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P38720

- 6PGD1_YEAST

UniProt

P38720 - 6PGD1_YEAST

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Protein

6-phosphogluconate dehydrogenase, decarboxylating 1

Gene

GND1

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

Functioni

Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO2, with concomitant reduction of NADP to NADPH.1 Publication

Catalytic activityi

6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH.1 Publication

Kineticsi

  1. KM=50 µM for 6-phosphogluconate1 Publication
  2. KM=35 µM for NADP1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei102 – 1021NADPBy similarity
Binding sitei102 – 1021SubstrateBy similarity
Active sitei182 – 1821Proton acceptorBy similarity
Active sitei189 – 1891Proton donorBy similarity
Binding sitei190 – 1901SubstrateBy similarity
Binding sitei259 – 2591Substrate; via amide nitrogenBy similarity
Binding sitei286 – 2861SubstrateBy similarity
Binding sitei446 – 4461Substrate; shared with dimeric partnerBy similarity
Binding sitei452 – 4521Substrate; shared with dimeric partnerBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi9 – 146NADPBy similarity
Nucleotide bindingi32 – 343NADPBy similarity
Nucleotide bindingi74 – 763NADPBy similarity

GO - Molecular functioni

  1. NADP binding Source: InterPro
  2. phosphogluconate dehydrogenase (decarboxylating) activity Source: SGD

GO - Biological processi

  1. cellular response to oxidative stress Source: SGD
  2. D-gluconate metabolic process Source: UniProtKB-KW
  3. pentose-phosphate shunt, oxidative branch Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Gluconate utilization, Pentose shunt

Keywords - Ligandi

NADP

Enzyme and pathway databases

BioCyciYEAST:YHR183W-MONOMER.
ReactomeiREACT_233695. Pentose phosphate pathway (hexose monophosphate shunt).
SABIO-RKP38720.
UniPathwayiUPA00115; UER00410.

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, decarboxylating 1 (EC:1.1.1.44)
Gene namesi
Name:GND1
Ordered Locus Names:YHR183W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome VIII

Organism-specific databases

CYGDiYHR183w.
SGDiS000001226. GND1.

Subcellular locationi

Cytoplasm 1 Publication

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 4894896-phosphogluconate dehydrogenase, decarboxylating 1PRO_0000090075Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei50 – 501Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP38720.
PaxDbiP38720.
PeptideAtlasiP38720.
PRIDEiP38720.

Expressioni

Gene expression databases

GenevestigatoriP38720.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi36616. 143 interactions.
DIPiDIP-6604N.
IntActiP38720. 109 interactions.
MINTiMINT-688249.
STRINGi4932.YHR183W.

Structurei

Secondary structure

1
489
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 85Combined sources
Helixi12 – 2312Combined sources
Beta strandi28 – 314Combined sources
Beta strandi33 – 353Combined sources
Helixi36 – 438Combined sources
Turni44 – 485Combined sources
Beta strandi49 – 524Combined sources
Helixi57 – 626Combined sources
Beta strandi69 – 724Combined sources
Helixi78 – 8710Combined sources
Helixi88 – 903Combined sources
Beta strandi96 – 994Combined sources
Helixi105 – 11713Combined sources
Beta strandi121 – 1299Combined sources
Helixi130 – 1367Combined sources
Beta strandi139 – 1446Combined sources
Helixi146 – 1483Combined sources
Helixi149 – 15911Combined sources
Beta strandi166 – 1683Combined sources
Helixi177 – 20529Combined sources
Helixi211 – 22212Combined sources
Turni223 – 2264Combined sources
Helixi229 – 23810Combined sources
Beta strandi245 – 2473Combined sources
Helixi248 – 2514Combined sources
Helixi261 – 27212Combined sources
Helixi277 – 29014Combined sources
Helixi292 – 30110Combined sources
Helixi315 – 34834Combined sources
Helixi354 – 3629Combined sources
Beta strandi363 – 3653Combined sources
Helixi370 – 38112Combined sources
Helixi388 – 3903Combined sources
Helixi392 – 41524Combined sources
Helixi420 – 43213Combined sources
Helixi439 – 44911Combined sources
Helixi458 – 4603Combined sources
Beta strandi463 – 4653Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2P4QX-ray2.37A1-489[»]
ProteinModelPortaliP38720.
SMRiP38720. Positions 1-476.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP38720.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni128 – 1303Substrate bindingBy similarity
Regioni185 – 1862Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0362.
GeneTreeiENSGT00390000009023.
HOGENOMiHOG000255147.
InParanoidiP38720.
KOiK00033.
OMAiEFNWNLP.
OrthoDBiEOG7F252Z.

Family and domain databases

Gene3Di1.10.1040.10. 1 hit.
1.20.5.320. 1 hit.
3.40.50.720. 1 hit.
InterProiIPR008927. 6-PGluconate_DH_C-like.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_decarbox.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR013328. DH_multihelical.
IPR012284. Fibritin/6PGD_C-extension.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000109. 6PGD. 1 hit.
SUPFAMiSSF48179. SSF48179. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P38720-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSADFGLIGL AVMGQNLILN AADHGFTVCA YNRTQSKVDH FLANEAKGKS
60 70 80 90 100
IIGATSIEDF ISKLKRPRKV MLLVKAGAPV DALINQIVPL LEKGDIIIDG
110 120 130 140 150
GNSHFPDSNR RYEELKKKGI LFVGSGVSGG EEGARYGPSL MPGGSEEAWP
160 170 180 190 200
HIKNIFQSIS AKSDGEPCCE WVGPAGAGHY VKMVHNGIEY GDMQLICEAY
210 220 230 240 250
DIMKRLGGFT DKEISDVFAK WNNGVLDSFL VEITRDILKF DDVDGKPLVE
260 270 280 290 300
KIMDTAGQKG TGKWTAINAL DLGMPVTLIG EAVFARCLSA LKNERIRASK
310 320 330 340 350
VLPGPEVPKD AVKDREQFVD DLEQALYASK IISYAQGFML IREAAATYGW
360 370 380 390 400
KLNNPAIALM WRGGCIIRSV FLGQITKAYR EEPDLENLLF NKFFADAVTK
410 420 430 440 450
AQSGWRKSIA LATTYGIPTP AFSTALSFYD GYRSERLPAN LLQAQRDYFG
460 470 480
AHTFRVLPEC ASDNLPVDKD IHINWTGHGG NVSSSTYQA
Length:489
Mass (Da):53,543
Last modified:February 1, 1995 - v1
Checksum:i55CAE5DACDC6A00B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z46631 Genomic DNA. Translation: CAA86600.1.
U00028 Genomic DNA. Translation: AAB68452.1.
U17155 Genomic DNA. Translation: AAA53637.1.
BK006934 Genomic DNA. Translation: DAA06875.1.
PIRiS46671.
RefSeqiNP_012053.3. NM_001179314.3.

Genome annotation databases

EnsemblFungiiYHR183W; YHR183W; YHR183W.
GeneIDi856589.
KEGGisce:YHR183W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z46631 Genomic DNA. Translation: CAA86600.1 .
U00028 Genomic DNA. Translation: AAB68452.1 .
U17155 Genomic DNA. Translation: AAA53637.1 .
BK006934 Genomic DNA. Translation: DAA06875.1 .
PIRi S46671.
RefSeqi NP_012053.3. NM_001179314.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2P4Q X-ray 2.37 A 1-489 [» ]
ProteinModelPortali P38720.
SMRi P38720. Positions 1-476.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 36616. 143 interactions.
DIPi DIP-6604N.
IntActi P38720. 109 interactions.
MINTi MINT-688249.
STRINGi 4932.YHR183W.

Proteomic databases

MaxQBi P38720.
PaxDbi P38720.
PeptideAtlasi P38720.
PRIDEi P38720.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YHR183W ; YHR183W ; YHR183W .
GeneIDi 856589.
KEGGi sce:YHR183W.

Organism-specific databases

CYGDi YHR183w.
SGDi S000001226. GND1.

Phylogenomic databases

eggNOGi COG0362.
GeneTreei ENSGT00390000009023.
HOGENOMi HOG000255147.
InParanoidi P38720.
KOi K00033.
OMAi EFNWNLP.
OrthoDBi EOG7F252Z.

Enzyme and pathway databases

UniPathwayi UPA00115 ; UER00410 .
BioCyci YEAST:YHR183W-MONOMER.
Reactomei REACT_233695. Pentose phosphate pathway (hexose monophosphate shunt).
SABIO-RK P38720.

Miscellaneous databases

EvolutionaryTracei P38720.
NextBioi 982464.

Gene expression databases

Genevestigatori P38720.

Family and domain databases

Gene3Di 1.10.1040.10. 1 hit.
1.20.5.320. 1 hit.
3.40.50.720. 1 hit.
InterProi IPR008927. 6-PGluconate_DH_C-like.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_decarbox.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR013328. DH_multihelical.
IPR012284. Fibritin/6PGD_C-extension.
IPR016040. NAD(P)-bd_dom.
[Graphical view ]
Pfami PF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view ]
PIRSFi PIRSF000109. 6PGD. 1 hit.
SUPFAMi SSF48179. SSF48179. 1 hit.
TIGRFAMsi TIGR00873. gnd. 1 hit.
PROSITEi PS00461. 6PGD. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Desouza M., Lobo Z., Maitra P.K.
    Submitted (NOV-1994) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. Cited for: PROTEIN SEQUENCE OF 41-47 AND 120-131.
    Strain: ATCC 204508 / S288c.
  5. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  7. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-50, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "Crystal structure of Saccharomyces cerevisiae 6-phosphogluconate dehydrogenase Gnd1."
    He W., Wang Y., Liu W., Zhou C.Z.
    BMC Struct. Biol. 7:38-38(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.37 ANGSTROMS) IN COMPLEX WITH CITRATE, CATALYTIC ACTIVITY, FUNCTION, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES.

Entry informationi

Entry namei6PGD1_YEAST
AccessioniPrimary (citable) accession number: P38720
Secondary accession number(s): D3DLD1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: November 26, 2014
This is version 137 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 101000 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

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

Documents

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

External Data

Dasty 3