1LNS | pdb_00001lns

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

• PDB DOI: https://doi.org/10.2210/pdb1LNS/pdb

• Classification: HYDROLASE
• Organism(s): Lactococcus lactis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-05-03 Released: 2002-11-06 
• Deposition Author(s): Rigolet, P., Mechin, I., Delage, M.M., Chich, J.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.223 (Depositor) 
• R-Value Work: 
  0.184 (Depositor), 0.197 (DCC) 

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

• PubMed: 12377124 
• DOI: https://doi.org/10.1016/s0969-2126(02)00851-1
• Primary Citation 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. 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.

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Organizational Affiliation: 
• L.U.R.E. Centre Universitaire Paris-Sud, Bât. 209D-BP 34, F-91898 Orsay Cedex, France. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 87.8 kDa 
• Atom Count: 6,505 
• Modeled Residue Count: 763 
• Deposited Residue Count: 763 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
X-PROLYL DIPEPTIDYL AMINOPEPTIDASE	A	763	Lactococcus lactis	Mutation(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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.223 (Depositor) 
• R-Value Work:  0.184 (Depositor), 0.197 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.5	α = 90
b = 102.5	β = 90
c = 101.5	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
ROTAVATA	data reduction
MLPHARE	phasing
CNS	refinement
CCP4	data scaling
ROTAVATA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-06 
Deposition Author(s): Rigolet, P., Mechin, I., Delage, M.M., Chich, J.F.

Revision History  

• 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
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references