ID GDPD4_HUMAN Reviewed; 623 AA.
AC Q6W3E5; Q7Z5B0;
DT 03-OCT-2006, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 24-JAN-2024, entry version 128.
DE RecName: Full=Glycerophosphodiester phosphodiesterase domain-containing protein 4;
DE EC=3.1.-.-;
DE AltName: Full=Glycerophosphodiester phosphodiesterase 6;
DE AltName: Full=UgpQ;
GN Name=GDPD4; Synonyms=GDE6, UGPQ;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
RA Shan Y.X., Huang C.Q., Guo Z.K., Ye M.G., Yu L.;
RT "Cloning and characterization of a novel GDPD gene.";
RL Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP VARIANT LYS-396.
RX PubMed=21248752; DOI=10.1038/nature09639;
RA Varela I., Tarpey P., Raine K., Huang D., Ong C.K., Stephens P., Davies H.,
RA Jones D., Lin M.L., Teague J., Bignell G., Butler A., Cho J.,
RA Dalgliesh G.L., Galappaththige D., Greenman C., Hardy C., Jia M.,
RA Latimer C., Lau K.W., Marshall J., McLaren S., Menzies A., Mudie L.,
RA Stebbings L., Largaespada D.A., Wessels L.F.A., Richard S., Kahnoski R.J.,
RA Anema J., Tuveson D.A., Perez-Mancera P.A., Mustonen V., Fischer A.,
RA Adams D.J., Rust A., Chan-On W., Subimerb C., Dykema K., Furge K.,
RA Campbell P.J., Teh B.T., Stratton M.R., Futreal P.A.;
RT "Exome sequencing identifies frequent mutation of the SWI/SNF complex gene
RT PBRM1 in renal carcinoma.";
RL Nature 469:539-542(2011).
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000305}; Multi-pass membrane
CC protein {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q6W3E5-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q6W3E5-2; Sequence=VSP_020811, VSP_020812;
CC -!- SIMILARITY: Belongs to the glycerophosphoryl diester phosphodiesterase
CC family. {ECO:0000305}.
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DR EMBL; AY313782; AAQ72549.1; -; mRNA.
DR EMBL; AY326450; AAP92403.1; -; mRNA.
DR CCDS; CCDS8249.1; -. [Q6W3E5-2]
DR RefSeq; NP_878253.1; NM_182833.1. [Q6W3E5-2]
DR AlphaFoldDB; Q6W3E5; -.
DR SMR; Q6W3E5; -.
DR BioGRID; 128619; 2.
DR IntAct; Q6W3E5; 1.
DR STRING; 9606.ENSP00000320815; -.
DR GlyCosmos; Q6W3E5; 2 sites, No reported glycans.
DR GlyGen; Q6W3E5; 2 sites.
DR iPTMnet; Q6W3E5; -.
DR PhosphoSitePlus; Q6W3E5; -.
DR BioMuta; GDPD4; -.
DR DMDM; 74710342; -.
DR PaxDb; 9606-ENSP00000320815; -.
DR PeptideAtlas; Q6W3E5; -.
DR DNASU; 220032; -.
DR Ensembl; ENST00000315938.5; ENSP00000320815.4; ENSG00000178795.10. [Q6W3E5-2]
DR Ensembl; ENST00000376217.6; ENSP00000365390.2; ENSG00000178795.10. [Q6W3E5-1]
DR GeneID; 220032; -.
DR KEGG; hsa:220032; -.
DR MANE-Select; ENST00000315938.5; ENSP00000320815.4; NM_182833.3; NP_878253.1. [Q6W3E5-2]
DR UCSC; uc001oyf.3; human. [Q6W3E5-1]
DR AGR; HGNC:24849; -.
DR CTD; 220032; -.
DR GeneCards; GDPD4; -.
DR HGNC; HGNC:24849; GDPD4.
DR HPA; ENSG00000178795; Tissue enhanced (retina, testis).
DR neXtProt; NX_Q6W3E5; -.
DR OpenTargets; ENSG00000178795; -.
DR PharmGKB; PA142671742; -.
DR VEuPathDB; HostDB:ENSG00000178795; -.
DR eggNOG; KOG2258; Eukaryota.
DR GeneTree; ENSGT00940000156251; -.
DR HOGENOM; CLU_024259_2_0_1; -.
DR InParanoid; Q6W3E5; -.
DR OMA; HDRRYVR; -.
DR OrthoDB; 203377at2759; -.
DR PhylomeDB; Q6W3E5; -.
DR TreeFam; TF313692; -.
DR PathwayCommons; Q6W3E5; -.
DR SignaLink; Q6W3E5; -.
DR BioGRID-ORCS; 220032; 4 hits in 1144 CRISPR screens.
DR GenomeRNAi; 220032; -.
DR Pharos; Q6W3E5; Tdark.
DR PRO; PR:Q6W3E5; -.
DR Proteomes; UP000005640; Chromosome 11.
DR RNAct; Q6W3E5; Protein.
DR Bgee; ENSG00000178795; Expressed in right testis and 84 other cell types or tissues.
DR GO; GO:0016020; C:membrane; IBA:GO_Central.
DR GO; GO:0008889; F:glycerophosphodiester phosphodiesterase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006629; P:lipid metabolic process; IEA:InterPro.
DR CDD; cd08610; GDPD_GDE6; 1.
DR Gene3D; 3.20.20.190; Phosphatidylinositol (PI) phosphodiesterase; 1.
DR InterPro; IPR030395; GP_PDE_dom.
DR InterPro; IPR017946; PLC-like_Pdiesterase_TIM-brl.
DR PANTHER; PTHR23344:SF13; GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE DOMAIN-CONTAINING PROTEIN 4; 1.
DR PANTHER; PTHR23344; GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE; 1.
DR Pfam; PF03009; GDPD; 1.
DR SUPFAM; SSF51695; PLC-like phosphodiesterases; 1.
DR PROSITE; PS51704; GP_PDE; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Glycoprotein; Hydrolase; Membrane; Metal-binding;
KW Reference proteome; Transmembrane; Transmembrane helix.
FT CHAIN 1..623
FT /note="Glycerophosphodiester phosphodiesterase domain-
FT containing protein 4"
FT /id="PRO_0000251938"
FT TOPO_DOM 1..17
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 18..38
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 39
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 40..60
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 61..69
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 70..90
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 91..109
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 110..130
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 131..162
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 163..183
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 184..468
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 469..489
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 490..623
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT DOMAIN 198..457
FT /note="GP-PDE"
FT BINDING 230
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 232
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 245
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT CARBOHYD 308
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 397
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT VAR_SEQ 514..520
FT /note="NLHIAMK -> SKNEEDR (in isoform 2)"
FT /evidence="ECO:0000303|Ref.1"
FT /id="VSP_020811"
FT VAR_SEQ 521..623
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|Ref.1"
FT /id="VSP_020812"
FT VARIANT 220
FT /note="K -> R (in dbSNP:rs2729772)"
FT /id="VAR_055872"
FT VARIANT 383
FT /note="H -> Y (in dbSNP:rs11237146)"
FT /id="VAR_055873"
FT VARIANT 390
FT /note="I -> V (in dbSNP:rs11237145)"
FT /id="VAR_055874"
FT VARIANT 396
FT /note="N -> K"
FT /evidence="ECO:0000269|PubMed:21248752"
FT /id="VAR_064764"
SQ SEQUENCE 623 AA; 71996 MW; 5C8C81D1B735A365 CRC64;
MLLFLWIETS SEYFNFDWVT FLGTGYWFFW SIFILSLARI LTAYSSLLLL LGFLLLWERI
ELYLHLCHKI LILLVILLCV ILMFIICKFW KERWLVAGLS MQIFAPYVHL VSITVMVILF
WPVAFYVACL EREVRMRRYR MTHSEKKRLK QCNVITRLRG LQVPVGLPFL LILLGLYLMP
LGIYSPCIQE KENLGPKPTI FGHRGAPMLG PENTMMSFEK AVEHGAHGLE TDIHLSYDHV
PFLMHDFDLK RTTNIGEVQP ESACENPAFF NWDFLSTLNA GKWFVKPELR PFYNMKPLSE
ADKERARNQS IPTLADLLTL AEKERKFVIF DLHRPPPKHP LRHTFVRQVV SVILASKIEQ
HLIFWLPAHD RQYVRSVAPG FQHVGRLVSI ETLAKNNISI INVDYKKLFP NGLRDYKAAN
IHINVYTVNE PWLFSLAWCS RINSVTTDNI GLLSQLDHPH FFMTPKFYVF MWLLADIISV
LFIVAIFCFH WRRETEKEKL FETSSTRTDT QSGNLHIAMK PPVRVVEGPW TLAALYPALP
KSGKEHQGHF NFAAPSKKLL PIKNAVTPLK PGKHEIQPPM PTVVFELTQA PTRQATSEAT
FQTTLPTLKV DKPTMPSIEV PYP
//
