3CPM

plant peptide deformylase PDF1B crystal structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

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

(2008) Biochem J 413: 417-427

  • DOI: https://doi.org/10.1042/BJ20071641
  • Primary Citation of Related Structures:  
    3CPM

  • PubMed 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.


  • Organizational Affiliation

    Plant Physiology/Biochemistry/Molecular Biology Program, Department of Horticulture, University of Kentucky, 441 Plant Science Building, Lexington, KY 40546-0312, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide deformylase, chloroplast193Arabidopsis thalianaMutation(s): 0 
Gene Names: PDF1B
EC: 3.5.1.88
UniProt
Find proteins for Q9FUZ2 (Arabidopsis thaliana)
Explore Q9FUZ2 
Go to UniProtKB:  Q9FUZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FUZ2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.902α = 90
b = 50.902β = 90
c = 144.783γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MAR345dtbdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations