PDBsum entry 4al2

Hydrolase

PDB id: 4al2

Contents

Protein chains

162 a.a.

Ligands

H2S ×3

Metals

_NI ×3

Waters ×54

PDB id:

4al2

Name:

Hydrolase

Title:

Peptide deformylase (ni-form) with hydrosulfide

Structure:

Peptide deformylase. Chain: a, b, c. Synonym: pdf, polypeptide deformylase. Engineered: yes. Other_details: c-terminal his tag

Source:

Escherichia coli. Organism_taxid: 469008. Strain: bl21(de3). Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: plyss.

Resolution:

2.60Å R-factor: 0.211 R-free: 0.298

Authors:

G.J.Palm,W.Hinrichs

Key ref:

M.Strianese et al. (2012). A FRET enzyme-based probe for monitoring hydrogen sulfide. Inorg Chem, 51, 11220-11222. PubMed id: 23072298

Date:

29-Feb-12 Release date: 04-Apr-12

Protein chains

P0A6K3  (DEF_ECOLI) -  Peptide deformylase from Escherichia coli (strain K12)

Seq: 169 a.a.

Struc: 162 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
• Cofactor: Fe(2+)

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

Key reference

Inorg Chem 51:11220-11222 (2012)

PubMed id: 23072298

A FRET enzyme-based probe for monitoring hydrogen sulfide.

M.Strianese, G.J.Palm, S.Milione, O.Kühl, W.Hinrichs, C.Pellecchia.

ABSTRACT

Fluorescently labeled cobalt peptide deformylase (Co-PDF) can be efficiently used as a fluorescence-resonance-energy-transfer-based sensing device for hydrogen sulfide (H(2)S). The proof of concept of our sensor system is substantiated by spectroscopic, structural, and theoretical results. Monohydrogen sulfide coordination to Co-PDF and Ni-PDF was verified by X-ray crystallography. Density functional theory calculations were performed to gain insight into the characteristics of the coordination adduct between H(2)S and the cobalt cofactor in Co-PDF.