PDBsum entry 2pd4

Oxidoreductase

PDB id: 2pd4

Contents

Protein chains

274 a.a. *

Ligands

NAD ×4

DCN ×4

Waters ×218

* Residue conservation analysis

PDB id:

2pd4

Name:

Oxidoreductase

Title:

Crystal structure of the helicobacter pylori enoyl-acyl carrier protein reductase in complex with hydroxydiphenyl ether compounds, triclosan and diclosan

Structure:

Enoyl-[acyl-carrier-protein] reductase [nadh]. Chain: a, b, c, d. Synonym: enoyl-acyl carrier protein reductase, nadh- dependent enoyl- acp reductase. Engineered: yes

Source:

Helicobacter pylori. Organism_taxid: 210. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.224 R-free: 0.248

Authors:

H.H.Lee,J.H.Moon,S.W.Suh

Key ref:

H.H.Lee et al. (2007). Crystal structure of the Helicobacter pylori enoyl-acyl carrier protein reductase in complex with hydroxydiphenyl ether compounds, triclosan and diclosan. Proteins, 69, 691-694. PubMed id: 17879346 DOI: 10.1002/prot.21586

Date:

31-Mar-07 Release date: 17-Apr-07

Supersedes:

1jw7

Protein chains

O24990  (FABI_HELPY) -  Enoyl-[acyl-carrier-protein] reductase [NADH] FabI from Helicobacter pylori (strain ATCC 700392 / 26695)

Seq: 275 a.a.

Struc: 274 a.a.

Enzyme reactions

• Enzyme class: E.C.1.3.1.9 - enoyl-[acyl-carrier-protein] reductase (NADH).
• Reaction: a 2,3-saturated acyl-[ACP] + NAD⁺ = a (2E)-enoyl-[ACP] + NADH + H⁺

2,3-saturated acyl-[ACP] + NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly) = (2E)-enoyl-[ACP] + NADH + H(+)

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

Added reference

DOI no: 10.1002/prot.21586

Proteins 69:691-694 (2007)

PubMed id: 17879346

Crystal structure of the Helicobacter pylori enoyl-acyl carrier protein reductase in complex with hydroxydiphenyl ether compounds, triclosan and diclosan.

H.H.Lee, J.Moon, S.W.Suh.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. Monomer and tetramer structures of H. pylori ENR and electron density maps of the bound ligands. (A) Monomer structure. Secondary structure elements were defined by PyMOL (DeLano, 2002, The PyMOL Molecular Graphics System, http://pymol.sourceforge.net/). NAD^+ and triclosan bound to the active site of subunit A are shown as ball-and-stick models. (B) Tetrameric architecture. NAD^+ and triclosan are shown. (C) 2F[o]-F[c] electron density maps of the bound ligands, superimposed on triclosan (subunit A), diclosan (subunit A), and NAD^+ (subunit A of the triclosan complex). (D) Superposition of triclosan (cyan) and diclosan (purple). Phenolic rings (ring A) of triclosan and diclosan are superimposed.

Figure 2.
Figure 2. Binding mode of triclosan, diclosan, and NAD^+. (A) Superposition of H. pylori ENR (subunit A of the triclosan complex, colored in red) with ENRs from E. coli (PDB ID code 1C14, colored in yellow), M. tuberculosis (PDB ID code 1P45, colored in pink), B. napus (PDB ID code 1D7O, colored in cyan), and P. falciparum (PDB ID code 1UH5, colored in green) ENRs (monomer A). (B) Binding site of triclosan and NAD^+ in subunit A. (C) Binding site of diclosan and NAD^+ in subunit A.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2007, 69, 691-694) copyright 2007.