PDBsum entry 1nvt

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
Jmol PyMol
Protein chains
287 a.a. *
NAP ×2
_ZN ×2
Waters ×139
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of shikimate dehydrogenase (aroe or mj1084) in complex with NADP+
Structure: Shikimate 5'-dehydrogenase. Chain: a, b. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: aroe. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.35Å     R-factor:   0.224     R-free:   0.260
Authors: A.K.Padyana,S.K.Burley,New York Sgx Research Center For Structural Genomics (Nysgxrc)
Key ref:
A.K.Padyana and S.K.Burley (2003). Crystal structure of shikimate 5-dehydrogenase (SDH) bound to NADP: insights into function and evolution. Structure, 11, 1005-1013. PubMed id: 12906831 DOI: 10.1016/S0969-2126(03)00159-X
04-Feb-03     Release date:   25-Mar-03    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q58484  (AROE_METJA) -  Shikimate dehydrogenase (NADP(+))
282 a.a.
287 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Shikimate dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Shikimate and Chorismate Biosynthesis
      Reaction: Shikimate + NADP+ = 3-dehydroshikimate + NADPH
Bound ligand (Het Group name = NAP)
corresponds exactly
= 3-dehydroshikimate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     3 terms  


DOI no: 10.1016/S0969-2126(03)00159-X Structure 11:1005-1013 (2003)
PubMed id: 12906831  
Crystal structure of shikimate 5-dehydrogenase (SDH) bound to NADP: insights into function and evolution.
A.K.Padyana, S.K.Burley.
The crystal structure of Methanococcus jannaschii shikimate 5-dehydrogenase (MjSDH) bound to the cofactor nicotinamide adenine dinucleotide phosphate (NADP) has been determined at 2.35 A resolution. Shikimate 5-dehydrogenase (SDH) is responsible for NADP-dependent catalysis of the fourth step in shikimate biosynthesis, which is essential for aromatic amino acid metabolism in bacteria, microbial eukaryotes, and plants. The structure of MjSDH is a compact alpha/beta sandwich with two distinct domains, responsible for binding substrate and the NADP cofactor, respectively. A phylogenetically conserved deep cleft on the protein surface corresponds to the enzyme active site. The structure reveals a topologically new domain fold within the N-terminal segment of the polypeptide chain, which binds substrate and supports dimerization. Insights gained from homology modeling and sequence/structure comparisons suggest that the SDHs represent a unique class of dehydrogenases. The structure provides a framework for further investigation to discover and develop novel inhibitors targeting this essential enzyme.
  Selected figure(s)  
Figure 1.
Figure 1. Reaction Pathway of Shikimate 5-Dehydrogenase

  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 1005-1013) copyright 2003.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21279669 R.M.Muir, A.M.Ibáñez, S.L.Uratsu, E.S.Ingham, C.A.Leslie, G.H.McGranahan, N.Batra, S.Goyal, J.Joseph, E.D.Jemmis, and A.M.Dandekar (2011).
Mechanism of gallic acid biosynthesis in bacteria (Escherichia coli) and walnut (Juglans regia).
  Plant Mol Biol, 75, 555-565.  
18260104 H.A.Arcuri, J.C.Borges, I.O.Fonseca, J.H.Pereira, J.R.Neto, L.A.Basso, D.S.Santos, and Azevedo (2008).
Structural studies of shikimate 5-dehydrogenase from Mycobacterium tuberculosis.
  Proteins, 72, 720-730.  
18566515 J.Schoepe, K.Niefind, and D.Schomburg (2008).
1.6 A structure of an NAD(+)-dependent quinate dehydrogenase from Corynebacterium glutamicum.
  Acta Crystallogr D Biol Crystallogr, 64, 803-809.
PDB code: 2nlo
16972983 C.Han, L.Wang, K.Yu, L.Chen, L.Hu, K.Chen, H.Jiang, and X.Shen (2006).
Biochemical characterization and inhibitor discovery of shikimate dehydrogenase from Helicobacter pylori.
  FEBS J, 273, 4682-4692.  
15596430 H.A.Lindner, G.Nadeau, A.Matte, G.Michel, R.Ménard, and M.Cygler (2005).
Site-directed mutagenesis of the active site region in the quinate/shikimate 5-dehydrogenase YdiB of Escherichia coli.
  J Biol Chem, 280, 7162-7169.  
15336409 S.Lim, I.Schröder, and H.G.Monbouquette (2004).
A thermostable shikimate 5-dehydrogenase from the archaeon Archaeoglobus fulgidus.
  FEMS Microbiol Lett, 238, 101-106.  
12906820 E.Vogan (2003).
Shikimate dehydrogenase structure reveals novel fold.
  Structure, 11, 902-903.  
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