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PDBsum entry 1h9a

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Oxidoreductase (choh(d) - NAD(p)) PDB id
1h9a
Jmol
Contents
Protein chain
485 a.a. *
Ligands
SO4
NAP
Waters ×191
* Residue conservation analysis
PDB id:
1h9a
Name: Oxidoreductase (choh(d) - NAD(p))
Title: Complex of active mutant (q365->c) of glucose 6-phosphate dehydrogenase from l. Mesenteroides with coenzyme NADP
Structure: Glucose 6-phosphate 1-dehydrogenase. Chain: a. Synonym: g6pd. Engineered: yes. Mutation: yes
Source: Leuconostoc mesenteroides. Organism_taxid: 1245. Strain: su294. Plasmid: plmz. Gene: g6pd. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: site directed mutagenesis
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.16Å     R-factor:   0.187     R-free:   0.226
Authors: M.J.Adams,C.E.Naylor,S.Gover
Key ref:
C.E.Naylor et al. (2001). NADP+ and NAD+ binding to the dual coenzyme specific enzyme Leuconostoc mesenteroides glucose 6-phosphate dehydrogenase: different interdomain hinge angles are seen in different binary and ternary complexes. Acta Crystallogr D Biol Crystallogr, 57, 635-648. PubMed id: 11320304 DOI: 10.1107/S0907444901003420
Date:
06-Mar-01     Release date:   03-May-01    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11411  (G6PD_LEUME) -  Glucose-6-phosphate 1-dehydrogenase
Seq:
Struc:
486 a.a.
485 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.49  - Glucose-6-phosphate dehydrogenase (NADP(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Pentose Phosphate Pathway (early stages)
      Reaction: D-glucose 6-phosphate + NADP+ = 6-phospho-D-glucono-1,5-lactone + NADPH
D-glucose 6-phosphate
+
NADP(+)
Bound ligand (Het Group name = NAP)
corresponds exactly
= 6-phospho-D-glucono-1,5-lactone
+ NADPH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     oxidoreductase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444901003420 Acta Crystallogr D Biol Crystallogr 57:635-648 (2001)
PubMed id: 11320304  
 
 
NADP+ and NAD+ binding to the dual coenzyme specific enzyme Leuconostoc mesenteroides glucose 6-phosphate dehydrogenase: different interdomain hinge angles are seen in different binary and ternary complexes.
C.E.Naylor, S.Gover, A.K.Basak, M.S.Cosgrove, H.R.Levy, M.J.Adams.
 
  ABSTRACT  
 
The reduced coenzymes NADH and NADPH only differ by one phosphate, but in the cell NADH provides reducing power for catabolism while NADPH is utilized in biosynthetic pathways. Enzymes almost invariably discriminate between the coenzymes, but glucose 6-phosphate dehydrogenase (G6PD) from Leuconostoc mesenteroides is rare in being functionally dual specific. In order to elucidate the coenzyme selectivity, the structures of NADP(+)- and NAD(+)-complexed L. mesenteroides G6PD have been determined including data to 2.2 and 2.5 A resolution, respectively, and compared with unliganded G6PD crystallized in the same space groups. Coenzyme binding is also compared with that in a ternary complex of a mutant in which Asp177 in the active site has been mutated to asparagine. There are no gross structural differences between the complexes. In both binary complexes, the enzyme interdomain hinge angle has opened. NADP(+) binds to the furthest open form; of the residues within the coenzyme domain, only Arg46 moves, interacting with the 2'-phosphate and adenine. NAD(+) is less well defined in the binding site; smaller hinge opening is seen but larger local changes: Arg46 is displaced, Thr14 bonds the 3'-hydroxyl and Gln47 bonds the 2'-hydroxyl. In the ternary complex, the hinge angle has closed; only the adenine nucleotide is ordered in the binding site. Arg46 again provides most binding interactions.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Stereo image of the final 2F[obs] - F[calc] electron-density map of the NAD^+ complex, crystallized in C2, in the region of the NAD^+ site, contoured at 1 . Difference electron density with NAD^+ omitted from F[calc], contoured at 2.5 .
Figure 4.
Figure 4 (a) Protein-NADP+ contacts, (b) protein-NADPH contacts, (c) protein-NAD^+ contacts. Coenzymes are shown with C atoms grey, N atoms blue, O atoms red and P atoms purple; waters are red-brown. (Atoms and bonds of the nicotinamide ring of NAD^+ are shown in white to indicate disorder.) Conserved protein residues are cyan; others are dark blue. Possible hydrogen bonds are drawn dotted in red; waters and certain residues discussed are labelled. (d) Atom-labelling convention for coenzyme.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 635-648) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19181802 T.Fuhrer, and U.Sauer (2009).
Different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism.
  J Bacteriol, 191, 2112-2121.  
16755587 V.Chaptal, V.Gueguen-Chaignon, S.Poncet, C.Lecampion, P.Meyer, J.Deutscher, A.Galinier, S.Nessler, and S.Moréra (2006).
Structural analysis of B. subtilis CcpA effector binding site.
  Proteins, 64, 814-816.
PDB code: 2fep
15340916 V.Z.Pletnev, C.M.Weeks, and W.L.Duax (2004).
Rational proteomics II: electrostatic nature of cofactor preference in the short-chain oxidoreductase (SCOR) enzyme family.
  Proteins, 57, 294-301.  
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.