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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Klebsiella pneumoniae
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.

Pathway: pentose phosphate pathway

This protein is involved in step 3 of the subpathway that synthesizes D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage).
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. Glucose-6-phosphate 1-dehydrogenase (zwf), Glucose-6-phosphate 1-dehydrogenase (zwf), Glucose-6-phosphate 1-dehydrogenase (zwf)
  2. 6-phosphogluconolactonase (pgl), 6-phosphogluconolactonase (6pgl), 6-phosphogluconolactonase (pgl), 6-phosphogluconolactonase (6pgl), 6-phosphogluconolactonase (6pgl), 6-phosphogluconolactonase (6pgl)
  3. 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (MC50_25615), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating, 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd)
This subpathway is part of the pathway pentose phosphate pathway, which is itself part of Carbohydrate degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage), the pathway pentose phosphate pathway and in Carbohydrate degradation.

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

GO - Biological processi

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
OrganismiKlebsiella pneumoniae
Taxonomic identifieri573 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeKlebsiella

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 4684686-phosphogluconate dehydrogenase, decarboxylatingPRO_0000090043Add
BLAST

Proteomic databases

PRIDEiP41576.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi272620.KPN_02499.

Structurei

3D structure databases

ProteinModelPortaliP41576.
SMRiP41576. Positions 1-466.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

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

Sequence similaritiesi

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.
IPR013328. 6PGD_dom_2.
IPR012284. 6PGD_dom_3.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_Gnd/GntZ.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR016040. NAD(P)-bd_dom.
IPR006183. Pgluconate_DH.
[Graphical view]
PfamiPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000109. 6PGD. 1 hit.
PRINTSiPR00076. 6PGDHDRGNASE.
SUPFAMiSSF48179. SSF48179. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P41576-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKQQIGVVG MAVMGRNLAL NIESRGYTVS VFNRSREKTE EVIAENTGKK
60 70 80 90 100
LVPYYTVQEF VESLETPRRI LLMVKAGAGT DSAIDSLKPY LDKGDIIIDG
110 120 130 140 150
GNTFFQDTIR RNRELSAEGF NFIGTGVSGG EEGALKGPSI MPGGQKEAYE
160 170 180 190 200
LVAPILKQIA AVAEDGEPCV TYIGADGAGH YVKMVHNGIE YGDMQLIAEA
210 220 230 240 250
YALLKGGLAL SNEELAQTFT EWNEGELSSY LIDITKDIFT KKDEEGKYLV
260 270 280 290 300
DVILDEAANK GTGKWTSQSS LDLGEPLSLI TESVFARYIS SLKDQRVAAS
310 320 330 340 350
KVLSGPQAQP VGDKAGFIEK VRRALYLGKI VSYAQGFSQL RAASDEYNWD
360 370 380 390 400
LNYGEIAKIF RAGCIIRAQF LQKITDAYAQ NAGIANLLLA PYFKQIADDY
410 420 430 440 450
QQALRDVVAY AVQNGIPVPT VSAAIAYYDS YRSAVLPANL IQAQRDYFGA
460
HTYKRTDKEG VFHTEWLE
Length:468
Mass (Da):51,328
Last modified:November 1, 1997 - v2
Checksum:iFF1EB5E7665FDC90
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti316 – 3161G → E in AAC43817 (PubMed:7937867).Curated
Sequence conflicti421 – 4211V → F in AAC43817 (PubMed:7937867).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D21242 Genomic DNA. Translation: BAA04786.1.
U14471 Genomic DNA. Translation: AAC43817.1.
PIRiD56146.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D21242 Genomic DNA. Translation: BAA04786.1.
U14471 Genomic DNA. Translation: AAC43817.1.
PIRiD56146.

3D structure databases

ProteinModelPortaliP41576.
SMRiP41576. Positions 1-466.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272620.KPN_02499.

Proteomic databases

PRIDEiP41576.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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.
IPR013328. 6PGD_dom_2.
IPR012284. 6PGD_dom_3.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_Gnd/GntZ.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR016040. NAD(P)-bd_dom.
IPR006183. Pgluconate_DH.
[Graphical view]
PfamiPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000109. 6PGD. 1 hit.
PRINTSiPR00076. 6PGDHDRGNASE.
SUPFAMiSSF48179. SSF48179. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Genomic organization of the Klebsiella pneumoniae cps region responsible for serotype K2 capsular polysaccharide synthesis in the virulent strain Chedid."
    Arakawa Y., Wacharotayankun R., Nagatsuka T., Ito H., Kato N., Ohta M.
    J. Bacteriol. 177:1788-1796(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: Chedid.
  2. "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: CW 7380.

Entry informationi

Entry namei6PGD_KLEPN
AccessioniPrimary (citable) accession number: P41576
Secondary accession number(s): Q48461
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1997
Last modified: June 24, 2015
This is version 77 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.