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P38720 (6PGD1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 134. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
6-phosphogluconate dehydrogenase, decarboxylating 1

EC=1.1.1.44
Gene names
Name:GND1
Ordered Locus Names:YHR183W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length489 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO2, with concomitant reduction of NADP to NADPH. Ref.8

Catalytic activity

6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH. Ref.8

Pathway

Carbohydrate degradation; pentose phosphate pathway; D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage): step 3/3.

Subunit structure

Homodimer. Ref.8

Subcellular location

Cytoplasm Ref.5.

Miscellaneous

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

Sequence similarities

Belongs to the 6-phosphogluconate dehydrogenase family.

Biophysicochemical properties

Kinetic parameters:

KM=50 µM for 6-phosphogluconate Ref.8

KM=35 µM for NADP

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 4894896-phosphogluconate dehydrogenase, decarboxylating 1
PRO_0000090075

Regions

Nucleotide binding9 – 146NADP By similarity
Nucleotide binding32 – 343NADP By similarity
Nucleotide binding74 – 763NADP By similarity
Region128 – 1303Substrate binding By similarity
Region185 – 1862Substrate binding By similarity

Sites

Active site1821Proton acceptor By similarity
Active site1891Proton donor By similarity
Binding site1021NADP By similarity
Binding site1021Substrate By similarity
Binding site1901Substrate By similarity
Binding site2591Substrate; via amide nitrogen By similarity
Binding site2861Substrate By similarity
Binding site4461Substrate; shared with dimeric partner By similarity
Binding site4521Substrate; shared with dimeric partner By similarity

Amino acid modifications

Modified residue501Phosphoserine Ref.7

Secondary structure

.................................................................... 489
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P38720 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: 55CAE5DACDC6A00B

FASTA48953,543
        10         20         30         40         50         60 
MSADFGLIGL AVMGQNLILN AADHGFTVCA YNRTQSKVDH FLANEAKGKS IIGATSIEDF 

        70         80         90        100        110        120 
ISKLKRPRKV MLLVKAGAPV DALINQIVPL LEKGDIIIDG GNSHFPDSNR RYEELKKKGI 

       130        140        150        160        170        180 
LFVGSGVSGG EEGARYGPSL MPGGSEEAWP HIKNIFQSIS AKSDGEPCCE WVGPAGAGHY 

       190        200        210        220        230        240 
VKMVHNGIEY GDMQLICEAY DIMKRLGGFT DKEISDVFAK WNNGVLDSFL VEITRDILKF 

       250        260        270        280        290        300 
DDVDGKPLVE KIMDTAGQKG TGKWTAINAL DLGMPVTLIG EAVFARCLSA LKNERIRASK 

       310        320        330        340        350        360 
VLPGPEVPKD AVKDREQFVD DLEQALYASK IISYAQGFML IREAAATYGW KLNNPAIALM 

       370        380        390        400        410        420 
WRGGCIIRSV FLGQITKAYR EEPDLENLLF NKFFADAVTK AQSGWRKSIA LATTYGIPTP 

       430        440        450        460        470        480 
AFSTALSFYD GYRSERLPAN LLQAQRDYFG AHTFRVLPEC ASDNLPVDKD IHINWTGHGG 


NVSSSTYQA 

« Hide

References

« Hide 'large scale' references
[1]Desouza M., Lobo Z., Maitra P.K.
Submitted (NOV-1994) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII."
Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z., Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T., Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P. expand/collapse author list , Louis E.J., Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L., St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P., Waterston R., Wilson R., Vaudin M.
Science 265:2077-2082(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Protein identifications for a Saccharomyces cerevisiae protein database."
Garrels J.I., Futcher B., Kobayashi R., Latter G.I., Schwender B., Volpe T., Warner J.R., McLaughlin C.S.
Electrophoresis 15:1466-1486(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 41-47 AND 120-131.
Strain: ATCC 204508 / S288c.
[5]"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].
[6]"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].
[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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z46631 Genomic DNA. Translation: CAA86600.1.
U00028 Genomic DNA. Translation: AAB68452.1.
U17155 Genomic DNA. Translation: AAA53637.1.
BK006934 Genomic DNA. Translation: DAA06875.1.
PIRS46671.
RefSeqNP_012053.3. NM_001179314.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2P4QX-ray2.37A1-489[»]
ProteinModelPortalP38720.
SMRP38720. Positions 1-476.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid36616. 142 interactions.
DIPDIP-6604N.
IntActP38720. 109 interactions.
MINTMINT-688249.
STRING4932.YHR183W.

Proteomic databases

MaxQBP38720.
PaxDbP38720.
PeptideAtlasP38720.
PRIDEP38720.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYHR183W; YHR183W; YHR183W.
GeneID856589.
KEGGsce:YHR183W.

Organism-specific databases

CYGDYHR183w.
SGDS000001226. GND1.

Phylogenomic databases

eggNOGCOG0362.
GeneTreeENSGT00390000009023.
HOGENOMHOG000255147.
KOK00033.
OMAEFNWNLP.
OrthoDBEOG7F252Z.

Enzyme and pathway databases

BioCycYEAST:YHR183W-MONOMER.
SABIO-RKP38720.
UniPathwayUPA00115; UER00410.

Gene expression databases

GenevestigatorP38720.

Family and domain databases

Gene3D1.10.1040.10. 1 hit.
1.20.5.320. 1 hit.
3.40.50.720. 1 hit.
InterProIPR008927. 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]
PfamPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFPIRSF000109. 6PGD. 1 hit.
SUPFAMSSF48179. SSF48179. 1 hit.
TIGRFAMsTIGR00873. gnd. 1 hit.
PROSITEPS00461. 6PGD. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP38720.
NextBio982464.

Entry information

Entry name6PGD1_YEAST
AccessionPrimary (citable) accession number: P38720
Secondary accession number(s): D3DLD1
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: May 14, 2014
This is version 134 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome VIII

Yeast (Saccharomyces cerevisiae) chromosome VIII: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways