5HRC

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
aspartate/glutamate racemase
A, B
235Escherichia coli O157:H7 str. SS52Mutation(s): 0 
Gene Names: ygeA, SS52_3985
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.779α = 90
b = 48.234β = 95.12
c = 114.784γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Funds of ChinaChina31300056
Foundation of Hebei Educational committeeChinaYQ2014007
Natural Science Foundation of HeBei ProvinceChinaC2014201039

Revision History  (Full details and data files)

  • 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