5HRA

Crystal structure of an aspartate/glutamate racemase in complex with D-aspartate

• PDB DOI: https://doi.org/10.2210/pdb5HRA/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli O157:H7 str. SS52
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-23 Released: 2016-04-20 
• Deposition Author(s): Liu, X., Gao, F., Ma, Y., Liu, S., Cui, Y., Yuan, Z., Kang, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.250 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 

Literature

Crystal structure and molecular mechanism of an aspartate/glutamate racemase from Escherichia coli O157

Liu, X., Gao, F., Ma, Y., Liu, S., Cui, Y., Yuan, Z., Kang, X.

(2016) FEBS Lett 590: 1262-1269

• PubMed: 27001440 
• DOI: https://doi.org/10.1002/1873-3468.12148
• Primary Citation of Related Structures:  
  5HQT, 5HRA, 5HRC


• PubMed Abstract: 
  

  EcL-DER, the aspartate/glutamate racemase from the pathogen Escherichia coli O157, exhibits racemase activity for l-aspartate and l-glutamate. This study reports the crystal structures of apo-EcL-DER, the EcL-DER-l-aspartate and the EcL-DER-d-aspartate complexes. The EcL-DER structure contains two domains, forming pseudo-mirror symmetry in the active site. A unique catalytic pair consisting of Thr(83) and Cys(197) exists in the active site. The characteristic conformations of l-Asp and d-Asp in the active site provide a straight structural evidence for the racemization mechanism of EcL-DER. In addition, the diversity of catalytic pairs implies that PLP-independent amino acid racemases adopt various catalytic mechanisms and are classified into different subgroups.

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Organizational Affiliation: 

College of Life Sciences, Hebei University, Baoding, China.

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: 52.25 kDa 
• Atom Count: 4,052 
• Modelled Residue Count: 465 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
aspartate/glutamate racemase	A, B	235	Escherichia coli O157:H7 str. SS52	Mutation(s): 0  Gene Names: ygeA, SS52_3985

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DAS	C [auth A], D [auth B]	D-ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-UWTATZPHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.250 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.938	α = 90
b = 48.248	β = 92.92
c = 116.289	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Liu, X., Gao, F., Ma, Y., Liu, S., Cui, Y., Yuan, Z., Kang, X.

Revision History  

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 1.1: 2016-05-18
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description