1LNS

Crystal Structure Analysis of the X-Prolyl Dipeptidyl Aminopeptidase From Lactococcus lactis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Structural Basis for Catalysis and Specificity of the X-prolyl dipepdidyl aminopeptidase from Lactococcus lactis

Rigolet, P.Mechin, I.Delage, M.M.Chich, J.F.

(2002) Structure 10: 1383-1394

  • DOI: 10.1016/s0969-2126(02)00851-1
  • Primary Citation of Related Structures:  
    1LNS

  • PubMed Abstract: 
  • The X-prolyl dipeptidyl aminopeptidase (X-PDAP) from Lactococcus lactis is a dimeric enzyme catalyzing the removal of Xaa-Pro dipeptides from the N terminus of peptides. The structure of the enzyme was solved at 2.2 A resolution and provides a model for the peptidase family S15 ...

    The X-prolyl dipeptidyl aminopeptidase (X-PDAP) from Lactococcus lactis is a dimeric enzyme catalyzing the removal of Xaa-Pro dipeptides from the N terminus of peptides. The structure of the enzyme was solved at 2.2 A resolution and provides a model for the peptidase family S15. Each monomer is composed of four domains. The larger one presents an alpha/beta hydrolase fold and comprises the active site serine. The specificity pocket is mainly built by residues from a small helical domain which is, together with the N-terminal domain, essential for dimerization. A C-terminal moiety probably plays a role in the tropism of X-PDAP toward the cellular membrane. These results give new insights for further exploration of the role of the enzymes of the SC clan.


    Organizational Affiliation

    L.U.R.E. Centre Universitaire Paris-Sud, Bât. 209D-BP 34, F-91898 Orsay Cedex, France. rigolet@lure.u-psud.fr



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
X-PROLYL DIPEPTIDYL AMINOPEPTIDASEA763Lactococcus lactisMutation(s): 0 
Gene Names: pepX (ORF2)
EC: 3.4.14.11
UniProt
Find proteins for P22346 (Lactococcus lactis subsp. cremoris)
Explore P22346 
Go to UniProtKB:  P22346
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22346
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.5α = 90
b = 102.5β = 90
c = 101.5γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
ROTAVATAdata reduction
MLPHAREphasing
CNSrefinement
CCP4data scaling
ROTAVATAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-06
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description