1AZW

PROLINE IMINOPEPTIDASE FROM XANTHOMONAS CAMPESTRIS PV. CITRI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of proline iminopeptidase from Xanthomonas campestris pv. citri: a prototype for the prolyl oligopeptidase family.

Medrano, F.J.Alonso, J.Garcia, J.L.Romero, A.Bode, W.Gomis-Ruth, F.X.

(1998) EMBO J. 17: 1-9

  • DOI: 10.1093/emboj/17.1.1

  • PubMed Abstract: 
  • The proline iminopeptidase from Xanthomonas campestris pv. citri is a serine peptidase that catalyses the removal of N-terminal proline residues from peptides with high specificity. We have solved its three-dimensional structure by multiple isomorpho ...

    The proline iminopeptidase from Xanthomonas campestris pv. citri is a serine peptidase that catalyses the removal of N-terminal proline residues from peptides with high specificity. We have solved its three-dimensional structure by multiple isomorphous replacement and refined it to a crystallographic R-factor of 19.2% using X-ray data to 2.7 A resolution. The protein is folded into two contiguous domains. The larger domain shows the general topology of the alpha/beta hydrolase fold, with a central eight-stranded beta-sheet flanked by two helices and the 11 N-terminal residues on one side, and by four helices on the other side. The smaller domain is placed on top of the larger domain and essentially consists of six helices. The active site, located at the end of a deep pocket at the interface between both domains, includes a catalytic triad of Ser110, Asp266 and His294. Cys269, located at the bottom of the active site very close to the catalytic triad, presumably accounts for the inhibition by thiol-specific reagents. The overall topology of this iminopeptidase is very similar to that of yeast serine carboxypeptidase. The striking secondary structure similarity to human lymphocytic prolyl oligopeptidase and dipeptidyl peptidase IV makes this proline iminopeptidase structure a suitable model for the three-dimensional structure of other peptidases of this family.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Analysis of Proline Iminopeptidase from Xanthomonas Campestris Pv. Citri
      Medrano, F.J.,Alonso, J.,Garcia, J.L.,Bode, W.,Gomis-Ruth, F.X.
      (1997) FEBS Lett. 400: 91


    Organizational Affiliation

    Max-Plank-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18, D-82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROLINE IMINOPEPTIDASE
A, B
313Xanthomonas citriGene Names: pip (xap)
EC: 3.4.11.5
Find proteins for P52279 (Xanthomonas citri)
Go to UniProtKB:  P52279
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.192 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 147.200α = 90.00
b = 167.800β = 90.00
c = 85.600γ = 90.00
Software Package:
Software NamePurpose
ROTAVATA)data scaling
X-PLORmodel building
CCP4data scaling
MOSFLMdata reduction
X-PLORphasing
X-PLORrefinement
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance