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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
Status
Reviewed-Annotation score: Annotation score: 3 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.By similarity

Catalytic activityi

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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei103 – 1031NADPBy similarity
Binding sitei103 – 1031SubstrateBy similarity
Active sitei183 – 1831Proton acceptorBy similarity
Active sitei190 – 1901Proton donorBy similarity
Binding sitei191 – 1911SubstrateBy similarity
Binding sitei263 – 2631Substrate; via amide nitrogenBy similarity
Binding sitei290 – 2901SubstrateBy similarity
Binding sitei449 – 4491Substrate; shared with dimeric partnerBy similarity
Binding sitei455 – 4551Substrate; shared with dimeric partnerBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi10 – 156NADPBy similarity
Nucleotide bindingi33 – 353NADPBy similarity
Nucleotide bindingi75 – 773NADPBy similarity

GO - Molecular functioni

  1. NADP binding Source: InterPro
  2. phosphogluconate dehydrogenase (decarboxylating) activity Source: UniProtKB-EC

GO - Biological processi

  1. D-gluconate metabolic process Source: UniProtKB-KW
  2. pentose-phosphate shunt Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Gluconate utilization, Pentose shunt

Keywords - Ligandi

NADP

Enzyme and pathway databases

BioCyciSYNEL:SYNPCC7942_0039-MONOMER.
UniPathwayiUPA00115; UER00410.

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, decarboxylating (EC:1.1.1.44)
Gene namesi
Name:gnd
Ordered Locus Names:Synpcc7942_0039
OrganismiSynechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
Taxonomic identifieri1140 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechococcus
ProteomesiUP000002717 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 4714716-phosphogluconate dehydrogenase, decarboxylatingPRO_0000090060Add
BLAST

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi1140.Synpcc7942_0039.

Structurei

3D structure databases

ProteinModelPortaliP21577.
SMRiP21577. Positions 1-471.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni129 – 1313Substrate bindingBy similarity
Regioni186 – 1872Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0362.
HOGENOMiHOG000255147.
KOiK00033.
OrthoDBiEOG6MSS4W.

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.

P21577-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALQQFGLIG LAVMGENLAL NIERNGFSLT VYNRTAEKTE AFMADRAQGK
60 70 80 90 100
NIVPAYSLED FVASLERPRR ILVMVKAGGP VDAVVEQLKP LLDPGDLIID
110 120 130 140 150
GGNSLFTDTE RRVKDLEALG LGFMGMGVSG GEEGALNGPS LMPGGTQAAY
160 170 180 190 200
EAVEPIVRSI AAQVDDGPCV TYIGPGGSGH YVKMVHNGIE YGDMQLIAEA
210 220 230 240 250
YDLLKSVAGL NASELHDVFA AWNKTPELDS FLIEITADIF TKVDDLGTGQ
260 270 280 290 300
PLVELILDAA GQKGTGRWTV ETALEIGVAI PTIIAAVNAR ILSSIKAERQ
310 320 330 340 350
AASEILSGPI TEPFSGDRQA FIDSVRDALY CSKICSYAQG MALLAKASQV
360 370 380 390 400
YNYGLNLGEL ARIWKGGCII RAGFLNKIKQ AYDADPTLAN LLLAPEFRQT
410 420 430 440 450
ILDRQLAWRR VIAIAAERGI PVPAFSASLD YFDSYRRDRL PQNLTQAQRD
460 470
YFGAHTYERT DRSGSFHAQW F
Length:471
Mass (Da):51,073
Last modified:April 17, 2006 - v4
Checksum:i0C75D58209E124E7
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti154 – 1596EPIVRS → SRSVPT in AAA27330 (PubMed:2113917).Curated
Sequence conflicti159 – 1591S → T in CAA41555 (Ref. 2) Curated
Sequence conflicti407 – 4071A → R in CAA41555 (Ref. 2) Curated
Sequence conflicti415 – 43925AAERG…YRRDR → RQNEEFRFRFQCFPGLLRQL PARS in CAA41555 (Ref. 2) CuratedAdd
BLAST
Sequence conflicti437 – 4415RDRLP → ASPA in AAA27330 (PubMed:2113917).Curated
Sequence conflicti450 – 4534DYFG → TTC in AAA27330 (PubMed:2113917).Curated
Sequence conflicti458 – 4658ERTDRSGS → KAPIALL in AAA27330 (PubMed:2113917).Curated
Sequence conflicti469 – 4702QW → M in AAA27330 (PubMed:2113917).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M55002 Genomic DNA. Translation: AAA27330.1.
X58719 Genomic DNA. Translation: CAA41555.1.
CP000100 Genomic DNA. Translation: ABB56071.1.
PIRiS14628.
RefSeqiYP_399058.1. NC_007604.1.

Genome annotation databases

EnsemblBacteriaiABB56071; ABB56071; Synpcc7942_0039.
KEGGisyf:Synpcc7942_0039.
PATRICi23785105. VBISynElo51371_0103.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M55002 Genomic DNA. Translation: AAA27330.1.
X58719 Genomic DNA. Translation: CAA41555.1.
CP000100 Genomic DNA. Translation: ABB56071.1.
PIRiS14628.
RefSeqiYP_399058.1. NC_007604.1.

3D structure databases

ProteinModelPortaliP21577.
SMRiP21577. Positions 1-471.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi1140.Synpcc7942_0039.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABB56071; ABB56071; Synpcc7942_0039.
KEGGisyf:Synpcc7942_0039.
PATRICi23785105. VBISynElo51371_0103.

Phylogenomic databases

eggNOGiCOG0362.
HOGENOMiHOG000255147.
KOiK00033.
OrthoDBiEOG6MSS4W.

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.
BioCyciSYNEL:SYNPCC7942_0039-MONOMER.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Genetic tagging, cloning, and DNA sequence of the Synechococcus sp. strain PCC 7942 gene (gnd) encoding 6-phosphogluconate dehydrogenase."
    Broedel S.E. Jr., Wolf R.E. Jr.
    J. Bacteriol. 172:4023-4031(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SUBSTRATE-BINDING SITE.
  2. "Amino acid sequence comparisons of 6-phosphogluconate dehydrogenase."
    Culler D.C., Krogmann D.W.
    Submitted (MAR-1991) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Complete sequence of chromosome 1 of Synechococcus elongatus PCC 7942."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Schmutz J., Larimer F., Land M., Kyrpides N., Lykidis A., Richardson P.
    Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: PCC 7942.

Entry informationi

Entry namei6PGD_SYNE7
AccessioniPrimary (citable) accession number: P21577
Secondary accession number(s): Q31S98
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 30, 1991
Last sequence update: April 17, 2006
Last modified: March 31, 2015
This is version 101 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.