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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: -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

Caution

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

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

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 lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDL022W
SGDiS000002180 GPD1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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
PaxDbiQ00055
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

Protein-protein interaction databases

BioGridi32033, 88 interactors
DIPiDIP-6393N
IntActiQ00055, 4 interactors
MINTiQ00055
STRINGi4932.YDL022W

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

Phylogenomic databases

GeneTreeiENSGT00390000003114
HOGENOMiHOG000246855
InParanoidiQ00055
KOiK00006
OMAiWLCKGFE
OrthoDBiEOG092C3ZQP

Family and domain databases

Gene3Di1.10.1040.10, 1 hit
InterProiView protein in InterPro
IPR008927 6-PGluconate_DH-like_C_sf
IPR013328 6PGD_dom2
IPR006168 G3P_DH_NAD-dep
IPR006109 G3P_DH_NAD-dep_C
IPR017751 G3P_DH_NAD-dep_euk
IPR011128 G3P_DH_NAD-dep_N
IPR036291 NAD(P)-bd_dom_sf
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

Similar proteinsi

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: May 23, 2018
This is version 184 of the entry and version 4 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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

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