PDBsum entry 3e12

Transferase

PDB id: 3e12

Contents

Protein chains

258 a.a. *

Ligands

PO4 ×2

KD0 ×2

ACT

Metals

_CU ×2

Waters ×543

* Residue conservation analysis

PDB id:

3e12

Name:

Transferase

Title:

Cu2+ substituted aquifex aeolicus kdo8ps in complex with kdo8p

Structure:

2-dehydro-3-deoxyphosphooctonate aldolase. Chain: a, b. Fragment: kdo8ps. Synonym: phospho-2-dehydro-3-deoxyoctonate aldolase, 3-deoxy-d-manno- octulosonic acid 8-phosphate synthetase, kdo-8-phosphate synthetase, kdo 8-p synthase, kdops. Engineered: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Gene: kdsa, aq_085. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.70Å R-factor: 0.168 R-free: 0.196

Authors:

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

Date:

01-Aug-08 Release date: 12-May-09

Protein chains

O66496  (KDSA_AQUAE) -  2-dehydro-3-deoxyphosphooctonate aldolase from Aquifex aeolicus (strain VF5)

Seq: 267 a.a.

Struc: 258 a.a.

Enzyme reactions

• Enzyme class: E.C.2.5.1.55 - 3-deoxy-8-phosphooctulonate synthase.
• Reaction: D-arabinose 5-phosphate + phosphoenolpyruvate + H2O = 3-deoxy-alpha-D- manno-2-octulosonate-8-phosphate + phosphate

D-arabinose 5-phosphate (Bound ligand (Het Group name = KD0) matches with 70.00% similarity) + phosphoenolpyruvate + H2O = 3-deoxy-alpha-D- manno-2-octulosonate-8-phosphate + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

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.

ABSTRACT

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.