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PDBsum entry 2pgd

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protein ligands links
Oxidoreductase (choh(d)-NADP+(a)) PDB id
2pgd
Jmol
Contents
Protein chain
473 a.a. *
Ligands
SO4 ×3
Waters ×346
* Residue conservation analysis
PDB id:
2pgd
Name: Oxidoreductase (choh(d)-NADP+(a))
Title: The structure of 6-phosphogluconate dehydrogenase refined at angstroms resolution
Structure: 6-phosphogluconate dehydrogenase. Chain: a. Engineered: yes
Source: Ovis aries. Sheep. Organism_taxid: 9940
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.198    
Authors: M.J.Adams,C.Phillips,S.Gover
Key ref: M.J.Adams et al. (1991). The structure of 6-phosphogluconate dehydrogenase refined at 2.5 A resolution. Acta Crystallogr B, 47, 817-820. PubMed id: 1793548
Date:
18-Jul-94     Release date:   27-Feb-95    
Supersedes: 1pgd
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00349  (6PGD_SHEEP) -  6-phosphogluconate dehydrogenase, decarboxylating
Seq:
Struc:
483 a.a.
473 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.44  - Phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Pentose Phosphate Pathway (early stages)
      Reaction: 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH
6-phospho-D-gluconate
+ NADP(+)
= D-ribulose 5-phosphate
+ CO(2)
+ NADPH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   3 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
Acta Crystallogr B 47:817-820 (1991)
PubMed id: 1793548  
 
 
The structure of 6-phosphogluconate dehydrogenase refined at 2.5 A resolution.
M.J.Adams, S.Gover, R.Leaback, C.Phillips, D.O.Somers.
 
  ABSTRACT  
 
The three-dimensional structure of ovine 6-phosphogluconate dehydrogenase, refined at 2.5 A resolution with a residual for all data of 18.5%, is reported. This model, based on improved diffraction data and a corrected sequence, supersedes that reported earlier. Each subunit of the dimer has three domains: a beta-alpha-beta domain binds NADP; an all alpha domain provides much of the dimer interface; the C-terminal tail burrows into the second subunit.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19177345 D.E.Tronrud, and B.W.Matthews (2009).
Sorting the chaff from the wheat at the PDB.
  Protein Sci, 18, 2-5.  
19500970 M.J.Sippl (2009).
Fold space unlimited.
  Curr Opin Struct Biol, 19, 312-320.  
17570834 W.He, Y.Wang, W.Liu, and C.Z.Zhou (2007).
Crystal structure of Saccharomyces cerevisiae 6-phosphogluconate dehydrogenase Gnd1.
  BMC Struct Biol, 7, 38.
PDB code: 2p4q
16284727 D.Ceyhan, A.Danişan, I.H.Oğüş, and N.Ozer (2005).
Purification and kinetic properties of 6-phosphogluconate dehydrogenase from rat small intestine.
  Protein J, 24, 293-301.  
15553090 G.N.Goulielmos, E.Eliopoulos, M.Loukas, and S.Tsakas (2004).
Functional constraints of 6-phosphogluconate dehydrogenase (6-PGD) based on sequence and structural information.
  J Mol Evol, 59, 358-371.  
11726492 E.Warkentin, B.Mamat, M.Sordel-Klippert, M.Wicke, R.K.Thauer, M.Iwata, S.Iwata, U.Ermler, and S.Shima (2001).
Structures of F420H2:NADP+ oxidoreductase with and without its substrates bound.
  EMBO J, 20, 6561-6569.
PDB codes: 1jax 1jay
7922042 M.J.Adams, G.H.Ellis, S.Gover, C.E.Naylor, and C.Phillips (1994).
Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism.
  Structure, 2, 651-668.
PDB codes: 1pgn 1pgo 1pgp 1pgq
7881907 P.Rowland, A.K.Basak, S.Gover, H.R.Levy, and M.J.Adams (1994).
The three-dimensional structure of glucose 6-phosphate dehydrogenase from Leuconostoc mesenteroides refined at 2.0 A resolution.
  Structure, 2, 1073-1087.
PDB code: 1dpg
  8298462 M.B.Swindells (1993).
Classification of doubly wound nucleotide binding topologies using automated loop searches.
  Protein Sci, 2, 2146-2153.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.