PDBsum entry 2h9c

Lyase

PDB id: 2h9c

Contents

Protein chains

88 a.a. *

Ligands

NO3 ×5

Waters ×55

* Residue conservation analysis

PDB id:

2h9c

Name:

Lyase

Title:

Native crystal structure of the isochorismate-pyruvate lyase from pseudomonas aeruginosa

Structure:

Salicylate biosynthesis protein pchb. Chain: a, b. Fragment: residues 1-99. Synonym: isochorismate-pyruvate lyase. Engineered: yes

Source:

Pseudomonas aeruginosa. Organism_taxid: 208964. Strain: pao1. Gene: pchb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.35Å R-factor: 0.224 R-free: 0.269

Authors:

A.L.Lamb,J.Zaitseva,J.Lu

Key ref:

J.Zaitseva et al. (2006). Two crystal structures of the isochorismate pyruvate lyase from Pseudomonas aeruginosa. J Biol Chem, 281, 33441-33449. PubMed id: 16914555 DOI: 10.1074/jbc.M605470200

Date:

09-Jun-06 Release date: 15-Aug-06

Protein chains

Q51507  (PCHB_PSEAE) -  Isochorismate pyruvate lyase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 101 a.a.

Struc: 88 a.a.

Enzyme reactions

• Enzyme class 2: E.C.4.2.99.21 - isochorismate lyase.
• Reaction: isochorismate = salicylate + pyruvate
• Enzyme class 3: E.C.5.4.99.5 - chorismate mutase.

Pathway:

• Reaction: chorismate = prephenate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1074/jbc.M605470200

J Biol Chem 281:33441-33449 (2006)

PubMed id: 16914555

Two crystal structures of the isochorismate pyruvate lyase from Pseudomonas aeruginosa.

J.Zaitseva, J.Lu, K.L.Olechoski, A.L.Lamb.

ABSTRACT

Enzymatic systems that exploit pericyclic reaction mechanisms are rare. A recent addition to this class is the enzyme PchB, an 11.4-kDa isochorismate pyruvate lyase from Pseudomonas aeruginosa. The apo and pyruvate-bound structures of PchB reveal that the enzyme is a structural homologue of chorismate mutases in the AroQalpha class despite low sequence identity (20%). The enzyme is an intertwined dimer of three helices with connecting loops, and amino acids from each monomer participate in each of two active sites. The apo structure (2.35 A resolution) has one dimer per asymmetric unit with nitrate bound in an open active site. The loop between the first and second helices is disordered, providing a gateway for substrate entry and product exit. The pyruvate-bound structure (1.95 A resolution) has two dimers per asymmetric unit. One has two open active sites like the apo structure, and the other has two closed active sites with the loop between the first and second helices ordered for catalysis. Determining the structure of PchB is part of a larger effort to elucidate protein structures involved in siderophore biosynthesis, as these enzymes are crucial for bacterial iron uptake and virulence and have been identified as antimicrobial drug targets.

Selected figure(s)

Figure 5.
FIGURE 5. Stereoviews of the active sites of apo PchB (a) with the closed pyruvate-bound PchB (b) and EcCM (c). The colors used are as described in Fig. 2. The amino acid legends in panel b indicate monomer name, residue number, and one-letter amino acid code and are in capital letters if they are conserved between PchB and EcCM and lowercase if they are not.

Figure 6.
FIGURE 6. Two-dimensional schematic representation of the protein-ligand contacts in the closed, pyruvate-bound structure (a) and the wrong-ligand crystallographic refinement model containing salicylate and pyruvate (b). The amino acid side chains are shown as sticks and labeled with the three-letter amino acid code, amino acid number, and monomer name. The pyruvate and salicylate molecules are depicted as ball-and-stick and are labeled "Pyr 1," "Pyr 2," and "SalI" with a monomer name of (E). The carbon atoms are black, and the oxygen atoms are white. This figure was generated with LIGPLOT (31).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 33441-33449) copyright 2006.

Figures were selected by the author.