PDBsum entry 3cmd

Hydrolase

PDB id: 3cmd

Contents

Protein chains

186 a.a. *

Ligands

MLI ×4

Metals

_FE ×2

_NA ×8

Waters ×207

* Residue conservation analysis

PDB id:

3cmd

Name:

Hydrolase

Title:

Crystal structure of peptide deformylase from vre-e.Faecium

Structure:

Peptide deformylase. Chain: a, b. Engineered: yes

Source:

Enterococcus faecium. Streptococcus faecium. Organism_taxid: 1352. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.70Å R-factor: 0.200 R-free: 0.229

Authors:

K.Y.Hwang,K.H.Nam

Key ref:

K.H.Nam et al. (2009). Insight into the antibacterial drug design and architectural mechanism of peptide recognition from the E. faecium peptide deformylase structure. Proteins, 74, 261-265. PubMed id: 18831047 DOI: 10.1002/prot.22257

Date:

21-Mar-08 Release date: 13-Jan-09

Protein chains

Q842S4  (Q842S4_ENTFC) -  Peptide deformylase from Enterococcus faecium

Seq: 187 a.a.

Struc: 186 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.1.88 - peptide deformylase.
• Reaction: N-terminal N-formyl-L-methionyl-[peptide] + H2O = N-terminal L-methionyl- [peptide] + formate

N-terminal N-formyl-L-methionyl-[peptide] + H2O = N-terminal L-methionyl- [peptide] (Bound ligand (Het Group name = MLI) matches with 42.86% similarity) + formate

• Cofactor: Fe(2+)

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

Key reference

DOI no: 10.1002/prot.22257

Proteins 74:261-265 (2009)

PubMed id: 18831047

Insight into the antibacterial drug design and architectural mechanism of peptide recognition from the E. faecium peptide deformylase structure.

K.H.Nam, J.I.Ham, A.Priyadarshi, E.E.Kim, N.Chung, K.Y.Hwang.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. Crystal structure of EfPDF. (a) Crystallographic packing of 75.4% solvent content. Twelve of the EfPDF monomers generated a large 80 Å pore. (b) Unfolded N-terminal expression tag peptides of all molecules accessed the active site pockets of neighboring molecules. The expression peptide has 82% buried surfaced area, but makes no contacts. A 2Fo-Fc electron density map contoured at 1 is shown in gray in the N-terminal region of the molecule. Molecules A and B are represented by green and cyan, respectively. The expression tag region is represented by dark-blue sticks. The surface of the active site pocket is represented in red. (c) Ribbon diagram of the EfPDF monomer structure. The unfolded expression tag peptide in the N-terminal region lies along the disordered region located between 2 and 3 (CD loop). Helices are represented in red, strands in yellow, loops in green and the expression tag peptide loop in light blue. The active site metal ion is represented by the orange sphere. (d) Malonic acid interacts with the metal ion and Glu158, which is the catalytic residue. The active site pocket is loosely associated with the malonic acid. The active site residues are shown by ball-and-stick representations. The metal ion is represented by the orange sphere.

Figure 2.
Figure 2. Proposed architectural mechanism of peptide recognition. Approximately 15 × 10 Å U shaped cavity in the EfPDF crystal structure. This shape prevents access by folded structures containing -helices or -sheets. Unfolded peptides can access the site from the side. The black dotted circle shows the region which prevents structurally folded proteins from entering, thus increasing the selectivity for unfolded peptides. The CD loop is located in the area of the red dotted circle. X indicates a route of entry that is likely to be inaccessible. Green ribbon is unfolded N-terminal expression tag peptides in our result.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2009, 74, 261-265) copyright 2009.