PDBsum entry 2go3

Hydrolase

PDB id: 2go3

Contents

Protein chains

266 a.a. *

Ligands

PLM

MYR ×2

IMD ×4

GOL ×4

Metals

_ZN ×5

_CL ×2

Waters ×410

* Residue conservation analysis

PDB id:

2go3

Name:

Hydrolase

Title:

Crystal structure of aquifex aeolicus lpxc complexed with imidazole.

Structure:

Udp-3-o-[3-hydroxymyristoyl] n-acetylglucosamine deacetylase. Chain: a, b. Fragment: delta 11 c-terminal deletion. Synonym: udp-3-o-acyl-glcnac deacetylase. Engineered: yes. Mutation: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Gene: lpxc, enva. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.195 R-free: 0.235

Authors:

H.A.Gennadios,D.A.Whittington,X.Li,C.A.Fierke,D.W.Christianson

Key ref:

H.A.Gennadios et al. (2006). Mechanistic inferences from the binding of ligands to LpxC, a metal-dependent deacetylase. Biochemistry, 45, 7940-7948. PubMed id: 16800620 DOI: 10.1021/bi060823m

Date:

12-Apr-06 Release date: 04-Jul-06

Protein chains

O67648  (LPXC_AQUAE) -  UDP-3-O-acyl-N-acetylglucosamine deacetylase from Aquifex aeolicus (strain VF5)

Seq: 282 a.a.

Struc: 266 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.5.1.108 - UDP-3-O-acyl-N-acetylglucosamine deacetylase.
• Reaction: a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + H2O = a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + acetate

UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + H2O = UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + acetate (Bound ligand (Het Group name = GOL) matches with 42.86% similarity)

• Cofactor: Zn(2+)

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

Key reference

DOI no: 10.1021/bi060823m

Biochemistry 45:7940-7948 (2006)

PubMed id: 16800620

Mechanistic inferences from the binding of ligands to LpxC, a metal-dependent deacetylase.

H.A.Gennadios, D.A.Whittington, X.Li, C.A.Fierke, D.W.Christianson.

ABSTRACT

The metal-dependent deacetylase LpxC catalyzes the first committed step of lipid A biosynthesis in Gram-negative bacteria. Accordingly, LpxC is an attractive target for the development of inhibitors that may serve as potential new antibiotics for the treatment of Gram-negative bacterial infections. Here, we report the 2.7 A resolution X-ray crystal structure of LpxC complexed with the substrate analogue inhibitor TU-514 and the 2.0 A resolution structure of LpxC complexed with imidazole. The X-ray crystal structure of LpxC complexed with TU-514 allows for a detailed examination of the coordination geometry of the catalytic zinc ion and other enzyme-inhibitor interactions in the active site. The hydroxamate group of TU-514 forms a bidentate chelate complex with the zinc ion and makes hydrogen bond interactions with conserved active site residues E78, H265, and T191. The inhibitor C-4 hydroxyl group makes direct hydrogen bond interactions with E197 and H58. Finally, the C-3 myristate moiety of the inhibitor binds in the hydrophobic tunnel of the active site. These intermolecular interactions provide a foundation for understanding structural aspects of enzyme-substrate and enzyme-inhibitor affinity. Comparison of the TU-514 complex with cacodylate and imidazole complexes suggests a possible substrate diphosphate binding site and highlights residues that may stabilize the tetrahedral intermediate and its flanking transition states in catalysis. Evidence of a catalytic zinc ion in the native zinc enzyme coordinated by H79, H238, D242, and two water molecules with square pyramidal geometry is also presented. These results suggest that the native state of this metallohydrolase may contain a pentacoordinate zinc ion, which contrasts with the native states of archetypical zinc hydrolases such as thermolysin and carboxypeptidase A.