4LUS

alanine racemase [Clostridium difficile 630]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural and biochemical analyses of alanine racemase from the multidrug-resistant Clostridium difficile strain 630.

Asojo, O.A.Nelson, S.K.Mootien, S.Lee, Y.Rezende, W.C.Hyman, D.A.Matsumoto, M.M.Reiling, S.Kelleher, A.Ledizet, M.Koski, R.A.Anthony, K.G.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1922-1933

  • DOI: https://doi.org/10.1107/S1399004714009419
  • Primary Citation of Related Structures:  
    4LUS, 4LUT, 4LUY

  • PubMed Abstract: 

    Clostridium difficile, a Gram-positive, spore-forming anaerobic bacterium, is the leading cause of infectious diarrhea among hospitalized patients. C. difficile is frequently associated with antibiotic treatment, and causes diseases ranging from antibiotic-associated diarrhea to life-threatening pseudomembranous colitis. The severity of C. difficile infections is exacerbated by the emergence of hypervirulent and multidrug-resistant strains, which are difficult to treat and are often associated with increased mortality rates. Alanine racemase (Alr) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes the reversible racemization of L- and D-alanine. Since D-alanine is an essential component of the bacterial cell-wall peptidoglycan, and there are no known Alr homologs in humans, this enzyme is being tested as an antibiotic target. Cycloserine is an antibiotic that inhibits Alr. In this study, the catalytic properties and crystal structures of recombinant Alr from the virulent and multidrug-resistant C. difficile strain 630 are presented. Three crystal structures of C. difficile Alr (CdAlr), corresponding to the complex with PLP, the complex with cycloserine and a K271T mutant form of the enzyme with bound PLP, are presented. The structures are prototypical Alr homodimers with two active sites in which the cofactor PLP and cycloserine are localized. Kinetic analyses reveal that the K271T mutant CdAlr has the highest catalytic constants reported to date for any Alr. Additional studies are needed to identify the basis for the high catalytic activity. The structural and activity data presented are first steps towards using CdAlr for the development of structure-based therapeutics for C. difficile infections.


  • Organizational Affiliation

    National School of Tropical Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alanine racemase
A, C, D
385Clostridioides difficile 630Mutation(s): 0 
Gene Names: alr2CD630_34630
EC: 5.1.1.1
UniProt
Find proteins for Q180W0 (Clostridioides difficile (strain 630))
Explore Q180W0 
Go to UniProtKB:  Q180W0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ180W0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Alanine racemase385Clostridioides difficile 630Mutation(s): 0 
Gene Names: alr2CD630_34630
EC: 5.1.1.1
UniProt
Find proteins for Q180W0 (Clostridioides difficile (strain 630))
Explore Q180W0 
Go to UniProtKB:  Q180W0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ180W0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TCE
Query on TCE

Download Ideal Coordinates CCD File 
F [auth B]3,3',3''-phosphanetriyltripropanoic acid
C9 H15 O6 P
PZBFGYYEXUXCOF-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, C, D
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
LLP
Query on LLP
A, C, D
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.15α = 90
b = 93.3β = 91
c = 107.09γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2014-06-04 
  • Deposition Author(s): Asojo, O.A.

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references
  • Version 1.2: 2015-01-28
    Changes: Structure summary
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-12-06
    Changes: Data collection