testis, present at lower level in brain. Weakly or not expreseed in other tissues (at protein level).1 Publication

Developmental stagei

Present at low level in male gonads in postnatal day 7 (P7) Expressed at higher level in P14, P21 and adult testes, correlating with the onset of meiosis (at protein level). Expressed in spermatogonia, spermatocytes and round spermatids, but not in elongating spermatids.2 Publications

Gene expression databases

BgeeiQ80VL1.
CleanExiMM_TDRKH.
ExpressionAtlasiQ80VL1. baseline and differential.
GenevisibleiQ80VL1. MM.

Interactioni

Subunit structurei

Interacts with (symmetrically methylated) PIWIL1, PIWIL2 and PIWIL4.3 Publications

Protein-protein interaction databases

IntActiQ80VL1. 1 interaction.
STRINGi10090.ENSMUSP00000041002.

Structurei

Secondary structure

1
560
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi120 – 1223Combined sources
Beta strandi124 – 1329Combined sources
Turni133 – 1353Combined sources
Helixi136 – 1405Combined sources
Beta strandi142 – 1443Combined sources
Helixi145 – 15410Combined sources
Beta strandi157 – 1604Combined sources
Beta strandi167 – 17913Combined sources
Helixi180 – 20526Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WE8NMR-A118-208[»]
ProteinModelPortaliQ80VL1.
SMRiQ80VL1. Positions 55-208, 307-490.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ80VL1.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini52 – 11564KH 1PROSITE-ProRule annotationAdd
BLAST
Domaini124 – 19067KH 2PROSITE-ProRule annotationAdd
BLAST
Domaini353 – 41260TudorPROSITE-ProRule annotationAdd
BLAST

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.
GeneTreeiENSGT00830000128334.
HOGENOMiHOG000037932.
HOVERGENiHBG055309.
InParanoidiQ80VL1.
KOiK18406.
OMAiLPTNGSW.
OrthoDBiEOG7HHWTM.
PhylomeDBiQ80VL1.
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]

Sequencei

Sequence statusi: Complete.

Q80VL1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTERTSWTN LSTIQKIALG LGIPASATVA YILYRRYRES REERLTFVGE
60 70 80 90 100
DDIEIEMRVP QEAVKLIIGR QGANIKQLRK QTGARIDVDT EDVGDERVLL
110 120 130 140 150
ISGFPVQVCK AKAAIHQILT ENTPVFEQLS VPQRSVGRII GRGGETIRSI
160 170 180 190 200
CKASGAKITC DKESEGTLLL SRLIKISGTQ KEVAAAKHLI LEKVSEDEEL
210 220 230 240 250
RKRIAHSAET RVPRKQPISV RREEVTEPGG AGEAALWKNT NSSMGPATPL
260 270 280 290 300
EVPLRKGGGD MVVVGPKEGS WEKPNDDSFQ NSGAQSSPET SMFEIPSPDF
310 320 330 340 350
SFHADEYLEV YVSASEHPNH FWIQIIGSRS LQLDKLVSEM TQHYENSLPE
360 370 380 390 400
DLTVHVGDIV AAPLSTNGSW YRARVLGTLE NGNLDLYFVD FGDNGDCALK
410 420 430 440 450
DLRALRSDFL SLPFQAIECS LARIAPTGEE WEEEALDEFD RLTHCADWKP
460 470 480 490 500
LVAKISSYVQ TGISTWPKIY LYDTSDEKKL DIGLELVRKG YAVELPEDME
510 520 530 540 550
ENRTVPNMLK DMATETDDSL ASILTETKKS PEEMPHTLSC LSLSEAASMS
560
GDDNLEDDLF
Length:560
Mass (Da):62,134
Last modified:June 1, 2003 - v1
Checksum:i57AB7B6F56D33128
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
GL456099 Genomic DNA. No translation available.
BC049363 mRNA. Translation: AAH49363.1.
CCDSiCCDS38534.1.
RefSeqiNP_082583.1. NM_028307.1.
XP_006502201.1. XM_006502138.2.
UniGeneiMm.331198.
Mm.470795.

Genome annotation databases

EnsembliENSMUST00000045245; ENSMUSP00000041002; ENSMUSG00000041912.
ENSMUST00000166032; ENSMUSP00000129635; ENSMUSG00000041912.
ENSMUST00000197901; ENSMUSP00000142561; ENSMUSG00000041912.
GeneIDi72634.
KEGGimmu:72634.
UCSCiuc008qge.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
GL456099 Genomic DNA. No translation available.
BC049363 mRNA. Translation: AAH49363.1.
CCDSiCCDS38534.1.
RefSeqiNP_082583.1. NM_028307.1.
XP_006502201.1. XM_006502138.2.
UniGeneiMm.331198.
Mm.470795.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WE8NMR-A118-208[»]
ProteinModelPortaliQ80VL1.
SMRiQ80VL1. Positions 55-208, 307-490.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ80VL1. 1 interaction.
STRINGi10090.ENSMUSP00000041002.

PTM databases

iPTMnetiQ80VL1.
PhosphoSiteiQ80VL1.

Proteomic databases

EPDiQ80VL1.
MaxQBiQ80VL1.
PaxDbiQ80VL1.
PRIDEiQ80VL1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000045245; ENSMUSP00000041002; ENSMUSG00000041912.
ENSMUST00000166032; ENSMUSP00000129635; ENSMUSG00000041912.
ENSMUST00000197901; ENSMUSP00000142561; ENSMUSG00000041912.
GeneIDi72634.
KEGGimmu:72634.
UCSCiuc008qge.1. mouse.

Organism-specific databases

CTDi11022.
MGIiMGI:1919884. Tdrkh.

Phylogenomic databases

eggNOGiKOG2279. Eukaryota.
ENOG410Z0DP. LUCA.
GeneTreeiENSGT00830000128334.
HOGENOMiHOG000037932.
HOVERGENiHBG055309.
InParanoidiQ80VL1.
KOiK18406.
OMAiLPTNGSW.
OrthoDBiEOG7HHWTM.
PhylomeDBiQ80VL1.
TreeFamiTF318292.

Enzyme and pathway databases

ReactomeiR-MMU-5601884. PIWI-interacting RNA (piRNA) biogenesis.

Miscellaneous databases

EvolutionaryTraceiQ80VL1.
PROiQ80VL1.
SOURCEiSearch...

Gene expression databases

BgeeiQ80VL1.
CleanExiMM_TDRKH.
ExpressionAtlasiQ80VL1. baseline and differential.
GenevisibleiQ80VL1. MM.

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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Eye.
  3. "Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members."
    Vagin V.V., Wohlschlegel J., Qu J., Jonsson Z., Huang X., Chuma S., Girard A., Sachidanandam R., Hannon G.J., Aravin A.A.
    Genes Dev. 23:1749-1762(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH PIWIL1 AND PIWIL4.
  4. "Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi."
    Chen C., Jin J., James D.A., Adams-Cioaba M.A., Park J.G., Guo Y., Tenaglia E., Xu C., Gish G., Min J., Pawson T.
    Proc. Natl. Acad. Sci. U.S.A. 106:20336-20341(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, INTERACTION WITH PIWIL1 AND PIWIL2.
  5. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Brown adipose tissue, Pancreas and Testis.
  6. "Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline."
    Saxe J.P., Chen M., Zhao H., Lin H.
    EMBO J. 32:1869-1885(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, DEVELOPMENTAL STAGE, INTERACTION WITH PIWIL1 AND PIWIL4.
  7. "Solution structure of KH domain in protein BAB28342."
    RIKEN structural genomics initiative (RSGI)
    Submitted (NOV-2004) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 118-208.

Entry informationi

Entry nameiTDRKH_MOUSE
AccessioniPrimary (citable) accession number: Q80VL1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 13, 2004
Last sequence update: June 1, 2003
Last modified: June 8, 2016
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.