PDBsum entry 3cpm

Hydrolase

PDB id: 3cpm

Contents

Protein chain

184 a.a. *

Ligands

SO4

Metals

_ZN ×4

Waters ×60

* Residue conservation analysis

PDB id:

3cpm

Name:

Hydrolase

Title:

Plant peptide deformylase pdf1b crystal structure

Structure:

Peptide deformylase, chloroplast. Chain: a. Fragment: residues 65-257. Synonym: pdf, polypeptide deformylase. Engineered: yes

Source:

Arabidopsis thaliana. Mouse-ear cress. Gene: pdf1b. Expressed in: escherichia coli.

Resolution:

2.40Å R-factor: 0.235 R-free: 0.297

Authors:

D.W.Rodgers,R.L.Houtz,L.M.A.Dirk,J.J.Schmidt,Y.Cai

Key ref:

L.M.Dirk et al. (2008). Insights into the substrate specificity of plant peptide deformylase, an essential enzyme with potential for the development of novel biotechnology applications in agriculture. Biochem J, 413, 417-427. PubMed id: 18412546

Date:

31-Mar-08 Release date: 22-Jul-08

Protein chain

Q9FUZ2  (DEF1B_ARATH) -  Peptide deformylase 1B, chloroplastic/mitochondrial from Arabidopsis thaliana

Seq: 273 a.a.

Struc: 184 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

Biochem J 413:417-427 (2008)

PubMed id: 18412546

Insights into the substrate specificity of plant peptide deformylase, an essential enzyme with potential for the development of novel biotechnology applications in agriculture.

L.M.Dirk, J.J.Schmidt, Y.Cai, J.C.Barnes, K.M.Hanger, N.R.Nayak, M.A.Williams, R.B.Grossman, R.L.Houtz, D.W.Rodgers.

ABSTRACT

The crystal structure of AtPDF1B [Arabidopsis thaliana PDF (peptide deformylase) 1B; EC 3.5.1.88], a plant specific deformylase, has been determined at a resolution of 2.4 A (1 A=0.1 nm). The overall fold of AtPDF1B is similar to other peptide deformylases that have been reported. Evidence from the crystal structure and gel filtration chromatography indicates that AtPDF1B exists as a symmetric dimer. PDF1B is essential in plants and has a preferred substrate specificity towards the PS II (photosystem II) D1 polypeptide. Comparative analysis of AtPDF1B, AtPDF1A, and the type 1B deformylase from Escherichia coli, identifies a number of differences in substrate binding subsites that might account for variations in sequence preference. A model of the N-terminal five amino acids from the D1 polypeptide bound in the active site of AtPDF1B suggests an influence of Tyr(178) as a structural determinant for polypeptide substrate specificity through hydrogen bonding with Thr(2) in the D1 sequence. Kinetic analyses using a polypeptide mimic of the D1 N-terminus was performed on AtPDF1B mutated at Tyr(178) to alanine, phenylalanine or arginine (equivalent residue in AtPDF1A). The results suggest that, whereas Tyr(178) can influence catalytic activity, other residues contribute to the overall preference for the D1 polypeptide.