Q00055 (GPD1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Glycerol-3-phosphate dehydrogenase [NAD(+)] 1
EC=1.1.1.8

Gene names

Name:	GPD1
Synonyms:	DAR1, HOR1, OSG1
Ordered Locus Names:	YDL022W
ORF Names:	D2830

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	391 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.2
Catalytic activity	sn-glycerol 3-phosphate + NAD+ = glycerone phosphate + NADH.
Subcellular location	Cytoplasm. Peroxisome Ref.12 Ref.14.
Induction	By osmotic stress and by methylglyoxal in a HOG pathway-dependent manner. Ref.2 Ref.15
Miscellaneous	Present with 807 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family.
Caution	Was originally (Ref.8) thought to be GUT2, the FAD-dependent glycerol-3-phosphate dehydrogenase.

Ontologies

Keywords
Biological process	Stress response
Cellular component	Cytoplasm Peroxisome
Ligand	NAD
Molecular function	Oxidoreductase
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	NADH oxidation Inferred from mutant phenotype PubMed 9171333. Source: SGD carbohydrate metabolic process Inferred from electronic annotation. Source: InterPro glycerol-3-phosphate catabolic process Inferred from electronic annotation. Source: InterPro intracellular accumulation of glycerol Inferred from mutant phenotype Ref.2. Source: SGD
Cellular_component	cytosol Inferred from direct assay Ref.14. Source: SGD glycerol-3-phosphate dehydrogenase complex Inferred from electronic annotation. Source: InterPro nucleus Inferred from direct assay PubMed 20026609. Source: SGD peroxisome Inferred from direct assay Ref.14. Source: SGD
Molecular_function	NAD binding Inferred from electronic annotation. Source: InterPro glycerol-3-phosphate dehydrogenase [NAD+] activity Inferred from mutant phenotype Ref.2. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.9

Chain

2 – 391

390

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

PRO_0000138100

Regions

Nucleotide binding

41 – 46

6

NAD By similarity

Region

310 – 311

2

Substrate binding By similarity

Sites

Active site

245

1

Proton acceptor By similarity

Binding site

129

1

NAD By similarity

Binding site

152

1

NAD; via amide nitrogen By similarity

Binding site

152

1

Substrate By similarity

Binding site

185

1

NAD; via amide nitrogen By similarity

Binding site

310

1

NAD By similarity

Binding site

339

1

NAD By similarity

Amino acid modifications

Modified residue

2

1

N-acetylserine Ref.9

Modified residue

12

1

Phosphoserine Ref.18

Modified residue

23

1

Phosphoserine Ref.17

Modified residue

24

1

Phosphoserine Ref.11 Ref.16 Ref.18

Modified residue

25

1

Phosphoserine Ref.17 Ref.18

Modified residue

27

1

Phosphoserine Ref.11 Ref.16 Ref.17 Ref.18

Natural variations

Natural variant

16

1

N → D in strain: WFB. Ref.4

Natural variant

143

1

S → A in strain: WFB. Ref.4

Natural variant

164

1

L → P in strain: WFB. Ref.4

Natural variant

183

1

N → S in strain: WFB. Ref.4

Natural variant

225

1

P → S in strain: WFB. Ref.4

Natural variant

256

1

E → V in strain: WFB. Ref.4

Experimental info

Sequence conflict

103 – 107

5

DNLVA → TIWLL in AAA18631. Ref.8

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

391

Helix Strand Turn

Details...

Beta strand

35 – 40

6

Helix

44 – 59

16

Turn

61 – 63

3

Beta strand

64 – 71

8

Beta strand

76 – 79

4

Helix

82 – 86

5

Turn

87 – 89

3

Turn

93 – 95

3

Beta strand

103 – 109

7

Helix

111 – 115

5

Beta strand

119 – 123

5

Helix

127 – 129

3

Helix

130 – 137

8

Turn

138 – 140

3

Beta strand

146 – 149

4

Beta strand

155 – 157

3

Beta strand

160 – 162

3

Helix

164 – 172

9

Beta strand

175 – 180

6

Helix

185 – 189

5

Beta strand

194 – 199

6

Beta strand

209 – 212

4

Helix

215 – 222

8

Beta strand

227 – 233

7

Helix

235 – 257

23

Helix

261 – 283

23

Helix

289 – 294

6

Turn

296 – 298

3

Helix

299 – 307

9

Helix

310 – 320

11

Helix

325 – 333

9

Helix

340 – 354

15

Helix

361 – 371

11

Helix

379 – 383

5

Sequences

	Sequence		Length	Mass (Da)
	Q00055 [UniParc]. Last modified January 23, 2007. Version 4. Checksum: F5F1F7F111F707D1	FASTA	391	42,869
	10 20 30 40 50 60 MSAAADRLNL TSGHLNAGRK RSSSSVSLKA AEKPFKVTVI GSGNWGTTIA KVVAENCKGY 70 80 90 100 110 120 PEVFAPIVQM WVFEEEINGE KLTEIINTRH QNVKYLPGIT LPDNLVANPD LIDSVKDVDI 130 140 150 160 170 180 IVFNIPHQFL PRICSQLKGH VDSHVRAISC LKGFEVGAKG VQLLSSYITE ELGIQCGALS 190 200 210 220 230 240 GANIATEVAQ EHWSETTVAY HIPKDFRGEG KDVDHKVLKA LFHRPYFHVS VIEDVAGISI 250 260 270 280 290 300 CGALKNVVAL GCGFVEGLGW GNNASAAIQR VGLGEIIRFG QMFFPESREE TYYQESAGVA 310 320 330 340 350 360 DLITTCAGGR NVKVARLMAT SGKDAWECEK ELLNGQSAQG LITCKEVHEW LETCGSVEDF 370 380 390 PLFEAVYQIV YNNYPMKNLP DMIEELDLHE D

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A gene encoding sn-glycerol 3-phosphate dehydrogenase (NAD+) complements an osmosensitive mutant of Saccharomyces cerevisiae." Larsson K., Ansell R., Eriksson P., Adler L. Mol. Microbiol. 10:1101-1111(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 30-49.
[2]	"GPD1, which encodes glycerol-3-phosphate dehydrogenase, is essential for growth under osmotic stress in Saccharomyces cerevisiae, and its expression is regulated by the high-osmolarity glycerol response pathway." Albertyn J., Hohmann S., Thevelein J.M., Prior B.A. Mol. Cell. Biol. 14:4135-4144(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INDUCTION.
[3]	"Cloning, sequence, and disruption of the Saccharomyces diastaticus DAR1 gene encoding a glycerol-3-phosphate dehydrogenase." Wang H.T., Rahaim P., Robbins P., Yocum R.R. J. Bacteriol. 176:7091-7095(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: Diastaticus / ATCC 62933 / NRC 5704 / J132b.
[4]	"Research on the mechanism of osmotolerance and thermotolerance of yeast." Ma X., Guo Y., Zhang F., Yu H., Kuang J., Yao J., Li Z., He G. Submitted (APR-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS ASP-16; ALA-143; PRO-164; SER-183; SER-225 AND VAL-256. Strain: FHS and WFB.
[5]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P. Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[6]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[7]	"The effects of co-expression of ScGPD1 and AtNHX1 on the salt tolerance of yeast." Fu C., Zheng D. Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[8]	"Cloning and characterisation of the Saccharomyces cerevisiae glycerol-3-phosphate dehydrogenase (GUT2) promoter." Sleep D., Ogden J.E., Roberts N.A., Goodey A.R. Gene 101:89-96(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-107.
[9]	Bienvenut W.V., Peters C. Submitted (JUN-2005) to UniProtKB Cited for: PROTEIN SEQUENCE OF 2-19 AND 271-278, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT SER-2, MASS SPECTROMETRY.
[10]	"Protein expression during exponential growth in 0.7 M NaCl medium of Saccharomyces cerevisiae." Norbeck J., Blomberg A. FEMS Microbiol. Lett. 137:1-8(1996) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 8-16; 95-108 AND 160-173. Strain: ATCC 38531 / Y41.
[11]	"Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae." Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., White F.M. Nat. Biotechnol. 20:301-305(2002) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-24 AND SER-27, MASS SPECTROMETRY. Strain: 2124.
[12]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[13]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[14]	"Distinct intracellular localization of Gpd1p and Gpd2p, the two yeast isoforms of NAD+-dependent glycerol-3-phosphate dehydrogenase, explains their different contributions to redox-driven glycerol production." Valadi A., Granath K., Gustafsson L., Adler L. J. Biol. Chem. 279:39677-39685(2004) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[15]	"The HOG MAP kinase pathway is required for the induction of methylglyoxal-responsive genes and determines methylglyoxal resistance in Saccharomyces cerevisiae." Aguilera J., Rodriguez-Vargas S., Prieto J.A. Mol. Microbiol. 56:228-239(2005) [PubMed] [Europe PMC] [Abstract] Cited for: INDUCTION.
[16]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-24 AND SER-27, MASS SPECTROMETRY. Strain: ADR376.
[17]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-23; SER-25 AND SER-27, MASS SPECTROMETRY.
[18]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-12; SER-24; SER-25 AND SER-27, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

S40059.

RefSeq

NP_010262.1. NM_001180081.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4FGW	X-ray	2.45	A/B	1-391	[»]

ProteinModelPortal

Q00055.

SMR

Q00055. Positions 33-385.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6393N.

IntAct

Q00055. 4 interactions.

MINT

MINT-2788005.

STRING

4932.YDL022W.

Proteomic databases

PaxDb

Q00055.

PeptideAtlas

Q00055.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDL022W; YDL022W; YDL022W.

GeneID

851539.

KEGG

sce:YDL022W.

Organism-specific databases

SGD

S000002180. GPD1.

Phylogenomic databases

eggNOG

COG0240.

GeneTree

ENSGT00390000003114.

HOGENOM

HOG000246855.

KO

K00006.

OMA

FHVNVIE.

OrthoDB

EOG4FBN2Q.

Enzyme and pathway databases

BRENDA

1.1.1.8. 984.

Gene expression databases

ArrayExpress

Q00055.

Genevestigator

Q00055.

GermOnline

YDL022W. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

1.10.1040.10. 1 hit.
3.40.50.720. 1 hit.

InterPro

IPR008927. 6-PGluconate_DH_C-like.
IPR013328. DH_multihelical.
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.
[Graphical view]

PANTHER

PTHR11728. PTHR11728. 1 hit.

Pfam

PF07479. NAD_Gly3P_dh_C. 1 hit.
PF01210. NAD_Gly3P_dh_N. 1 hit.
[Graphical view]

PIRSF

PIRSF000114. Glycerol-3-P_dh. 1 hit.

PRINTS

PR00077. GPDHDRGNASE.

SUPFAM

SSF48179. 6DGDH_C_like. 1 hit.

TIGRFAMs

TIGR03376. glycerol3P_DH. 1 hit.

PROSITE

PS00957. NAD_G3PDH. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

968943.

Entry information

Entry name

GPD1_YEAST

Accession

Primary (citable) accession number: Q00055
Secondary accession number(s): A5YWB0 , D6VRW8, Q6J5J2, Q6J5J5

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1993
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 138 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program