PDBsum entry 1fwt

Lyase

PDB id: 1fwt

Contents

Protein chains

263 a.a. *

Ligands

PEP ×2

E4P

PO4

Metals

_CD ×2

Waters ×223

* Residue conservation analysis

PDB id:

1fwt

Name:

Lyase

Title:

Aquifex aeolicus kdo8p synthase in complex with pep, e4p and cadmium

Structure:

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

1.90Å R-factor: 0.197 R-free: 0.222

Authors:

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

Key ref:

H.S.Duewel et al. (2001). Substrate and metal complexes of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Aquifex aeolicus at 1.9-A resolution. Implications for the condensation mechanism. J Biol Chem, 276, 8393-8402. PubMed id: 11115499 DOI: 10.1074/jbc.M007884200

Date:

24-Sep-00 Release date: 21-Apr-01

Protein chains

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

Seq: 267 a.a.

Struc: 263 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 = E4P) matches with 85.71% similarity) + phosphoenolpyruvate + H2O (Bound ligand (Het Group name = PEP) corresponds exactly) = 3-deoxy-alpha-D- manno-2-octulosonate-8-phosphate + phosphate

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

reference

DOI no: 10.1074/jbc.M007884200

J Biol Chem 276:8393-8402 (2001)

PubMed id: 11115499

Substrate and metal complexes of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Aquifex aeolicus at 1.9-A resolution. Implications for the condensation mechanism.

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

ABSTRACT

3-Deoxy-D-manno-octulosonate-8-phosphate synthase (KDO8PS) from the hyperthermophilic bacterium Aquifex aeolicus differs from its Escherichia coli counterpart in the requirement of a divalent metal for activity (Duewel, H. S., and Woodard, R. W. (2000) J. Biol. Chem. 275, 22824-22831). Here we report the crystal structure of the A. aeolicus enzyme, which was determined by molecular replacement using E. coli KDO8PS as a model. The structures of the metal-free and Cd(2+) forms of the enzyme were determined in the uncomplexed state and in complex with various combinations of phosphoenolpyruvate (PEP), arabinose 5-phosphate (A5P), and erythrose 4-phosphate (E4P). Like the E. coli enzyme, A. aeolicus KDO8PS is a homotetramer containing four distinct active sites at the interface between subunits. The active site cavity is open in the substrate-free enzyme or when either A5P alone or PEP alone binds, and becomes isolated from the aqueous phase when both PEP and A5P (or E4P) bind together. In the presence of metal, the enzyme is asymmetric and appears to alternate catalysis between the active sites located on one face of the tetramer and those located on the other face. In the absence of metal, the asymmetry is lost. Details of the active site that may be important for catalysis are visible at the high resolution achieved in these structures. Most notably, the shape of the PEP-binding pocket forces PEP to assume a distorted geometry at C-2, which might anticipate the conversion from sp(2) to sp(3) hybridization occurring during intermediate formation and which may modulate PEP reactivity toward A5P. Two water molecules are located in van der Waals contact with the si and re sides of C-2(PEP), respectively. Abstraction of a proton from either of these water molecules by a protein group is expected to elicit a nucleophilic attack of the resulting hydroxide ion on the nearby C-2(PEP), thus triggering the beginning of the catalytic cycle.

Selected figure(s)

Figure 3.
Fig. 3. Metal-binding site of A. aeolicus KDO8PS. The C- trace and side chains of the Cd^2+ enzyme are shown with salmon and white bonds, respectively. The C- trace and side chains of the metal-free enzyme are shown with transparent light-blue bonds. The coordination of the Cd^2+ ion is shown as transparent light-green bonds. Phosphate ions are labeled PO[4]-1 and PO[4]-2. Blue, nitrogen; red, oxygen; yellow, sulfur; pale blue, phosphorus; cyan, cadmium. WAT, water.

Figure 4.
Fig. 4. PEP-binding site. A, polar contacts of PEP inside the active site. The C- trace and side chains of the Cd^2+ enzyme are shown with salmon and white bonds, respectively. Cd^2+ coordination is shown as transparent bonds. PEP is shown as ball-and-sticks with gold bonds; the si side of PEP is pointing up and to the left, and the re side is pointing down and to the right. Blue, nitrogen; red, oxygen; yellow, sulfur; pale blue, phosphorus; orange, carbon. B, details of PEP geometry inside the active site. PEP is shown with its si side pointing up. The angle between the plane defined by C-2, C-1, and C-3 (blue triangle) and the plane defined by C-1, C-3, and O-2 (yellow triangle) is ~12°, indicating that the geometry of C-2 is intermediate between trigonal and tetrahedral. WAT, water.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 8393-8402) copyright 2001.

Figures were selected by an automated process.