spacer
spacer
Go to PDB code: 
protein Protein-protein interface(s) links
Oxidoreductase PDB id
1p74
Jmol
Contents
Protein chains
267 a.a. *
Waters ×133
* Residue conservation analysis
PDB id:
1p74
Name: Oxidoreductase
Title: Crystal structure of shikimate dehydrogenase (aroe) from haemophilus influenzae
Structure: Shikimate 5-dehydrogenase. Chain: a, b. Engineered: yes
Source: Haemophilus influenzae. Organism_taxid: 727. Gene: aroe or hi0655. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.40Å     R-factor:   0.231     R-free:   0.276
Authors: S.Ye,F.Von Delft,A.Brooun,M.W.Knuth,R.V.Swanson,D.E.Mcree
Key ref: S.Ye et al. (2003). The crystal structure of shikimate dehydrogenase (AroE) reveals a unique NADPH binding mode. J Bacteriol, 185, 4144-4151. PubMed id: 12837789 DOI: 10.1128/JB.185.14.4144-4151.2003
Date:
30-Apr-03     Release date:   12-Aug-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P43876  (AROE_HAEIN) -  Shikimate dehydrogenase
Seq:
Struc: 		272 a.a.
267 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.25  - Shikimate dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Shikimate and Chorismate Biosynthesis
      Reaction: Shikimate + NADP+ = 3-dehydroshikimate + NADPH
Shikimate
 + NADP(+)
 = 3-dehydroshikimate
 + 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   3 terms 
  Biochemical function     nucleotide binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1128/JB.185.14.4144-4151.2003 J Bacteriol 185:4144-4151 (2003)
PubMed id: 12837789  
 
 
The crystal structure of shikimate dehydrogenase (AroE) reveals a unique NADPH binding mode.
S.Ye, F.Von Delft, A.Brooun, M.W.Knuth, R.V.Swanson, D.E.McRee.
 
  ABSTRACT  
 
Shikimate dehydrogenase catalyzes the NADPH-dependent reversible reduction of 3-dehydroshikimate to shikimate. We report the first X-ray structure of shikimate dehydrogenase from Haemophilus influenzae to 2.4-A resolution and its complex with NADPH to 1.95-A resolution. The molecule contains two domains, a catalytic domain with a novel open twisted alpha/beta motif and an NADPH binding domain with a typical Rossmann fold. The enzyme contains a unique glycine-rich P-loop with a conserved sequence motif, GAGGXX, that results in NADPH adopting a nonstandard binding mode with the nicotinamide and ribose moieties disordered in the binary complex. A deep pocket with a narrow entrance between the two domains, containing strictly conserved residues primarily contributed by the catalytic domain, is identified as a potential 3-dehydroshikimate binding pocket. The flexibility of the nicotinamide mononucleotide portion of NADPH may be necessary for the substrate 3-dehydroshikimate to enter the pocket and for the release of the product shikimate.
 

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.  
19376919 H.Teramoto, M.Inui, and H.Yukawa (2009).
Regulation of expression of genes involved in quinate and shikimate utilization in Corynebacterium glutamicum.
  Appl Environ Microbiol, 75, 3461-3468.  
19735225 M.J.Duckworth, A.S.Okoli, and G.L.Mendz (2009).
Novel Helicobacter pylori therapeutic targets: the unusual suspects.
  Expert Rev Anti Infect Ther, 7, 835-867.  
19234762 Y.Kim, P.Quartey, R.Ng, T.I.Zarembinski, and A.Joachimiak (2009).
Crystal structure of YfeU protein from Haemophilus influenzae: a predicted etherase involved in peptidoglycan recycling.
  J Struct Funct Genomics, 10, 151-156.  
18260104 H.A.Arcuri, J.C.Borges, I.O.Fonseca, J.H.Pereira, J.R.Neto, L.A.Basso, D.S.Santos, and W.F.de 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.  
17090918 O.Adachi, Y.Ano, H.Toyama, and K.Matsushita (2006).
Purification and properties of NADP-dependent shikimate dehydrogenase from Gluconobacter oxydans IFO 3244 and its application to enzymatic shikimate production.
  Biosci Biotechnol Biochem, 70, 2786-2789.  
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.  
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.