4LUS | pdb_00004lus

alanine racemase [Clostridium difficile 630]

• PDB DOI: https://doi.org/10.2210/pdb4LUS/pdb

• Classification: ISOMERASE
• Organism(s): Clostridioides difficile 630
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2013-07-25 Released: 2014-06-04 
• Deposition Author(s): Asojo, O.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.266 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

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

• PubMed: 25004969 
• DOI: https://doi.org/10.1107/S1399004714009419
• Primary Citation 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.

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Organizational Affiliation: 
• National School of Tropical Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.
L2 Diagnostics LLC, 300 George Street, New Haven, CT 06511, USA.
Pathology and Microbiology Department, University of Nebraska Medical Center, Omaha, NE 68105, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 174.84 kDa 
• Atom Count: 12,484 
• Modeled Residue Count: 1,498 
• Deposited Residue Count: 1,540 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine racemase	A, C, D	385	Clostridioides difficile 630	Mutation(s): 0  Gene Names: alr2, CD630_34630 EC: 5.1.1.1
UniProt
Find proteins for Q180W0 (Clostridioides difficile (strain 630)) Explore Q180W0  Go to UniProtKB:  Q180W0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine racemase	B	385	Clostridioides difficile 630	Mutation(s): 0  Gene Names: alr2, CD630_34630 EC: 5.1.1.1
UniProt
Find proteins for Q180W0 (Clostridioides difficile (strain 630)) Explore Q180W0  Go to UniProtKB:  Q180W0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TCE	F [auth B]	3,3',3''-phosphanetriyltripropanoic acid C9 H15 O6 P PZBFGYYEXUXCOF-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, C, D	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS
LLP	A, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.266 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.15	α = 90
b = 93.3	β = 91
c = 107.09	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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