4QHR | pdb_00004qhr

The structure of alanine racemase from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb4QHR/pdb
• Entry: 4QHR supersedes: 4TLO

• Classification: ISOMERASE
• Organism(s): Acinetobacter baumannii ACICU
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-29 Released: 2015-05-06 
• Deposition Author(s): Davis, E., Scaletti-Hutchinson, E., Nakatani, Y., Krause, K.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.234 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

The structure of alanine racemase from Acinetobacter baumannii

Davis, E., Scaletti-Hutchinson, E., Opel-Reading, H., Nakatani, Y., Krause, K.L.

(2014) Acta Crystallogr F Struct Biol Commun 70: 1199-1205

• PubMed: 25195891 
• DOI: https://doi.org/10.1107/S2053230X14017725
• Primary Citation Related Structures: 
  4QHR


• PubMed Abstract: 
  

  Acinetobacter baumannii is an opportunistic Gram-negative bacterium which is a common cause of hospital-acquired infections. Numerous antibiotic-resistant strains exist, emphasizing the need for the development of new antimicrobials. Alanine racemase (Alr) is a pyridoxal 5'-phosphate dependent enzyme that is responsible for racemization between enantiomers of alanine. As D-alanine is an essential component of the bacterial cell wall, its inhibition is lethal to prokaryotes, making it an excellent antibiotic drug target. The crystal structure of A. baumannii alanine racemase (AlrAba) from the highly antibiotic-resistant NCTC13302 strain has been solved to 1.9 Å resolution. Comparison of AlrAba with alanine racemases from closely related bacteria demonstrates a conserved overall fold. The substrate entryway and active site of the enzymes were shown to be highly conserved. The structure of AlrAba will provide the template required for future structure-based drug-design studies.

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Organizational Affiliation: 
• Department of Biochemistry, University of Otago, Dunedin, New Zealand.

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)

Macromolecule Content 

• Total Structure Weight: 79.73 kDa 
• Atom Count: 5,902 
• Modeled Residue Count: 693 
• Deposited Residue Count: 712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine racemase	A, B	356	Acinetobacter baumannii ACICU	Mutation(s): 0  Gene Names: ACICU_02378 EC: 5.1.1.1
UniProt
Find proteins for A0A0M3KKV7 (Acinetobacter baumannii (strain ACICU)) Explore A0A0M3KKV7  Go to UniProtKB:  A0A0M3KKV7

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.234 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.99	α = 90
b = 82.98	β = 97.09
c = 93.32	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-06 
Deposition Author(s): Davis, E., Scaletti-Hutchinson, E., Nakatani, Y., Krause, K.L.
• This entry supersedes: 4TLO

Revision History  

• Version 1.0: 2015-05-06
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary