7K3U

X-ray crystallographic structure model of Lactococcus lactis prolidase mutant R293S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.203 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystallographic structure of recombinant Lactococcus lactis prolidase to support proposed structure-function relationships.

Kgosisejo, O.Chen, J.A.Grochulski, P.Tanaka, T.

(2017) Biochim Biophys Acta Proteins Proteom 1865: 473-480

  • DOI: https://doi.org/10.1016/j.bbapap.2017.02.004
  • Primary Citation of Related Structures:  
    6XMR, 7K3U, 7N02

  • PubMed Abstract: 

    Lactococcus lactis prolidase (Xaa-Pro dipeptidase; EC.3.4.13.9) is unique from other prolidases by showing allosteric behaviour, substrate inhibition, and metal-dependent substrate specificity. We have previously shown several critical residues for these characteristics using site-directed mutagenesis and amino acid sequence-based models. In this present study, the three-dimensional structure of recombinant L. lactis prolidase was determined by X-ray crystallography at 2.25Å resolution in order to provide evidences of the proposed mechanism. Three molecules are located in the crystal asymmetric unit where molecule A forms a dimer with molecule B, while molecule C forms a dimer with molecule C' in the adjacent asymmetric unit. Of all the three molecules, molecule C is less defined and incomplete. While this fact compromises the overall quality of the refined model, the functional interpretation of the structure is not compromised since the biologically-functional homodimeric configuration of L. lactis prolidase is represented by well-defined molecules A and B. The refined model confirmed that there is a twelve-residue (residues 32-43) loop structure from one subunit over the active site of the other subunit, proving the existence of the putative loop structure in our previous study. This loop is three amino acids longer than the loops of prolidases of Pyrococcus furious (1pv9) and Pyrococcus horikoshii OT3 (1wy2). The crystal structure shows the loop structure can form two states ("open" and "closed" states) through interaction between the loop and active site proximity. It supports the proposed formation of allosteric site by the loop and Arg 293.


  • Organizational Affiliation

    Department of Food and Bioproduct Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminopeptidase P family protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
362Lactococcus lactisMutation(s): 1 
Gene Names: pepQAMHIJAGA_00052BW151_08640FNJ58_07375
EC: 3.4.13.9
UniProt
Find proteins for A8WBX8 (Lactococcus lactis)
Explore A8WBX8 
Go to UniProtKB:  A8WBX8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8WBX8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth G],
M [auth A],
P [auth B],
S [auth C],
V [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth G]
DA [auth H]
EA [auth H]
FA [auth I]
AA [auth G],
BA [auth G],
DA [auth H],
EA [auth H],
FA [auth I],
GA [auth I],
HA [auth J],
IA [auth J],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
Q [auth C],
R [auth C],
T [auth D],
U [auth D],
W [auth E],
X [auth E],
Y [auth F],
Z [auth F]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.3α = 90
b = 80β = 102.03
c = 187.15γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-06209-2016

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description