PDBsum entry 2a21

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
Protein chains
263 a.a. *
PO4 ×2
PEP ×2
_ZN ×2
Waters ×550
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Aquifex aeolicus kdo8ps in complex with pep, po4, and zn2+
Structure: 2-dehydro-3-deoxyphosphooctonate aldolase. Chain: a, b. Synonym: phospho-2-dehydro-3-deoxyoctonate aldolase, 3-deox octulosonic acid 8-phosphate synthetase, kdo-8-phosphate sy kdo 8-p synthase, kdops. Engineered: yes
Source: Aquifex aeolicus. Organism_taxid: 63363. Gene: kdsa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PDB file)
1.80Å     R-factor:   0.184     R-free:   0.210
Authors: F.Kona,X.Xu,J.Lu,P.Martin,D.L.Gatti
Key ref: F.Kona et al. (2009). Electronic structure of the metal center in the Cd(2+), Zn(2+), and Cu(2+) substituted forms of KDO8P synthase: implications for catalysis. Biochemistry, 48, 3610-3630. PubMed id: 19228070 DOI: 10.1021/bi801955h
21-Jun-05     Release date:   20-Jun-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
O66496  (KDSA_AQUAE) -  2-dehydro-3-deoxyphosphooctonate aldolase
267 a.a.
263 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 3-deoxy-8-phosphooctulonate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Phosphoenolpyruvate + D-arabinose 5-phosphate + H2O = 2-dehydro-3- deoxy-D-octonate 8-phosphate + phosphate
Bound ligand (Het Group name = PEP)
corresponds exactly
+ D-arabinose 5-phosphate
+ H(2)O
= 2-dehydro-3- deoxy-D-octonate 8-phosphate
Bound ligand (Het Group name = PO4)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     3 terms  


DOI no: 10.1021/bi801955h Biochemistry 48:3610-3630 (2009)
PubMed id: 19228070  
Electronic structure of the metal center in the Cd(2+), Zn(2+), and Cu(2+) substituted forms of KDO8P synthase: implications for catalysis.
F.Kona, P.Tao, P.Martin, X.Xu, D.L.Gatti.
Aquifex aeolicus 3-deoxy-d-manno-octulosonate 8-phosphate synthase (KDO8PS) is active with a variety of different divalent metal ions bound in the active site. The Cd(2+), Zn(2+), and Cu(2+) substituted enzymes display similar values of k(cat) and similar dependence of K(m)(PEP) and K(m)(A5P) on both substrate and product concentrations. However, the flux-control coefficients for some of the catalytically relevant reaction steps are different in the presence of Zn(2+) or Cu(2+), suggesting that the type of metal bound in the active site affects the behavior of the enzyme in vivo. The type of metal also affects the rate of product release in the crystal environment. For example, the crystal structure of the Cu(2+) enzyme incubated with phosphoenolpyruvate (PEP) and arabinose 5-phosphate (A5P) shows the formed product, 3-deoxy-d-manno-octulosonate 8-phosphate (KDO8P), still bound in the active site in its linear conformation. This observation completes our structural studies of the condensation reaction, which altogether have provided high-resolution structures for the reactants, the intermediate, and the product bound forms of KDO8PS. The crystal structures of the Cd(2+), Zn(2+), and Cu(2+) substituted enzymes show four residues (Cys-11, His-185, Glu-222, and Asp-233) and a water molecule as possible metal ligands. Combined quantum mechanics/molecular mechanics (QM/MM) geometry optimizations reveal that the metal centers have a delocalized electronic structure, and that their true geometry is square pyramidal for Cd(2+) and Zn(2+) and distorted octahedral or distorted tetrahedral for Cu(2+). These geometries are different from those obtained by QM optimization in the gas phase (tetrahedral for Cd(2+) and Zn(2+), distorted tetrahedral for Cu(2+)) and may represent conformations of the metal center that minimize the reorganization energy between the substrate-bound and product-bound states. The QM/MM calculations also show that when only PEP is bound to the enzyme the electronic structure of the metal center is optimized to prevent a wasteful reaction of PEP with water.