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P57081 (WDR4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 116. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4
Alternative name(s):
WD repeat-containing protein 4
Gene names
Name:WDR4
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length412 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Required for the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. In the complex, it is required to stabilize and induce conformational changes of the catalytic subunit. Ref.7

Pathway

tRNA modification; N(7)-methylguanine-tRNA biosynthesis. HAMAP-Rule MF_03056

Subunit structure

Forms a heterodimer with the catalytic subunit METTL1.

Subcellular location

Nucleus Ref.8.

Sequence similarities

Belongs to the WD repeat TRM82 family.

Contains 5 WD repeats.

Ontologies

Keywords
   Biological processtRNA processing
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
Polymorphism
   DomainRepeat
WD repeat
   PTMAcetylation
Phosphoprotein
   Technical termComplete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processRNA (guanine-N7)-methylation

Inferred from electronic annotation. Source: InterPro

tRNA methylation

Inferred from electronic annotation. Source: UniProtKB-HAMAP

tRNA modification

Inferred from direct assay Ref.8. Source: UniProtKB

   Cellular_componentcytoplasm

Inferred from direct assay. Source: HPA

nucleoplasm

Inferred from direct assay PubMed 16780588. Source: UniProtKB

nucleus

Inferred from direct assay Ref.8. Source: UniProtKB

   Molecular_functionprotein binding

Inferred from physical interaction Ref.8. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P57081-1)

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.
Isoform 2 (identifier: P57081-2)

The sequence of this isoform differs from the canonical sequence as follows:
     243-243: Missing.
Note: No experimental confirmation available.
Isoform 3 (identifier: P57081-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-146: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.6
Chain2 – 412411tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 HAMAP-Rule MF_03056
PRO_0000051348

Regions

Repeat59 – 9840WD 1 HAMAP-Rule MF_03056
Repeat100 – 13940WD 2 HAMAP-Rule MF_03056
Repeat143 – 18341WD 3 HAMAP-Rule MF_03056
Repeat186 – 22641WD 4 HAMAP-Rule MF_03056
Repeat287 – 32741WD 5 HAMAP-Rule MF_03056

Amino acid modifications

Modified residue21N-acetylalanine Ref.6
Modified residue3911Phosphoserine Ref.12
Modified residue4111Phosphoserine Ref.9

Natural variations

Alternative sequence1 – 146146Missing in isoform 3.
VSP_036935
Alternative sequence2431Missing in isoform 2.
VSP_036936
Natural variant711K → N. Ref.2 Ref.4
Corresponds to variant rs2248490 [ dbSNP | Ensembl ].
VAR_020120
Natural variant2661P → S. Ref.2 Ref.5
Corresponds to variant rs15736 [ dbSNP | Ensembl ].
VAR_033121
Natural variant3901R → Q.
Corresponds to variant rs6586250 [ dbSNP | Ensembl ].
VAR_033122

Experimental info

Sequence conflict1411E → K in CAB93144. Ref.1
Sequence conflict1411E → K in CAB93145. Ref.1
Sequence conflict1491L → V in CAB93144. Ref.1
Sequence conflict1491L → V in CAB93145. Ref.1
Sequence conflict2361V → A in BAG37500. Ref.2
Sequence conflict3181R → K in BAG60319. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified February 11, 2002. Version 2.
Checksum: 394B11A2AFB1CADB

FASTA41245,490
        10         20         30         40         50         60 
MAGSVGLALC GQTLVVRGGS RFLATSIASS DDDSLFIYDC SAAEKKSQEN KGEDAPLDQG 

        70         80         90        100        110        120 
SGAILASTFS KSGSYFALTD DSKRLILFRT KPWQCLSVRT VARRCTALTF IASEEKVLVA 

       130        140        150        160        170        180 
DKSGDVYSFS VLEPHGCGRL ELGHLSMLLD VAVSPDDRFI LTADRDEKIR VSWAAAPHSI 

       190        200        210        220        230        240 
ESFCLGHTEF VSRISVVPTQ PGLLLSSSGD GTLRLWEYRS GRQLHCCHLA SLQELVDPQA 

       250        260        270        280        290        300 
PQKFAASRIA FWCQENCVAL LCDGTPVVYI FQLDARRQQL VYRQQLAFQH QVWDVAFEET 

       310        320        330        340        350        360 
QGLWVLQDCQ EAPLVLYRPV GDQWQSVPES TVLKKVSGVL RGNWAMLEGS AGADASFSSL 

       370        380        390        400        410 
YKATFDNVTS YLKKKEERLQ QQLEKKQRRR SPPPGPDGHA KKMRPGEATL SC 

« Hide

Isoform 2 [UniParc].

Checksum: A32E06F66CE6574F
Show »

FASTA41145,362
Isoform 3 [UniParc].

Checksum: 121DF7AE95363BD0
Show »

FASTA26629,946

References

« Hide 'large scale' references
[1]"Isolation and characterization of a human chromosome 21q22.3 gene (WDR4) and its mouse homologue that code for a WD-repeat protein."
Michaud J., Kudoh J., Berry A., Bonne-Tamir B., Lalioti M.D., Rossier C., Shibuya K., Kawasaki K., Asakawa S., Minoshima S., Shimizu N., Antonarakis S.E., Scott H.S.
Genomics 68:71-79(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 1).
[2]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2 AND 3), VARIANTS ASN-71 AND SER-266.
Tissue: Lung and Trachea.
[3]"The DNA sequence of human chromosome 21."
Hattori M., Fujiyama A., Taylor T.D., Watanabe H., Yada T., Park H.-S., Toyoda A., Ishii K., Totoki Y., Choi D.-K., Groner Y., Soeda E., Ohki M., Takagi T., Sakaki Y., Taudien S., Blechschmidt K., Polley A. expand/collapse author list , Menzel U., Delabar J., Kumpf K., Lehmann R., Patterson D., Reichwald K., Rump A., Schillhabel M., Schudy A., Zimmermann W., Rosenthal A., Kudoh J., Shibuya K., Kawasaki K., Asakawa S., Shintani A., Sasaki T., Nagamine K., Mitsuyama S., Antonarakis S.E., Minoshima S., Shimizu N., Nordsiek G., Hornischer K., Brandt P., Scharfe M., Schoen O., Desario A., Reichelt J., Kauer G., Bloecker H., Ramser J., Beck A., Klages S., Hennig S., Riesselmann L., Dagand E., Wehrmeyer S., Borzym K., Gardiner K., Nizetic D., Francis F., Lehrach H., Reinhardt R., Yaspo M.-L.
Nature 405:311-319(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT ASN-71.
[5]"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] (ISOFORMS 1 AND 3), VARIANT SER-266.
Tissue: Lung and Uterus.
[6]Bienvenut W.V.
Submitted (JAN-2010) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 2-17 AND 105-116, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY.
Tissue: Ovarian carcinoma.
[7]"Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA."
Alexandrov A., Martzen M.R., Phizicky E.M.
RNA 8:1253-1266(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH METTL1.
[8]"The tRNA methylase METTL1 is phosphorylated and inactivated by PKB and RSK in vitro and in cells."
Cartlidge R.A., Knebel A., Peggie M., Alexandrov A., Phizicky E.M., Cohen P.
EMBO J. 24:1696-1705(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, INTERACTION WITH METTL1.
[9]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-411, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[10]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[11]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-391, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AJ243912 mRNA. Translation: CAB93144.1.
AJ243913 mRNA. Translation: CAB93145.1.
AK056343 mRNA. Translation: BAG51684.1.
AK292923 mRNA. Translation: BAF85612.1.
AK298015 mRNA. Translation: BAG60319.1.
AK315008 mRNA. Translation: BAG37500.1.
AB039887 Genomic DNA. Translation: BAB13726.1.
AP001629 Genomic DNA. No translation available.
CH471079 Genomic DNA. Translation: EAX09528.1.
CH471079 Genomic DNA. Translation: EAX09529.1.
BC001074 mRNA. Translation: AAH01074.1.
BC006341 mRNA. Translation: AAH06341.1.
CCDSCCDS13691.1. [P57081-1]
RefSeqNP_001247403.1. NM_001260474.1. [P57081-2]
NP_001247404.1. NM_001260475.1. [P57081-3]
NP_001247405.1. NM_001260476.1. [P57081-3]
NP_001247406.1. NM_001260477.1. [P57081-3]
NP_061139.2. NM_018669.5. [P57081-1]
NP_387510.1. NM_033661.4. [P57081-1]
XP_006724022.1. XM_006723959.1. [P57081-1]
UniGeneHs.248815.
Hs.711744.

3D structure databases

ProteinModelPortalP57081.
SMRP57081. Positions 70-292.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid116001. 36 interactions.
IntActP57081. 1 interaction.
MINTMINT-1440842.
STRING9606.ENSP00000328671.

PTM databases

PhosphoSiteP57081.

Polymorphism databases

DMDM20141943.

Proteomic databases

MaxQBP57081.
PaxDbP57081.
PeptideAtlasP57081.
PRIDEP57081.

Protocols and materials databases

DNASU10785.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000330317; ENSP00000328671; ENSG00000160193. [P57081-1]
ENST00000398208; ENSP00000381266; ENSG00000160193. [P57081-1]
GeneID10785.
KEGGhsa:10785.
UCSCuc002zci.4. human. [P57081-1]
uc010gpg.2. human. [P57081-2]

Organism-specific databases

CTD10785.
GeneCardsGC21M044263.
HGNCHGNC:12756. WDR4.
HPAHPA017381.
MIM605924. gene.
neXtProtNX_P57081.
PharmGKBPA37360.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG253533.
HOVERGENHBG022880.
InParanoidP57081.
KOK15443.
OMATIANSND.
OrthoDBEOG7GXPCK.
PhylomeDBP57081.
TreeFamTF105877.

Enzyme and pathway databases

SignaLinkP57081.
UniPathwayUPA00989.

Gene expression databases

BgeeP57081.
CleanExHS_WDR4.
GenevestigatorP57081.

Family and domain databases

Gene3D2.130.10.10. 1 hit.
HAMAPMF_03056. TRM82.
InterProIPR028884. Trm82.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamPF00400. WD40. 2 hits.
[Graphical view]
SMARTSM00320. WD40. 4 hits.
[Graphical view]
SUPFAMSSF50978. SSF50978. 1 hit.
PROSITEPS50082. WD_REPEATS_2. 1 hit.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSWDR4. human.
GeneWikiWDR4.
GenomeRNAi10785.
NextBio40960.
PROP57081.
SOURCESearch...

Entry information

Entry nameWDR4_HUMAN
AccessionPrimary (citable) accession number: P57081
Secondary accession number(s): A8KA58 expand/collapse secondary AC list , B2RCA3, B4DNQ7, D3DSK3, Q9BVM5, Q9HCR3
Entry history
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: February 11, 2002
Last modified: July 9, 2014
This is version 116 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 21

Human chromosome 21: entries, gene names and cross-references to MIM