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Protein

PDZ domain-containing protein 4

Gene

PDZD4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

GO - Molecular functioni

  1. ubiquitin protein ligase activity Source: GO_Central

GO - Biological processi

  1. protein ubiquitination Source: GO_Central
Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
PDZ domain-containing protein 4
Alternative name(s):
PDZ domain-containing RING finger protein 4-like protein
Gene namesi
Name:PDZD4
Synonyms:KIAA1444, PDZK4, PDZRN4L
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome X

Organism-specific databases

HGNCiHGNC:21167. PDZD4.

Subcellular locationi

  1. Cytoplasmcell cortex 1 Publication

  2. Note: Mainly localized under the plasma membrane.

GO - Cellular componenti

  1. cell cortex Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134896313.

Polymorphism and mutation databases

BioMutaiPDZD4.
DMDMi62288846.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 769769PDZ domain-containing protein 4PRO_0000055921Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei236 – 2361Phosphoserine1 Publication
Modified residuei454 – 4541Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ76G19.
PRIDEiQ76G19.

PTM databases

PhosphoSiteiQ76G19.

Expressioni

Tissue specificityi

Brain-specific. Expressed in fetal and adult brain. Up-regulated in synovial carcinomas.1 Publication

Gene expression databases

BgeeiQ76G19.
CleanExiHS_PDZD4.
ExpressionAtlasiQ76G19. baseline and differential.
GenevestigatoriQ76G19.

Organism-specific databases

HPAiHPA003878.

Interactioni

Protein-protein interaction databases

BioGridi121646. 3 interactions.
IntActiQ76G19. 2 interactions.
MINTiMINT-2875333.
STRINGi9606.ENSP00000164640.

Structurei

3D structure databases

ProteinModelPortaliQ76G19.
SMRiQ76G19. Positions 12-53, 118-226.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini130 – 21485PDZPROSITE-ProRule annotationAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili389 – 41931Sequence AnalysisAdd
BLAST

Sequence similaritiesi

Contains 1 PDZ (DHR) domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiNOG318730.
GeneTreeiENSGT00510000046421.
HOGENOMiHOG000231379.
HOVERGENiHBG053554.
InParanoidiQ76G19.
KOiK15682.
OMAiCLREQQN.
OrthoDBiEOG70ZZNP.
PhylomeDBiQ76G19.
TreeFamiTF315909.

Family and domain databases

Gene3Di2.30.42.10. 2 hits.
InterProiIPR001478. PDZ.
[Graphical view]
PfamiPF00595. PDZ. 1 hit.
[Graphical view]
SMARTiSM00228. PDZ. 1 hit.
[Graphical view]
SUPFAMiSSF50156. SSF50156. 1 hit.
PROSITEiPS50106. PDZ. 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: Q76G19-1) [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
MGCNMCVVQK PEEQYKVMLQ VNGKELSKLS QEQTLQALRS SKEPLVIQVL
60 70 80 90 100
RRSPRLRGDS SCHDLQLVDS GTQTDITFEH IMALGKLRPP TPPMVILEPP
110 120 130 140 150
PISHEYYDPA EFMEGGPQEA DRLDELEYEE VELYKSSHRD KLGLMVCYRT
160 170 180 190 200
DDEEDLGIYV GEVNPNSIAA KDGRIREGDR IIQINGVDVQ NREEAVAILS
210 220 230 240 250
QEENTNISLL VARPESQLAK RWKDSDRDDF LDDFGSENEG ELRARKLKSP
260 270 280 290 300
PAQQPGNEEE KGAPDAGPGL SNSQELDSGV GRTDESTRNE ESSEHDLLGD
310 320 330 340 350
EPPSSTNTPG SLRKFGLQGD ALQSRDFHFS MDSLLAEGAG LGGGDVPGLT
360 370 380 390 400
DEEYERYREL LEIKCHLENG NQLGLLFPRA SGGNSALDVN RNESLGHEMA
410 420 430 440 450
MLEEELRHLE FKCRNILRAQ KMQQLRERCM KAWLLEEESL YDLAASEPKK
460 470 480 490 500
HELSDISELP EKSDKDSTSA YNTGESCRST PLLVEPLPES PLRRAMAGNS
510 520 530 540 550
NLNRTPPGPA VATPAKAAPP PGSPAKFRSL SRDPEAGRRQ HAEERGRRNP
560 570 580 590 600
KTGLTLERVG PESSPYLSRR HRGQGQEGEH YHSCVQLAPT RGLEELGHGP
610 620 630 640 650
LSLAGGPRVG GVAAAATEAP RMEWKVKVRS DGTRYVAKRP VRDRLLKARA
660 670 680 690 700
LKIREERSGM TTDDDAVSEM KMGRYWSKEE RKQHLIRARE QRKRREFMMQ
710 720 730 740 750
SRLECLREQQ NGDSKPELNI IALSHRKTMK KRNKKILDNW ITIQEMLAHG
760
ARSADGKRVY NPLLSVTTV
Length:769
Mass (Da):86,171
Last modified:July 5, 2004 - v1
Checksum:i9C6788FD289154CD
GO
Isoform 2 (identifier: Q76G19-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     21-129: Missing.

Note: No experimental confirmation available.

Show »
Length:660
Mass (Da):73,877
Checksum:i781514567F6CB369
GO

Sequence cautioni

The sequence BAC03666.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti374 – 3741G → D in BAC03666 (PubMed:14702039).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti39 – 391R → C in a breast cancer sample; somatic mutation. 1 Publication
VAR_035952

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei21 – 129109Missing in isoform 2. 1 PublicationVSP_054521Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB103478 mRNA. Translation: BAD16631.1.
AK091444 mRNA. Translation: BAC03666.1. Different initiation.
AK127016 mRNA. Translation: BAG54423.1.
U52111 Genomic DNA. No translation available.
CH471172 Genomic DNA. Translation: EAW72805.1.
BC002606 mRNA. Translation: AAH02606.2.
BC080584 mRNA. Translation: AAH80584.1.
BC143459 mRNA. Translation: AAI43460.1.
AB040877 mRNA. Translation: BAA95968.1.
CCDSiCCDS14732.1. [Q76G19-1]
RefSeqiNP_115901.2. NM_032512.3. [Q76G19-1]
UniGeneiHs.92732.

Genome annotation databases

EnsembliENST00000164640; ENSP00000164640; ENSG00000067840. [Q76G19-1]
ENST00000544474; ENSP00000442033; ENSG00000067840. [Q76G19-2]
GeneIDi57595.
KEGGihsa:57595.
UCSCiuc004fiz.1. human. [Q76G19-1]
uc011mze.1. human.

Polymorphism and mutation databases

BioMutaiPDZD4.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB103478 mRNA. Translation: BAD16631.1.
AK091444 mRNA. Translation: BAC03666.1. Different initiation.
AK127016 mRNA. Translation: BAG54423.1.
U52111 Genomic DNA. No translation available.
CH471172 Genomic DNA. Translation: EAW72805.1.
BC002606 mRNA. Translation: AAH02606.2.
BC080584 mRNA. Translation: AAH80584.1.
BC143459 mRNA. Translation: AAI43460.1.
AB040877 mRNA. Translation: BAA95968.1.
CCDSiCCDS14732.1. [Q76G19-1]
RefSeqiNP_115901.2. NM_032512.3. [Q76G19-1]
UniGeneiHs.92732.

3D structure databases

ProteinModelPortaliQ76G19.
SMRiQ76G19. Positions 12-53, 118-226.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121646. 3 interactions.
IntActiQ76G19. 2 interactions.
MINTiMINT-2875333.
STRINGi9606.ENSP00000164640.

PTM databases

PhosphoSiteiQ76G19.

Polymorphism and mutation databases

BioMutaiPDZD4.
DMDMi62288846.

Proteomic databases

PaxDbiQ76G19.
PRIDEiQ76G19.

Protocols and materials databases

DNASUi57595.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000164640; ENSP00000164640; ENSG00000067840. [Q76G19-1]
ENST00000544474; ENSP00000442033; ENSG00000067840. [Q76G19-2]
GeneIDi57595.
KEGGihsa:57595.
UCSCiuc004fiz.1. human. [Q76G19-1]
uc011mze.1. human.

Organism-specific databases

CTDi57595.
GeneCardsiGC0XM153067.
HGNCiHGNC:21167. PDZD4.
HPAiHPA003878.
MIMi300634. gene.
neXtProtiNX_Q76G19.
PharmGKBiPA134896313.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG318730.
GeneTreeiENSGT00510000046421.
HOGENOMiHOG000231379.
HOVERGENiHBG053554.
InParanoidiQ76G19.
KOiK15682.
OMAiCLREQQN.
OrthoDBiEOG70ZZNP.
PhylomeDBiQ76G19.
TreeFamiTF315909.

Miscellaneous databases

GeneWikiiPDZD4.
GenomeRNAii57595.
NextBioi35481214.
PROiQ76G19.
SOURCEiSearch...

Gene expression databases

BgeeiQ76G19.
CleanExiHS_PDZD4.
ExpressionAtlasiQ76G19. baseline and differential.
GenevestigatoriQ76G19.

Family and domain databases

Gene3Di2.30.42.10. 2 hits.
InterProiIPR001478. PDZ.
[Graphical view]
PfamiPF00595. PDZ. 1 hit.
[Graphical view]
SMARTiSM00228. PDZ. 1 hit.
[Graphical view]
SUPFAMiSSF50156. SSF50156. 1 hit.
PROSITEiPS50106. PDZ. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Identification of PDZK4, a novel human gene with PDZ domains, that is upregulated in synovial sarcomas."
    Nagayama S., Iiizumi M., Katagiri T., Toguchida J., Nakamura Y.
    Oncogene 23:5551-5557(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
  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.
    , 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] (ISOFORM 1).
    Tissue: Brain.
  3. "The DNA sequence of the human X chromosome."
    Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C.
    , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R.
    Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  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] (ISOFORM 2), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 535-769 (ISOFORM 1).
    Tissue: Brain.
  6. "Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
    Nagase T., Kikuno R., Ishikawa K., Hirosawa M., Ohara O.
    DNA Res. 7:143-150(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 132-547 (ISOFORM 1/2).
    Tissue: Brain.
  7. "Identification and characterization of human PDZRN4L gene and mouse Pdzrn4l gene in silico."
    Katoh M., Katoh M.
    Int. J. Mol. Med. 13:923-927(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  8. "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-236 AND SER-454, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. Cited for: VARIANT [LARGE SCALE ANALYSIS] CYS-39.

Entry informationi

Entry nameiPDZD4_HUMAN
AccessioniPrimary (citable) accession number: Q76G19
Secondary accession number(s): B3KXB1
, B7ZKY3, Q8NB75, Q9BUH9, Q9P284
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 2005
Last sequence update: July 5, 2004
Last modified: April 29, 2015
This is version 97 of the entry and version 1 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome X
    Human chromosome X: 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. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.