PDBsum entry: 1jcx

Lyase

PDB id: 1jcx

Contents

Protein chains

255 a.a. *

Ligands

PAI ×2

Metals

_CD ×2

Waters ×228

* Residue conservation analysis

PDB id:

1jcx

Name:

Lyase

Title:

Aquifex aeolicus kdo8p synthase in complex with api and cadm

Structure:

2-dehydro-3-deoxyphosphooctonate aldolase. Chain: a, b. Synonym: kdo8p synthase, phospho-2-dehydro-3-deoxyoctonate 3-deoxy-d-manno-octulosonic acid 8-phosphate synthetase, kd phosphate synthetase. Engineered: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.80Å R-factor: 0.206 R-free: 0.229

Authors:

J.Wang,H.S.Duewel,R.W.Woodard,D.L.Gatti

Key ref:

J.Wang et al. (2001). Structures of Aquifex aeolicus KDO8P synthase in complex with R5P and PEP, and with a bisubstrate inhibitor: role of active site water in catalysis. Biochemistry, 40, 15676-15683. PubMed id: 11747443 DOI: 10.1021/bi015568e

Date:

11-Jun-01 Release date: 16-Jan-02

Protein chains

O66496  (KDSA_AQUAE) -  2-dehydro-3-deoxyphosphooctonate aldolase

Seq: 267 a.a.

Struc: 255 a.a.

Enzyme reactions

• Enzyme class: E.C.2.5.1.55 - 3-deoxy-8-phosphooctulonate synthase.
• Reaction: Phosphoenolpyruvate + D-arabinose 5-phosphate + H₂O = 2-dehydro-3- deoxy-D-octonate 8-phosphate + phosphate

Phosphoenolpyruvate + D-arabinose 5-phosphate (Bound ligand (Het Group name = PAI) matches with 56.00% similarity) + H(2)O = 2-dehydro-3- deoxy-D-octonate 8-phosphate + phosphate

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: metabolic process (3 terms)
• Biochemical function: catalytic activity (3 terms)

reference

DOI no: 10.1021/bi015568e

Biochemistry 40:15676-15683 (2001)

PubMed id: 11747443

Structures of Aquifex aeolicus KDO8P synthase in complex with R5P and PEP, and with a bisubstrate inhibitor: role of active site water in catalysis.

J.Wang, H.S.Duewel, R.W.Woodard, D.L.Gatti.

ABSTRACT

We have determined the crystal structures of the metalloenzyme 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase from Aquifex aeolicus in complex with phosphoenolpyruvate (PEP) and ribose 5-phosphate (R5P), and with a bisubstrate inhibitor that mimics the postulated linear reaction intermediate. R5P, which is not a substrate for KDO8P synthase, binds in a manner similar to that of arabinose 5-phosphate (A5P), which is the natural substrate. The lack of reactivity of R5P appears to be primarily a consequence of the loss of a water molecule coordinated to Cd(2+) and located on the si side of PEP. This water molecule is no longer present because it cannot form a hydrogen bond with C2-OH(R5P), which is oriented in a different direction from C2-OH(A5P). The bisubstrate inhibitor binds with its phosphate and phosphonate moieties occupying the positions of the phosphate groups of A5P and PEP, respectively. One of the inhibitor hydroxyls replaces water as a ligand of Cd(2+). The current work supports a mechanism for the synthesis of KDO8P, in which a hydroxide ion on the si side of PEP attacks C2(PEP), forming a tetrahedral-like intermediate with a buildup of negative charge at C3(PEP). The ensuing condensation of C3(PEP) with C1(A5P) would be favored by a proton transfer from the phosphate moiety of PEP to the aldehyde carbonyl of A5P to generate the hydroxyl. Overall, the process can be described as a syn addition of water and A5P to the si side of PEP.