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Protein

Glycerophosphodiester phosphodiesterase domain-containing protein 5

Gene

GDPD5

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

Functioni

Promotes neurite formation. Cooperates with PRDX1 to drive postmitotic motor neuron differentiation. The glycerophosphodiester phosphodiesterase activity may be required for its role in neuronal differentiation. May contribute to the osmotic regulation of cellular glycerophosphocholine.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Neurogenesis

Enzyme and pathway databases

BRENDAi3.1.4.46. 2681.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycerophosphodiester phosphodiesterase domain-containing protein 5 (EC:3.1.-.-)
Alternative name(s):
Glycerophosphodiester phosphodiesterase 2
Gene namesi
Name:GDPD5
Synonyms:GDE2
ORF Names:PP6037, PP9363, UNQ1850/PRO3580
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

HGNCiHGNC:28804. GDPD5.

Subcellular locationi

  • Endomembrane system By similarity; Multi-pass membrane protein Sequence analysis
  • Cytoplasmperinuclear region By similarity
  • Cell projectiongrowth cone By similarity

  • Note: In a punctate perinuclear pattern.By similarity

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 4242CytoplasmicSequence analysisAdd
BLAST
Transmembranei43 – 6321HelicalSequence analysisAdd
BLAST
Topological domaini64 – 8926ExtracellularSequence analysisAdd
BLAST
Transmembranei90 – 11021HelicalSequence analysisAdd
BLAST
Topological domaini111 – 12515CytoplasmicSequence analysisAdd
BLAST
Transmembranei126 – 14621HelicalSequence analysisAdd
BLAST
Topological domaini147 – 16014ExtracellularSequence analysisAdd
BLAST
Transmembranei161 – 18121HelicalSequence analysisAdd
BLAST
Topological domaini182 – 19211CytoplasmicSequence analysisAdd
BLAST
Transmembranei193 – 21321HelicalSequence analysisAdd
BLAST
Topological domaini214 – 496283ExtracellularSequence analysisAdd
BLAST
Transmembranei497 – 51721HelicalSequence analysisAdd
BLAST
Topological domaini518 – 60588CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell projection, Cytoplasm, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA142671743.

Polymorphism and mutation databases

BioMutaiGDPD5.
DMDMi115502213.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 605605Glycerophosphodiester phosphodiesterase domain-containing protein 5PRO_0000251941Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi15 ↔ 18Sequence analysis
Disulfide bondi25 ↔ 571By similarity
Glycosylationi301 – 3011N-linked (GlcNAc...)Sequence analysis
Glycosylationi336 – 3361N-linked (GlcNAc...)Sequence analysis
Glycosylationi352 – 3521N-linked (GlcNAc...)Sequence analysis
Glycosylationi374 – 3741N-linked (GlcNAc...)Sequence analysis
Glycosylationi448 – 4481N-linked (GlcNAc...)Sequence analysis

Post-translational modificationi

Intramolecular disulfide bond between Cys-25 and Cys-571 is reduced by PRDX1.By similarity

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

EPDiQ8WTR4.
PaxDbiQ8WTR4.
PRIDEiQ8WTR4.

Expressioni

Gene expression databases

BgeeiQ8WTR4.
CleanExiHS_GDPD5.
ExpressionAtlasiQ8WTR4. baseline and differential.
GenevisibleiQ8WTR4. HS.

Interactioni

Subunit structurei

Interacts with PRDX1; forms a mixed-disulfide with PRDX1, leading to disrupt intramolecular disulfide bond between Cys-25 and Cys-571.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
PEX5P505423EBI-2833203,EBI-597835
SIAH1Q8IUQ43EBI-2833203,EBI-747107

Protein-protein interaction databases

BioGridi123512. 40 interactions.
IntActiQ8WTR4. 3 interactions.
STRINGi9606.ENSP00000337972.

Structurei

3D structure databases

ProteinModelPortaliQ8WTR4.
SMRiQ8WTR4. Positions 228-476.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini228 – 485258GP-PDEAdd
BLAST

Sequence similaritiesi

Contains 1 GP-PDE domain.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG2258. Eukaryota.
COG0584. LUCA.
GeneTreeiENSGT00510000046457.
HOVERGENiHBG081551.
InParanoidiQ8WTR4.
OMAiWEVHNDY.
OrthoDBiEOG7F511B.
PhylomeDBiQ8WTR4.
TreeFamiTF313692.

Family and domain databases

Gene3Di3.20.20.190. 1 hit.
InterProiIPR004129. GlyceroP-diester-Pdiesterase.
IPR030395. GP_PDE_dom.
IPR017946. PLC-like_Pdiesterase_TIM-brl.
[Graphical view]
PANTHERiPTHR23344. PTHR23344. 1 hit.
PfamiPF03009. GDPD. 1 hit.
[Graphical view]
SUPFAMiSSF51695. SSF51695. 1 hit.
PROSITEiPS51704. GP_PDE. 1 hit.
[Graphical view]

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8WTR4-1) [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
MVRHQPLQYY EPQLCLSCLT GIYGCRWKRY QRSHDDTTPW ERLWFLLLTF
60 70 80 90 100
TFGLTLTWLY FWWEVHNDYD EFNWYLYNRM GYWSDWPVPI LVTTAAAFAY
110 120 130 140 150
IAGLLVLALC HIAVGQQMNL HWLHKIGLVV ILASTVVAMS AVAQLWEDEW
160 170 180 190 200
EVLLISLQGT APFLHVGAVA AVTMLSWIVA GQFARAERTS SQVTILCTFF
210 220 230 240 250
TVVFALYLAP LTISSPCIME KKDLGPKPAL IGHRGAPMLA PEHTLMSFRK
260 270 280 290 300
ALEQKLYGLQ ADITISLDGV PFLMHDTTLR RTTNVEEEFP ELARRPASML
310 320 330 340 350
NWTTLQRLNA GQWFLKTDPF WTASSLSPSD HREAQNQSIC SLAELLELAK
360 370 380 390 400
GNATLLLNLR DPPREHPYRS SFINVTLEAV LHSGFPQHQV MWLPSRQRPL
410 420 430 440 450
VRKVAPGFQQ TSGSKEAVAS LRRGHIQRLN LRYTQVSRQE LRDYASWNLS
460 470 480 490 500
VNLYTVNAPW LFSLLWCAGV PSVTSDNSHA LSQVPSPLWI MPPDEYCLMW
510 520 530 540 550
VTADLVSFTL IVGIFVLQKW RLGGIRSYNP EQIMLSAAVR RTSRDVSIMK
560 570 580 590 600
EKLIFSEISD GVEVSDVLSV CSDNSYDTYA NSTATPVGPR GGGSHTKTLI

ERSGR
Length:605
Mass (Da):68,586
Last modified:October 3, 2006 - v2
Checksum:iA4AC52A6773FB7EF
GO
Isoform 2 (identifier: Q8WTR4-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     40-158: Missing.

Show »
Length:486
Mass (Da):54,523
Checksum:i2946647BCA4D62DA
GO
Isoform 3 (identifier: Q8WTR4-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-138: Missing.

Show »
Length:467
Mass (Da):52,139
Checksum:iB5CF612BBBCCF38B
GO
Isoform 4 (identifier: Q8WTR4-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-218: Missing.

Show »
Length:387
Mass (Da):43,468
Checksum:i4ACF7C4116F4B9DE
GO
Isoform 5 (identifier: Q8WTR4-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-245: Missing.

Show »
Length:360
Mass (Da):40,577
Checksum:iAED99694192208EF
GO

Sequence cautioni

The sequence AAP97686.1 differs from that shown. Reason: Erroneous initiation. Curated
The sequence BAC11242.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti233 – 2331H → N in AAH33391 (PubMed:15489334).Curated
Sequence conflicti397 – 3993QRP → GS in AAP97686 (Ref. 6) Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti480 – 4801A → T.4 Publications
Corresponds to variant rs571353 [ dbSNP | Ensembl ].
VAR_027733

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 245245Missing in isoform 5. 1 PublicationVSP_020813Add
BLAST
Alternative sequencei1 – 218218Missing in isoform 4. 1 PublicationVSP_020814Add
BLAST
Alternative sequencei1 – 138138Missing in isoform 3. 1 PublicationVSP_020815Add
BLAST
Alternative sequencei40 – 158119Missing in isoform 2. 1 PublicationVSP_020816Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF318351 mRNA. Translation: AAL55858.1.
AF318377 mRNA. Translation: AAL55884.1.
AY358477 mRNA. Translation: AAQ88841.1.
AK098808 mRNA. Translation: BAC05418.1.
BC018771 mRNA. Translation: AAH18771.1.
BC033391 mRNA. Translation: AAH33391.1.
AK074848 mRNA. Translation: BAC11242.1. Different initiation.
AF451987 mRNA. Translation: AAP97686.1. Different initiation.
CCDSiCCDS8238.1. [Q8WTR4-1]
RefSeqiNP_110419.5. NM_030792.6. [Q8WTR4-1]
XP_006718760.1. XM_006718697.2. [Q8WTR4-1]
XP_011543587.1. XM_011545285.1. [Q8WTR4-3]
XP_011543589.1. XM_011545287.1. [Q8WTR4-5]
UniGeneiHs.503297.

Genome annotation databases

EnsembliENST00000336898; ENSP00000337972; ENSG00000158555. [Q8WTR4-1]
ENST00000526177; ENSP00000434050; ENSG00000158555. [Q8WTR4-3]
ENST00000529721; ENSP00000433214; ENSG00000158555. [Q8WTR4-1]
ENST00000533784; ENSP00000437049; ENSG00000158555. [Q8WTR4-2]
ENST00000533805; ENSP00000435196; ENSG00000158555. [Q8WTR4-5]
GeneIDi81544.
KEGGihsa:81544.
UCSCiuc001own.5. human. [Q8WTR4-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF318351 mRNA. Translation: AAL55858.1.
AF318377 mRNA. Translation: AAL55884.1.
AY358477 mRNA. Translation: AAQ88841.1.
AK098808 mRNA. Translation: BAC05418.1.
BC018771 mRNA. Translation: AAH18771.1.
BC033391 mRNA. Translation: AAH33391.1.
AK074848 mRNA. Translation: BAC11242.1. Different initiation.
AF451987 mRNA. Translation: AAP97686.1. Different initiation.
CCDSiCCDS8238.1. [Q8WTR4-1]
RefSeqiNP_110419.5. NM_030792.6. [Q8WTR4-1]
XP_006718760.1. XM_006718697.2. [Q8WTR4-1]
XP_011543587.1. XM_011545285.1. [Q8WTR4-3]
XP_011543589.1. XM_011545287.1. [Q8WTR4-5]
UniGeneiHs.503297.

3D structure databases

ProteinModelPortaliQ8WTR4.
SMRiQ8WTR4. Positions 228-476.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi123512. 40 interactions.
IntActiQ8WTR4. 3 interactions.
STRINGi9606.ENSP00000337972.

Polymorphism and mutation databases

BioMutaiGDPD5.
DMDMi115502213.

Proteomic databases

EPDiQ8WTR4.
PaxDbiQ8WTR4.
PRIDEiQ8WTR4.

Protocols and materials databases

DNASUi81544.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000336898; ENSP00000337972; ENSG00000158555. [Q8WTR4-1]
ENST00000526177; ENSP00000434050; ENSG00000158555. [Q8WTR4-3]
ENST00000529721; ENSP00000433214; ENSG00000158555. [Q8WTR4-1]
ENST00000533784; ENSP00000437049; ENSG00000158555. [Q8WTR4-2]
ENST00000533805; ENSP00000435196; ENSG00000158555. [Q8WTR4-5]
GeneIDi81544.
KEGGihsa:81544.
UCSCiuc001own.5. human. [Q8WTR4-1]

Organism-specific databases

CTDi81544.
GeneCardsiGDPD5.
HGNCiHGNC:28804. GDPD5.
MIMi609632. gene.
neXtProtiNX_Q8WTR4.
PharmGKBiPA142671743.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2258. Eukaryota.
COG0584. LUCA.
GeneTreeiENSGT00510000046457.
HOVERGENiHBG081551.
InParanoidiQ8WTR4.
OMAiWEVHNDY.
OrthoDBiEOG7F511B.
PhylomeDBiQ8WTR4.
TreeFamiTF313692.

Enzyme and pathway databases

BRENDAi3.1.4.46. 2681.

Miscellaneous databases

ChiTaRSiGDPD5. human.
GenomeRNAii81544.
NextBioi71781.
PROiQ8WTR4.
SOURCEiSearch...

Gene expression databases

BgeeiQ8WTR4.
CleanExiHS_GDPD5.
ExpressionAtlasiQ8WTR4. baseline and differential.
GenevisibleiQ8WTR4. HS.

Family and domain databases

Gene3Di3.20.20.190. 1 hit.
InterProiIPR004129. GlyceroP-diester-Pdiesterase.
IPR030395. GP_PDE_dom.
IPR017946. PLC-like_Pdiesterase_TIM-brl.
[Graphical view]
PANTHERiPTHR23344. PTHR23344. 1 hit.
PfamiPF03009. GDPD. 1 hit.
[Graphical view]
SUPFAMiSSF51695. SSF51695. 1 hit.
PROSITEiPS51704. GP_PDE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Large-scale cDNA transfection screening for genes related to cancer development and progression."
    Wan D., Gong Y., Qin W., Zhang P., Li J., Wei L., Zhou X., Li H., Qiu X., Zhong F., He L., Yu J., Yao G., Jiang H., Qian L., Yu Y., Shu H., Chen X.
    , Xu H., Guo M., Pan Z., Chen Y., Ge C., Yang S., Gu J.
    Proc. Natl. Acad. Sci. U.S.A. 101:15724-15729(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT THR-480.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), VARIANT THR-480.
  3. "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 5), VARIANT THR-480.
    Tissue: Thyroid.
  4. "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 3 AND 4), VARIANT THR-480.
    Tissue: Eye and Testis.
  5. "Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries."
    Otsuki T., Ota T., Nishikawa T., Hayashi K., Suzuki Y., Yamamoto J., Wakamatsu A., Kimura K., Sakamoto K., Hatano N., Kawai Y., Ishii S., Saito K., Kojima S., Sugiyama T., Ono T., Okano K., Yoshikawa Y.
    , Aotsuka S., Sasaki N., Hattori A., Okumura K., Nagai K., Sugano S., Isogai T.
    DNA Res. 12:117-126(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 142-605.
    Tissue: Teratocarcinoma.
  6. Guo J.H., Zan Q., Yu L.
    Submitted (NOV-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 166-605.
    Tissue: Brain.

Entry informationi

Entry nameiGDPD5_HUMAN
AccessioniPrimary (citable) accession number: Q8WTR4
Secondary accession number(s): Q49AQ5
, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: October 3, 2006
Last modified: May 11, 2016
This is version 103 of the entry and version 2 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 11
    Human chromosome 11: 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

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.