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UniProtKB - Q00055 (GPD1_YEAST)

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Protein

Glycerol-3-phosphate dehydrogenase [NAD(+)] 1

Gene

GPD1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the production and accumulation of glycerol during hyperosmotic stress conditions. Glycerol acts as a osmoregulator that prevents loss of water and turgor of the cells.1 Publication

Miscellaneous

Present with 807 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

sn-glycerol 3-phosphate + NAD+ = glycerone phosphate + NADH.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei129NADBy similarity1
Binding sitei152NAD; via amide nitrogenBy similarity1
Binding sitei152SubstrateBy similarity1
Binding sitei185NAD; via amide nitrogenBy similarity1
Active sitei245Proton acceptorBy similarity1
Binding sitei310NADBy similarity1
Binding sitei339NADBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi41 – 46NADBy similarity6

GO - Molecular functioni

  • glycerol-3-phosphate dehydrogenase [NAD+] activity Source: SGD
  • NAD binding Source: InterPro
  • protein homodimerization activity Source: InterPro
Complete GO annotation...

GO - Biological processi

  • carbohydrate metabolic process Source: InterPro
  • glycerol-3-phosphate catabolic process Source: InterPro
  • intracellular accumulation of glycerol Source: SGD
  • NADH oxidation Source: SGD
  • protein import into peroxisome matrix Source: SGD
Complete GO annotation...

Keywordsi

Molecular functionOxidoreductase
Biological processStress response
LigandNAD

Enzyme and pathway databases

BioCyciMetaCyc:YDL022W-MONOMER.
YEAST:YDL022W-MONOMER.
BRENDAi1.1.1.8. 984.
ReactomeiR-SCE-1483166. Synthesis of PA.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycerol-3-phosphate dehydrogenase [NAD(+)] 1 (EC:1.1.1.8)
Gene namesi
Name:GPD1
Synonyms:DAR1, HOR1, OSG1
Ordered Locus Names:YDL022W
ORF Names:D2830
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDL022W.
SGDiS000002180. GPD1.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
  • glycerol-3-phosphate dehydrogenase complex Source: InterPro
  • nucleus Source: SGD
  • peroxisome Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Peroxisome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001381002 – 391Glycerol-3-phosphate dehydrogenase [NAD(+)] 1Add BLAST390

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserine1 Publication1
Modified residuei24PhosphoserineCombined sources1
Modified residuei27PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ00055.
PRIDEiQ00055.
TopDownProteomicsiQ00055.

PTM databases

iPTMnetiQ00055.

Expressioni

Inductioni

By osmotic stress and by methylglyoxal in a HOG pathway-dependent manner.2 Publications

Interactioni

GO - Molecular functioni

Complete GO annotation...

Protein-protein interaction databases

BioGridi32033. 86 interactors.
DIPiDIP-6393N.
IntActiQ00055. 3 interactors.
MINTiMINT-2788005.

Structurei

Secondary structure

1391
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi35 – 40Combined sources6
Helixi44 – 59Combined sources16
Turni61 – 63Combined sources3
Beta strandi64 – 71Combined sources8
Beta strandi76 – 79Combined sources4
Helixi82 – 86Combined sources5
Turni87 – 89Combined sources3
Turni93 – 95Combined sources3
Beta strandi103 – 109Combined sources7
Helixi111 – 115Combined sources5
Beta strandi119 – 123Combined sources5
Helixi127 – 129Combined sources3
Helixi130 – 137Combined sources8
Turni138 – 140Combined sources3
Beta strandi146 – 149Combined sources4
Beta strandi155 – 157Combined sources3
Beta strandi160 – 162Combined sources3
Helixi164 – 172Combined sources9
Beta strandi175 – 180Combined sources6
Helixi185 – 189Combined sources5
Beta strandi194 – 199Combined sources6
Beta strandi209 – 212Combined sources4
Helixi215 – 222Combined sources8
Beta strandi227 – 233Combined sources7
Helixi235 – 257Combined sources23
Helixi261 – 283Combined sources23
Helixi289 – 294Combined sources6
Turni296 – 298Combined sources3
Helixi299 – 307Combined sources9
Helixi310 – 320Combined sources11
Helixi325 – 333Combined sources9
Helixi340 – 354Combined sources15
Helixi361 – 371Combined sources11
Helixi379 – 383Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4FGWX-ray2.45A/B1-391[»]
ProteinModelPortaliQ00055.
SMRiQ00055.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni310 – 311Substrate bindingBy similarity2

Sequence similaritiesi

Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000003114.
HOGENOMiHOG000246855.
InParanoidiQ00055.
KOiK00006.
OMAiNMIGKGY.
OrthoDBiEOG092C3ZQP.

Family and domain databases

Gene3Di1.10.1040.10. 1 hit.
InterProiView protein in InterPro
IPR008927. 6-PGluconate_DH_C-like.
IPR013328. 6PGD_dom_2.
IPR006168. G3P_DH_NAD-dep.
IPR006109. G3P_DH_NAD-dep_C.
IPR017751. G3P_DH_NAD-dep_euk.
IPR011128. G3P_DH_NAD-dep_N.
IPR016040. NAD(P)-bd_dom.
PfamiView protein in Pfam
PF07479. NAD_Gly3P_dh_C. 1 hit.
PF01210. NAD_Gly3P_dh_N. 1 hit.
PIRSFiPIRSF000114. Glycerol-3-P_dh. 1 hit.
PRINTSiPR00077. GPDHDRGNASE.
SUPFAMiSSF48179. SSF48179. 1 hit.
SSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR03376. glycerol3P_DH. 1 hit.
PROSITEiView protein in PROSITE
PS00957. NAD_G3PDH. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q00055-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSAAADRLNL TSGHLNAGRK RSSSSVSLKA AEKPFKVTVI GSGNWGTTIA 
        60         70         80         90        100
KVVAENCKGY PEVFAPIVQM WVFEEEINGE KLTEIINTRH QNVKYLPGIT 
       110        120        130        140        150
LPDNLVANPD LIDSVKDVDI IVFNIPHQFL PRICSQLKGH VDSHVRAISC 
       160        170        180        190        200
LKGFEVGAKG VQLLSSYITE ELGIQCGALS GANIATEVAQ EHWSETTVAY 
       210        220        230        240        250
HIPKDFRGEG KDVDHKVLKA LFHRPYFHVS VIEDVAGISI CGALKNVVAL 
       260        270        280        290        300
GCGFVEGLGW GNNASAAIQR VGLGEIIRFG QMFFPESREE TYYQESAGVA 
       310        320        330        340        350
DLITTCAGGR NVKVARLMAT SGKDAWECEK ELLNGQSAQG LITCKEVHEW 
       360        370        380        390 
LETCGSVEDF PLFEAVYQIV YNNYPMKNLP DMIEELDLHE D
Length:391
Mass (Da):42,869
Last modified:January 23, 2007 - v4
Checksum:iF5F1F7F111F707D1
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti103 – 107DNLVA → TIWLL in AAA18631 (PubMed:1676389).Curated5

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti16N → D in strain: WFB. 1 Publication1
Natural varianti143S → A in strain: WFB. 1 Publication1
Natural varianti164L → P in strain: WFB. 1 Publication1
Natural varianti183N → S in strain: WFB. 1 Publication1
Natural varianti225P → S in strain: WFB. 1 Publication1
Natural varianti256E → V in strain: WFB. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z24454 Genomic DNA. Translation: CAA80827.1.
X76859 Genomic DNA. Translation: CAA54189.1.
U04621 Genomic DNA. Translation: AAA64936.1.
AY598965 Genomic DNA. Translation: AAT27375.1.
AY598968 Genomic DNA. Translation: AAT27378.1.
Z48432 Genomic DNA. Translation: CAA88337.1.
Z74071 Genomic DNA. Translation: CAA98582.1.
EF596737 Genomic DNA. Translation: ABQ58864.1.
M38740 Genomic DNA. Translation: AAA18631.1.
BK006938 Genomic DNA. Translation: DAA11828.1.
PIRiS40059.
RefSeqiNP_010262.1. NM_001180081.1.

Genome annotation databases

EnsemblFungiiYDL022W; YDL022W; YDL022W.
GeneIDi851539.
KEGGisce:YDL022W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z24454 Genomic DNA. Translation: CAA80827.1.
X76859 Genomic DNA. Translation: CAA54189.1.
U04621 Genomic DNA. Translation: AAA64936.1.
AY598965 Genomic DNA. Translation: AAT27375.1.
AY598968 Genomic DNA. Translation: AAT27378.1.
Z48432 Genomic DNA. Translation: CAA88337.1.
Z74071 Genomic DNA. Translation: CAA98582.1.
EF596737 Genomic DNA. Translation: ABQ58864.1.
M38740 Genomic DNA. Translation: AAA18631.1.
BK006938 Genomic DNA. Translation: DAA11828.1.
PIRiS40059.
RefSeqiNP_010262.1. NM_001180081.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4FGWX-ray2.45A/B1-391[»]
ProteinModelPortaliQ00055.
SMRiQ00055.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32033. 86 interactors.
DIPiDIP-6393N.
IntActiQ00055. 3 interactors.
MINTiMINT-2788005.

PTM databases

iPTMnetiQ00055.

Proteomic databases

MaxQBiQ00055.
PRIDEiQ00055.
TopDownProteomicsiQ00055.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL022W; YDL022W; YDL022W.
GeneIDi851539.
KEGGisce:YDL022W.

Organism-specific databases

EuPathDBiFungiDB:YDL022W.
SGDiS000002180. GPD1.

Phylogenomic databases

GeneTreeiENSGT00390000003114.
HOGENOMiHOG000246855.
InParanoidiQ00055.
KOiK00006.
OMAiNMIGKGY.
OrthoDBiEOG092C3ZQP.

Enzyme and pathway databases

BioCyciMetaCyc:YDL022W-MONOMER.
YEAST:YDL022W-MONOMER.
BRENDAi1.1.1.8. 984.
ReactomeiR-SCE-1483166. Synthesis of PA.

Miscellaneous databases

PROiPR:Q00055.

Family and domain databases

Gene3Di1.10.1040.10. 1 hit.
InterProiView protein in InterPro
IPR008927. 6-PGluconate_DH_C-like.
IPR013328. 6PGD_dom_2.
IPR006168. G3P_DH_NAD-dep.
IPR006109. G3P_DH_NAD-dep_C.
IPR017751. G3P_DH_NAD-dep_euk.
IPR011128. G3P_DH_NAD-dep_N.
IPR016040. NAD(P)-bd_dom.
PfamiView protein in Pfam
PF07479. NAD_Gly3P_dh_C. 1 hit.
PF01210. NAD_Gly3P_dh_N. 1 hit.
PIRSFiPIRSF000114. Glycerol-3-P_dh. 1 hit.
PRINTSiPR00077. GPDHDRGNASE.
SUPFAMiSSF48179. SSF48179. 1 hit.
SSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR03376. glycerol3P_DH. 1 hit.
PROSITEiView protein in PROSITE
PS00957. NAD_G3PDH. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiGPD1_YEAST
AccessioniPrimary (citable) accession number: Q00055
Secondary accession number(s): A5YWB0
, D6VRW8, Q6J5J2, Q6J5J5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: January 23, 2007
Last modified: June 7, 2017
This is version 175 of the entry and version 4 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Caution

Was originally thought to be GUT2, the FAD-dependent glycerol-3-phosphate dehydrogenase.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

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.