PDBsum entry 2vzk

Transferase

PDB id: 2vzk

Contents

Protein chains

173 a.a. *

213 a.a. *

197 a.a. *

Ligands

TRS ×2

ACT ×2

Waters ×292

* Residue conservation analysis

PDB id:

2vzk

Name:

Transferase

Title:

Structure of the acyl-enzyme complex of an n-terminal nucleophile (ntn) hydrolase, oat2

Structure:

Glutamate n-acetyltransferase 2 alpha chain. Chain: a, c, e, g. Fragment: residues 8-180. Synonym: ornithine acetyl transferase, oat2. Engineered: yes. Glutamate n-acetyltransferase 2 beta chain. Chain: b. Synonym: ornithine acetyl transferase, oat2. Engineered: yes.

Source:

Streptomyces clavuligerus. Organism_taxid: 1901. Atcc: 3585. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.33Å R-factor: 0.255 R-free: 0.284

Authors:

A.Iqbal,I.J.Clifton,C.J.Schofield

Key ref:

A.Iqbal et al. (2009). Anatomy of a simple acyl intermediate in enzyme catalysis: combined biophysical and modeling studies on ornithine acetyl transferase. J Am Chem Soc, 131, 749-757. PubMed id: 19105697

Date:

01-Aug-08 Release date: 16-Sep-08

Protein chains

P0DJQ5  (GNAT2_STRCL) -  Glutamate N-acetyltransferase 2 from Streptomyces clavuligerus

Seq: 393 a.a.

Struc: 173 a.a.

Protein chains

P0DJQ5  (GNAT2_STRCL) -  Glutamate N-acetyltransferase 2 from Streptomyces clavuligerus

Seq: 393 a.a.

Struc: 213 a.a.

Protein chains

P0DJQ5  (GNAT2_STRCL) -  Glutamate N-acetyltransferase 2 from Streptomyces clavuligerus

Seq: 393 a.a.

Struc: 197 a.a.*

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

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H: E.C.2.3.1.35 - glutamate N-acetyltransferase.
• Reaction: N₂-acetyl-L-ornithine + L-glutamate = N-acetyl-L-glutamate + L-ornithine

N(2)-acetyl-L-ornithine (Bound ligand (Het Group name = ACT) matches with 40.00% similarity) + L-glutamate = N-acetyl-L-glutamate (Bound ligand (Het Group name = TRS) matches with 41.67% similarity) + L-ornithine

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

reference

J Am Chem Soc 131:749-757 (2009)

PubMed id: 19105697

Anatomy of a simple acyl intermediate in enzyme catalysis: combined biophysical and modeling studies on ornithine acetyl transferase.

A.Iqbal, I.J.Clifton, M.Bagonis, N.J.Kershaw, C.Domene, T.D.Claridge, C.W.Wharton, C.J.Schofield.

ABSTRACT

Acyl-enzyme complexes are intermediates in reactions catalyzed by many hydrolases and related enzymes which employ nucleophilic catalysis. However, most of the reported structural data on acyl-enzyme complexes has been acquired under noncatalytic conditions. Recent IR analyses have indicated that some acyl-enzyme complexes may be more flexible than most crystallographic analyses have implied. OAT2 is a member of the N-terminal nucleophile (Ntn) hydrolase enzyme superfamily and catalyzes the reversible transfer of an acetyl group between the alpha-amino groups of ornithine and glutamate in a mechanism proposed to involve an acyl-enzyme complex. We have carried out biophysical analyses on ornithine acetyl transferase (OAT2), both in solution and in the crystalline state. Mass spectrometric studies identified Thr-181 as the residue acetylated during OAT2 catalysis; (13)C NMR analyses implied the presence of an acyl-enzyme complex in solution. Crystallization of OAT2 in the presence of N-alpha-acetyl-L-glutamate led to a structure in which Thr-181 was acetylated; the carbonyl oxygen of the acyl-enzyme complex was located in an oxyanion hole and positioned to hydrogen bond with the backbone amide NH of Gly-112 and the alcohol of Thr-111. While the crystallographic analyses revealed only one structure, IR spectroscopy demonstrated the presence of two distinct acyl-enzyme complex structures with carbonyl stretching frequencies at 1691 and 1701 cm(-1). Modeling studies implied two possible acyl-enzyme complex structures, one of which correlates with that observed in the crystal structure and with the 1691 cm(-1) IR absorption. The second acyl-enzyme complex structure, which has only a single oxyanion hole hydrogen bond, is proposed to give rise to the 1701 cm(-1) IR absorption. The two acyl-enzyme complex structures can interconvert by movement of the Thr-111 side-chain alcohol hydrogen away from the oxyanion hole to hydrogen bond with the backbone carbonyl of the acylated residue, Thr-181. Overall, the results reveal that acyl-enzyme complex structures may be more dynamic than previously thought and support the use of a comprehensive biophysical and modeling approach in studying such intermediates.