5X5H

Crystal structure of metB from Corynebacterium glutamicum

Summary for 5X5H

• Entry DOI: 10.2210/pdb5x5h/pdb
• Descriptor: Cystathionine beta-lyases/cystathionine gamma-synthases, PYRIDOXAL-5'-PHOSPHATE, GLYCEROL, ... (5 entities in total)
• Functional Keywords: plp-binding domain, transferase
• Biological source: Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
• Total number of polymer chains: 1
• Total formula weight: 43099.87

Authors

Sagong, H.-Y.,Kim, K.-J. (deposition date: 2017-02-16, release date: 2017-03-01, Last modification date: 2023-11-22)

Primary citation

Sagong, H.-Y.,Kim, K.-J.
Structural Insights into Substrate Specificity of Cystathionine gamma-Synthase from Corynebacterium glutamicum
J. Agric. Food Chem., 65:6002-6008, 2017

PubMed Abstract: Cystathionine γ-synthase (MetB) condenses O-acetyl-l-homoserine (OAHS) or O-succinyl-l-homoserine (OSHS) with cysteine to produce cystathionine. To investigate the molecular mechanisms and substrate specificity of MetB from Corynebacterium glutamicum (CgMetB), we determined its crystal structure at 1.5 Å resolution. The pyridoxal phosphate cofactor is covalently bound to Lys204 via a Schiff base linkage in the deep cavity. Superposition with the structure of MetB from Nicotiana tabacum in complex with its inhibitor dl-(E)-2-amino-5-phosphono-3-pentenoic acid revealed that Thr347 from the β10-β11 connecting loop, located at the entrance of the active site, is speculated to be a main contributor for stabilization of the acetyl group of OAHS. Moreover, on the basis of structural comparison of CgMetB with EcMetB utilizing OSHS as a main substrate, we propose that the conformation of the β10-β11 connecting loops determines the size and shape of the acetyl- or succinyl-group binding site and ultimately determines the substrate specificity of MetBs toward OAHS or OSHS.

PubMed: 28675039
DOI: 10.1021/acs.jafc.7b02391

Experimental method

X-RAY DIFFRACTION (1.51 Å)