ISDA

Deposition Date 2016-01-23

Release Date 2016-04-20

Last Version Date 2023-11-08

Entry Detail

PDB ID:

5HRA

Keywords:

ISOMERASE

Title:

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

Biological Source:

Source Organism:

Escherichia coli O157:H7 str. SS52 (Taxon ID: 1330457)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.60 Å

R-Value Free:

0.24

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 1 21 1

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:aspartate/glutamate racemase
Chain IDs:A, B
Chain Length:235
Number of Molecules:2
Biological Source:Escherichia coli O157:H7 str. SS52

UniProt ID:A0A0H3JGH6 Pfam ID:PF01177

Ligand Molecules

DAS

Primary Citation

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.Show

Febs Lett. 590 1262 1269 (2016)

PMID: 27001440 DOI: 10.1002/1873-3468.12148

Abstact

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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Primary Citation of related structures