6A2F | pdb_00006a2f

Crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb6A2F/pdb

• Classification: ISOMERASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-11 Released: 2018-08-08 
• Deposition Author(s): Dong, H., Li, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Enzymatic characterization and crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa PAO1.

Dong, H., Han, Q., Guo, Y., Ju, J., Wang, S., Yuan, C., Long, W., He, X., Xu, S., Li, S.

(2018) Biochem Biophys Res Commun 503: 2319-2325

• PubMed: 29964014 
• DOI: https://doi.org/10.1016/j.bbrc.2018.06.155
• Primary Citation Related Structures: 
  6A2F


• PubMed Abstract: 
  

  Alanine racemase is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that reversibly catalyzes the conversion of l-alanine to d-alanine. d-alanine is an essential constituent in many prokaryotic cell structures. Inhibition of alanine racemase is lethal to prokaryotes, creating an attractive target for designing antibacterial drugs. Here we report the crystal structure of biosynthetic alanine racemase (Alr) from a pathogenic bacteria Pseudomonas aeruginosa PAO1. Structural studies showed that P. aeruginosa Alr (PaAlr) adopts a conserved homodimer structure. A guest substrate d-lysine was observed in the active site and refined to dual-conformation. Two buffer ions, malonate and acetate, were bound in the proximity to d-lysine. Biochemical characterization revealed the optimal reaction conditions for PaAlr.

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Organizational Affiliation: 
• Key Laboratory of Tianjin Radiation and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300192, China.
College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China. Electronic address: [e-mail].
Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China. Electronic address: [e-mail].

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 Evidence: homology

Macromolecule Content 

• Total Structure Weight: 77.78 kDa 
• Atom Count: 5,826 
• Modeled Residue Count: 716 
• Deposited Residue Count: 716 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine racemase, biosynthetic	A, B	358	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: alr, PA4930 EC: 5.1.1.1
UniProt
Find proteins for Q9HUN4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HUN4  Go to UniProtKB:  Q9HUN4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DLY	D [auth A], F [auth B]	D-LYSINE C6 H14 N2 O2 KDXKERNSBIXSRK-RXMQYKEDSA-N
MLI	C [auth A], H [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
ACT	E [auth A], G [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 2.50 Å
• R-Value Free:  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.24	α = 90
b = 78.3	β = 90
c = 154.07	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Dong, H., Li, S.

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2020-01-29
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description