PDBsum entry 2g3f

Hydrolase

PDB id: 2g3f

Contents

Protein chains

414 a.a. *

Ligands

IZC ×2

Metals

_ZN ×2

Waters ×405

* Residue conservation analysis

PDB id:

2g3f

Name:

Hydrolase

Title:

Crystal structure of imidazolonepropionase complexed with imidazole-4- acetic acid sodium salt, a substrate homologue

Structure:

Imidazolonepropionase. Chain: a, b. Synonym: imidazolone-5-propionate hydrolase. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Strain: 168. Gene: huti. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.185 R-free: 0.216

Authors:

Y.Yu,Y.H.Liang,X.D.Su

Key ref:

Y.Yu et al. (2006). A catalytic mechanism revealed by the crystal structures of the imidazolonepropionase from Bacillus subtilis. J Biol Chem, 281, 36929-36936. PubMed id: 16990261 DOI: 10.1074/jbc.M607703200

Date:

19-Feb-06 Release date: 26-Sep-06

Protein chains

P42084  (HUTI_BACSU) -  Imidazolonepropionase from Bacillus subtilis (strain 168)

Seq: 421 a.a.

Struc: 414 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.2.7 - imidazolonepropionase.
• Pathway: Histidine Catabolism
• Reaction: 4-imidazolone-5-propanoate + H2O = N-formimidoyl-L-glutamate

4-imidazolone-5-propanoate + H2O = N-formimidoyl-L-glutamate (Bound ligand (Het Group name = IZC) matches with 75.00% similarity)

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

Added reference

DOI no: 10.1074/jbc.M607703200

J Biol Chem 281:36929-36936 (2006)

PubMed id: 16990261

A catalytic mechanism revealed by the crystal structures of the imidazolonepropionase from Bacillus subtilis.

Y.Yu, Y.H.Liang, E.Brostromer, J.M.Quan, S.Panjikar, Y.H.Dong, X.D.Su.

ABSTRACT

Imidazolonepropionase (EC 3.5.2.7) catalyzes the third step in the universal histidine degradation pathway, hydrolyzing the carbon-nitrogen bonds in 4-imidazolone-5-propionic acid to yield N-formimino-l-glutamic acid. Here we report the crystal structures of the Bacillus subtilis imidazolonepropionase and its complex at 2.0-A resolution with substrate analog imidazole-4-acetic acid sodium (I4AA). The structure of the native enzyme contains two domains, a TIM (triose-phosphate isomerase) barrel domain with two insertions and a small beta-sandwich domain. The TIM barrel domain is quite similar to the members of the alpha/beta barrel metallo-dependent hydrolase superfamily, especially to Escherichia coli cytosine deaminase. A metal ion was found in the central cavity of the TIM barrel and was tightly coordinated to residues His-80, His-82, His-249, Asp-324, and a water molecule. X-ray fluorescence scan analysis confirmed that the bound metal ion was a zinc ion. An acetate ion, 6 A away from the zinc ion, was also found in the potential active site. In the complex structure with I4AA, a substrate analog, I4AA replaced the acetate ion and contacted with Arg-89, Try-102, Tyr-152, His-185, and Glu-252, further defining and confirming the active site. The detailed structural studies allowed us to propose a zinc-activated nucleophilic attack mechanism for the hydrolysis reaction catalyzed by the enzyme.

Selected figure(s)

Figure 1.
FIGURE 1. A, the chemical reaction catalyzed by the imidazolonepropionase. B, imidazole-4-acetic acid sodium salt, an analog of 4-imidazolone-5-propionic acid (the substrate of imidazolonepropionase).

Figure 4.
FIGURE 4. The schematic diagram of a proposed mechanism for the hydrolysis reaction catalyzed by the family of imidazolonepropionase (see under "Results and Discussion").

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 36929-36936) copyright 2006.

Figures were selected by an automated process.