PDBsum entry 2q3c

Transferase

PDB id: 2q3c

Contents

Protein chain

300 a.a. *

Ligands

ASP-PHE-SER-ILE

MPD

Waters ×163

* Residue conservation analysis

PDB id:

2q3c

Name:

Transferase

Title:

2.1 a resolution crystal structure of o-acetylserine sulfhydrylase (oass) holoenzyme from mycobacterium tuberculosis in complex with the inhibitory peptide dfsi

Structure:

Cysteine synthase a. Chain: a. Synonym: o-acetylserine sulfhydrylase a, o-acetylserine thiol, lyase a, csase a. Engineered: yes. Dfsi inhibitory peptide. Chain: b. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Strain: rv2334. Gene: cysk. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Organism_taxid: 1773

Resolution:

2.10Å R-factor: 0.188 R-free: 0.207

Authors:

G.Schneider,R.Schnell

Key ref:

R.Schnell et al. (2007). Structural insights into catalysis and inhibition of O-acetylserine sulfhydrylase from Mycobacterium tuberculosis. Crystal structures of the enzyme alpha-aminoacrylate intermediate and an enzyme-inhibitor complex. J Biol Chem, 282, 23473-23481. PubMed id: 17567578 DOI: 10.1074/jbc.M703518200

Date:

30-May-07 Release date: 12-Jun-07

Protein chain

P9WP55  (CYSK_MYCTU) -  O-acetylserine sulfhydrylase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 310 a.a.

Struc: 300 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.2.5.1.47 - cysteine synthase.
• Reaction: O-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate

O-acetyl-L-serine + hydrogen sulfide (Bound ligand (Het Group name = SER) matches with 60.00% similarity) = L-cysteine (Bound ligand (Het Group name = ASP) matches with 50.00% similarity) + acetate (Bound ligand (Het Group name = ILE) matches with 60.00% similarity)

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PHE) matches with 42.11% similarity)

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

reference

DOI no: 10.1074/jbc.M703518200

J Biol Chem 282:23473-23481 (2007)

PubMed id: 17567578

Structural insights into catalysis and inhibition of O-acetylserine sulfhydrylase from Mycobacterium tuberculosis. Crystal structures of the enzyme alpha-aminoacrylate intermediate and an enzyme-inhibitor complex.

R.Schnell, W.Oehlmann, M.Singh, G.Schneider.

ABSTRACT

Cysteine biosynthetic genes are up-regulated in the persistent phase of Mycobacterium tuberculosis, and the corresponding enzymes are therefore of interest as potential targets for novel antibacterial agents. cysK1 is one of these genes and has been annotated as coding for an O-acetylserine sulfhydrylase. Recombinant CysK1 is a pyridoxal phosphate (PLP)-dependent enzyme that catalyzes the conversion of O-acetylserine to cysteine. The crystal structure of the enzyme was determined to 1.8A resolution. CysK1 belongs to the family of fold type II PLP enzymes and is similar in structure to other O-acetylserine sulfhydrylases. We were able to trap the alpha-aminoacrylate reaction intermediate and determine its structure by cryocrystallography. Formation of the aminoacrylate complex is accompanied by a domain rotation resulting in active site closure. The aminoacrylate moiety is bound in the active site via the covalent linkage to the PLP cofactor and by hydrogen bonds of its carboxyl group to several enzyme residues. The catalytic lysine residue is positioned such that it can protonate the Calpha-carbon atom of the aminoacrylate only from the si-face, resulting in the formation of L-cysteine. CysK1 is competitively inhibited by a four-residue peptide derived from the C-terminal of serine acetyl transferase. The crystallographic analysis reveals that the peptide binds to the enzyme active site, suggesting that CysK1 forms an bi-enzyme complex with serine acetyl transferase, in a similar manner to other bacterial and plant O-acetylserine sulfhydrylases. The structure of the enzyme-peptide complex provides a framework for the design of strong binding inhibitors.

Selected figure(s)

Figure 3.
FIGURE 3. Structure of the complex of CysK1 with -aminoacrylate. A, superposition of holo-CysK1 (blue) and the CysK1-aminoacrylate complex (red) illustrating the conformational changes of the N-terminal domain leading to the closure of the active site. The covalent intermediate forming the external Schiff base with PLP is shown as a stick model (yellow). B, part of the 2F[o] - F[o] electron density map, contoured at 1.2 , showing formation of the -aminoacrylate intermediate. C, schematic showing the interactions of the reaction intermediate with enzyme residues in the active site. Hydrogen bonds are indicated by dashed lines. D, stereo view of the active site of the CysK1- -aminoacrylate intermediate complex. The red spheres indicate the positions of bound water molecules.

Figure 6.
FIGURE 6. Structure of the CysK1-peptide complex. A, stereo view of the active site of CysK1 with the bound DFSI peptide, shown in green. CysK1 amino acid residues are shown in yellow, and water molecules are shown as red spheres. B, part of the 2F[o] - F[o] electron density map at the peptide binding site in CysK1, contoured at 1.4 .

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 23473-23481) copyright 2007.

Figures were selected by the author.