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P96789 (6PGD_LACLM) Reviewed, UniProtKB/Swiss-Prot

Last modified November 13, 2013. Version 96. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | 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

EC=1.1.1.44
Gene names
Name:gnd
Ordered Locus Names:llmg_0586
OrganismLactococcus lactis subsp. cremoris (strain MG1363) [Complete proteome] [HAMAP]
Taxonomic identifier416870 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeLactococcus

Protein attributes

Sequence length472 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 By similarity.

Catalytic activity

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

Pathway

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

Subunit structure

Homodimer By similarity. Ref.3

Sequence similarities

Belongs to the 6-phosphogluconate dehydrogenase family.

Ontologies

Keywords
   Biological processGluconate utilization
Pentose shunt
   LigandNADP
   Molecular functionOxidoreductase
   Technical term3D-structure
Complete proteome
Gene Ontology (GO)
   Biological_processD-gluconate metabolic process

Inferred from electronic annotation. Source: UniProtKB-KW

pentose-phosphate shunt

Inferred from electronic annotation. Source: UniProtKB-UniPathway

   Molecular_functionNADP binding

Inferred from electronic annotation. Source: InterPro

phosphogluconate dehydrogenase (decarboxylating) activity

Inferred from electronic annotation. Source: UniProtKB-EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 4724726-phosphogluconate dehydrogenase, decarboxylating
PRO_0000090046

Regions

Nucleotide binding10 – 156NADP
Nucleotide binding33 – 353NADP
Nucleotide binding74 – 763NADP
Region128 – 1303Substrate binding
Region187 – 1882Substrate binding

Sites

Active site1841Proton acceptor Ref.3
Active site1911Proton donor Ref.3
Binding site1021NADP By similarity
Binding site1021Substrate
Binding site1921Substrate
Binding site2621Substrate; via amide nitrogen
Binding site2891Substrate
Binding site4471Substrate; shared with dimeric partner
Binding site4531Substrate; shared with dimeric partner

Experimental info

Sequence conflict431Y → F in AAC12804. Ref.1

Secondary structure

...................................................................... 472
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P96789 [UniParc].

Last modified May 1, 2007. Version 3.
Checksum: A0075C9F46171F1C

FASTA47252,460
        10         20         30         40         50         60 
MAQANFGVVG MAVMGKNLAL NVESRGYTVA IYNRTTSKTE EVYKEHQDKN LVFTKTLEEF 

        70         80         90        100        110        120 
VGSLEKPRRI MLMVQAGAAT DATIKSLLPL LDIGDILIDG GNTHFPDTMR RNAELADSGI 

       130        140        150        160        170        180 
NFIGTGVSGG EKGALLGPSM MPGGQKEAYD LVAPIFEQIA AKAPQDGKPC VAYMGANGAG 

       190        200        210        220        230        240 
HYVKMVHNGI EYGDMQLIAE SYDLLKRILG LSNAEIQAIF EEWNEGELDS YLIEITKEVL 

       250        260        270        280        290        300 
KRKDDEGEGY IVDKILDKAG NKGTGKWTSE SALDLGVPLP LITESVFARY ISTYKDERVK 

       310        320        330        340        350        360 
ASKVLSGPAL DFSGDKKEVI EKIRKALYFS KIMSYAQGFA QLRKASEEFD WDLPYGTIAQ 

       370        380        390        400        410        420 
IWRAGCIIRA EFLQNITDAF DKDSELENLL LDDYFVDITK RYQEAVRDVV SLAVQAGTPI 

       430        440        450        460        470 
PTFTSAISYY DSYRSENLPA NLIQAQRDYF GAHTYERTDK AGIFHYDWYT ED 

« Hide

References

« Hide 'large scale' references
[1]"6-phosphogluconate dehydrogenase from Lactococcus lactis: a role for arginine residues in binding substrate and coenzyme."
Tetaud E., Hanau S., Wells J.M., Le Page R.W.F., Adams M.J., Arkison S., Barrett M.P.
Biochem. J. 338:55-60(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The complete genome sequence of the lactic acid bacterial paradigm Lactococcus lactis subsp. cremoris MG1363."
Wegmann U., O'Connell-Motherway M., Zomer A., Buist G., Shearman C., Canchaya C., Ventura M., Goesmann A., Gasson M.J., Kuipers O.P., van Sinderen D., Kok J.
J. Bacteriol. 189:3256-3270(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: MG1363.
[3]"Crystal structures of a bacterial 6-phosphogluconate dehydrogenase reveal aspects of specificity, mechanism and mode of inhibition by analogues of high-energy reaction intermediates."
Sundaramoorthy R., Iulek J., Barrett M.P., Bidet O., Ruda G.F., Gilbert I.H., Hunter W.N.
FEBS J. 274:275-286(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE; PRODUCT; INHIBITORS AND NADP, SUBUNIT, ACTIVE SITE.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U74322 Genomic DNA. Translation: AAC12804.1.
AM406671 Genomic DNA. Translation: CAL97186.1.
RefSeqYP_001031931.1. NC_009004.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2IYOX-ray2.40A1-472[»]
2IYPX-ray2.79A/B/C1-472[»]
2IZ0X-ray2.60A/B/C1-472[»]
2IZ1X-ray2.30A/B/C1-472[»]
ProteinModelPortalP96789.
SMRP96789. Positions 1-470.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING416870.llmg_0586.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCAL97186; CAL97186; llmg_0586.
GeneID4798708.
KEGGllm:llmg_0586.
PATRIC22282257. VBILacLac4574_0596.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0362.
HOGENOMHOG000255147.
KOK00033.
OMAKQQIGVI.
OrthoDBEOG6MSS4W.
ProtClustDBPRK09287.

Enzyme and pathway databases

BioCycLLAC416870:GCDT-613-MONOMER.
SABIO-RKP96789.
UniPathwayUPA00115; UER00410.

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

EvolutionaryTraceP96789.

Entry information

Entry name6PGD_LACLM
AccessionPrimary (citable) accession number: P96789
Secondary accession number(s): A2RIU0
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 1, 2007
Last modified: November 13, 2013
This is version 96 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

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