PDBsum entry 1kpi

Transferase

PDB id: 1kpi

Contents

Protein chain

291 a.a. *

Ligands

CO3

SO4 ×4

SAH

10A

Waters ×62

* Residue conservation analysis

PDB id:

1kpi

Name:

Transferase

Title:

Crystal structure of mycolic acid cyclopropane synthase cmaa2 complexed with sah and dddmab

Structure:

Cyclopropane-fatty-acyl-phospholipid synthase 2. Chain: a. Synonym: cyclopropane fatty acid synthase. Cfa synthase. Cyclopropane mycolic acid synthase. Cmaa2. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: cmaa2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.65Å R-factor: 0.208 R-free: 0.242

Authors:

C.-C.Huang,C.V.Smith,W.R.Jacobs Jr.,M.S.Glickman,J.C.Sacchettini,Tb Structural Genomics Consortium (Tbsgc)

Key ref:

C.C.Huang et al. (2002). Crystal structures of mycolic acid cyclopropane synthases from Mycobacterium tuberculosis. J Biol Chem, 277, 11559-11569. PubMed id: 11756461 DOI: 10.1074/jbc.M111698200

Date:

30-Dec-01 Release date: 11-Jan-02

Protein chain

P9WPB5  (CMAS2_MYCTU) -  Cyclopropane mycolic acid synthase 2 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 302 a.a.

Struc: 291 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.1.1.79 - cyclopropane-fatty-acyl-phospholipid synthase.
• Reaction: a 1-acyl-2-(9Z)-enoyl-sn-glycero-3-phospholipid + S-adenosyl-L-methionine = a 1-acyl-2-(9-cyclopronane)-acyl-sn-glycero-3-phospholipid + S-adenosyl-L-homocysteine + H⁺

1-acyl-2-(9Z)-enoyl-sn-glycero-3-phospholipid + S-adenosyl-L-methionine = 1-acyl-2-(9-cyclopronane)-acyl-sn-glycero-3-phospholipid + S-adenosyl-L-homocysteine + H(+) (Bound ligand (Het Group name = SAH) corresponds exactly)

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

Added reference

DOI no: 10.1074/jbc.M111698200

J Biol Chem 277:11559-11569 (2002)

PubMed id: 11756461

Crystal structures of mycolic acid cyclopropane synthases from Mycobacterium tuberculosis.

C.C.Huang, C.V.Smith, M.S.Glickman, W.R.Jacobs, J.C.Sacchettini.

ABSTRACT

Mycolic acids are major components of the cell wall of Mycobacterium tuberculosis. Several studies indicate that functional groups in the acyl chain of mycolic acids are important for pathogenesis and persistence. There are at least three mycolic acid cyclopropane synthases (PcaA, CmaA1, and CmaA2) that are responsible for these site-specific modifications of mycolic acids. To derive information on the specificity and enzyme mechanism of the family of proteins, the crystal structures of CmaA1, CmaA2, and PcaA were solved to 2-, 2-, and 2.65-A resolution, respectively. All three enzymes have a seven-stranded alpha/beta fold similar to other methyltransferases with the location and interactions with the cofactor S-adenosyl-l-methionine conserved. The structures of the ternary complexes demonstrate the position of the mycolic acid substrate binding site. Close examination of the active site reveals electron density that we believe represents a bicarbonate ion. The structures support the hypothesis that these enzymes catalyze methyl transfer via a carbocation mechanism in which the bicarbonate ion acts as a general base. In addition, comparison of the enzyme structures reveals a possible mechanism for substrate specificity. These structures provide a foundation for rational-drug design, which may lead to the development of new inhibitors effective against persistent bacteria.

Selected figure(s)

Figure 3.
Fig. 3. Structure of apoCmaA1. a, superimposition of C[ ]atoms of structures of apoCmaA1 (gray) and CmaAl-SAH-DDDMAB (blue) using residues 20-170. Residues 136-145 and residues 170-210 of apoCmaA1 are colored in green. b, comparison of the active site cavities in apoCmaA1 and CmaAl-SAH-DDDMAB.

Figure 4.
Fig. 4. a, interactions between cofactor SAH and CmaA1. The detailed interactions are also listed in Table II. The figure was prepared using LIGPLOT(54). b, interactions between 7 amino acid insertions (residues 153-159) of CmaA2 (orange) and the N terminus compared with CmaA1 (blue). c, active site architecture. SAH and DDDMAB are shown in green. Residues 136-140 are shown in orange. DDDMAB in CmaA2-SAH-DDDMAB structure is superimposed with CmaA1-SAH-DDDMAB structure and is shown in gray. The bicarbonate ion in the active site is shown interacting with His-167, Cys-35, and Glu-140. The carbocation intermediate of the reaction mechanism may be stabilized by cation- interactions during catalysis, specifically by the aromatic ring of the Tyr-33.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 11559-11569) copyright 2002.

Figures were selected by an automated process.