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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Shigella flexneri
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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 sitei102 – 1021NADPBy similarity
Binding sitei102 – 1021SubstrateBy similarity
Active sitei183 – 1831Proton acceptorBy similarity
Active sitei190 – 1901Proton donorBy similarity
Binding sitei191 – 1911SubstrateBy similarity
Binding sitei260 – 2601Substrate; via amide nitrogenBy similarity
Binding sitei287 – 2871SubstrateBy similarity
Binding sitei445 – 4451Substrate; shared with dimeric partnerBy similarity
Binding sitei451 – 4511Substrate; shared with dimeric partnerBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi10 – 156NADPBy similarity
Nucleotide bindingi33 – 353NADPBy similarity
Nucleotide bindingi74 – 763NADPBy similarity

GO - Molecular functioni

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

GO - Biological processi

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

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Gluconate utilization, Pentose shunt

Keywords - Ligandi

NADP

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, decarboxylating (EC:1.1.1.44)
Gene namesi
Name:gnd
Ordered Locus Names:SF2091, S2212
OrganismiShigella flexneri
Taxonomic identifieri623 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeShigella
ProteomesiUP000001006: Chromosome, UP000002673: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 4684686-phosphogluconate dehydrogenase, decarboxylatingPRO_0000090050Add
BLAST

Proteomic databases

PaxDbiP37756.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi198214.SF2091.

Structurei

3D structure databases

ProteinModelPortaliP37756.
SMRiP37756. Positions 1-466.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni128 – 1303Substrate bindingBy similarity
Regioni186 – 1872Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0362.
HOGENOMiHOG000255147.
KOiK00033.
OMAiSDEYNWD.
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.

P37756-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKQQIGVVG MAVMGRNLAL NIESRGYTVS IFNRSREKTE EVIAENPGKK
60 70 80 90 100
LAPYYTVKEF VESLETPRRI LLMVKAGAGT DAAIDSLKPY LDKGDIIIDG
110 120 130 140 150
GNTFFQDTIR RNRELSAEGF NFIGTGVSGG EEGALKGPSI MPGGQKEAYE
160 170 180 190 200
LVAPILTKIA AVAEDGEPCV TYIGADGAGH YVKMVHNGIE YGDMQLIAEA
210 220 230 240 250
YSLLKGGLNL SNEELAQTFT EWNNGELSSY LIDITKDIFT KKDEDGNYLV
260 270 280 290 300
DVILDEAANK GTGKWTSQSA LDLGEPLSLI TESVFARYIS SLKDQRVAAS
310 320 330 340 350
KVLSGPQAQS AGDKAEFIEK VRSALYLGKI VSYAQGFSQL RAASEEYNWD
360 370 380 390 400
LNYGEIAKIF RAGCIIRAQF LQKITDAYAE NPQIANLLLA PYFKQIADDY
410 420 430 440 450
QQALRDVVAY AVQNGIPVPT FAAAVAYYDS YRAAVLPANL IQAQRDYFGA
460
HTYKRIDKEG VFHTEWLD
Length:468
Mass (Da):51,344
Last modified:October 1, 1994 - v1
Checksum:i2203A0D82120CD61
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X71970 Genomic DNA. Translation: CAA50781.1.
AE005674 Genomic DNA. Translation: AAN43630.1.
AE014073 Genomic DNA. Translation: AAP17458.1.
U14468 Genomic DNA. Translation: AAC43834.1.
RefSeqiNP_707923.1. NC_004337.2.
NP_837649.1. NC_004741.1.
WP_000043429.1. NZ_JMRK01000046.1.

Genome annotation databases

EnsemblBacteriaiAAN43630; AAN43630; SF2091.
AAP17458; AAP17458; S2212.
GeneIDi1025304.
1078514.
KEGGisfl:SF2091.
sfx:S2212.
PATRICi18705945. VBIShiFle31049_2451.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X71970 Genomic DNA. Translation: CAA50781.1.
AE005674 Genomic DNA. Translation: AAN43630.1.
AE014073 Genomic DNA. Translation: AAP17458.1.
U14468 Genomic DNA. Translation: AAC43834.1.
RefSeqiNP_707923.1. NC_004337.2.
NP_837649.1. NC_004741.1.
WP_000043429.1. NZ_JMRK01000046.1.

3D structure databases

ProteinModelPortaliP37756.
SMRiP37756. Positions 1-466.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi198214.SF2091.

Proteomic databases

PaxDbiP37756.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN43630; AAN43630; SF2091.
AAP17458; AAP17458; S2212.
GeneIDi1025304.
1078514.
KEGGisfl:SF2091.
sfx:S2212.
PATRICi18705945. VBIShiFle31049_2451.

Phylogenomic databases

eggNOGiCOG0362.
HOGENOMiHOG000255147.
KOiK00033.
OMAiSDEYNWD.
OrthoDBiEOG6MSS4W.

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.

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. "Characterization of the rfc region of Shigella flexneri."
    Morona R., Mavris M., Fallarino A., Manning P.A.
    J. Bacteriol. 176:733-747(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: PE577 / Serotype 2a.
  2. "Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157."
    Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J., Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L., Xue Y.
    , Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H., Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J.
    Nucleic Acids Res. 30:4432-4441(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 301 / Serotype 2a.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700930 / 2457T / Serotype 2a.
  4. "Intergeneric transfer and recombination of the 6-phosphogluconate dehydrogenase gene (gnd) in enteric bacteria."
    Nelson K., Selander R.K.
    Proc. Natl. Acad. Sci. U.S.A. 91:10227-10231(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 12-456.
    Strain: ATCC 29903.

Entry informationi

Entry namei6PGD_SHIFL
AccessioniPrimary (citable) accession number: P37756
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: January 7, 2015
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete 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.