4Y9X

Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate-glucose (UDP-Glc) and phosphoglyceric acid (PGA) - GpgS Mn2+ UDP-Glc PGA-3

Summary for 4Y9X

• Entry DOI: 10.2210/pdb4y9x/pdb
• Related: 4Y6N 4Y6U 4Y7F 4Y7G
• Descriptor: Glucosyl-3-phosphoglycerate synthase, MANGANESE (II) ION, CHLORIDE ION, ... (7 entities in total)
• Functional Keywords: transferase
• Biological source: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
• Total number of polymer chains: 1
• Total formula weight: 35712.51

Authors

Albesa-Jove, D.,Rodrigo-Unzueta, A.,Cifuente, J.O.,Urresti, S.,Comino, N.,Sancho-Vaello, E.,Guerin, M.E. (deposition date: 2015-02-17, release date: 2015-07-15, Last modification date: 2024-01-10)

Primary citation

Albesa-Jove, D.,Mendoza, F.,Rodrigo-Unzueta, A.,Gomollon-Bel, F.,Cifuente, J.O.,Urresti, S.,Comino, N.,Gomez, H.,Romero-Garcia, J.,Lluch, J.M.,Sancho-Vaello, E.,Biarnes, X.,Planas, A.,Merino, P.,Masgrau, L.,Guerin, M.E.
A Native Ternary Complex Trapped in a Crystal Reveals the Catalytic Mechanism of a Retaining Glycosyltransferase.
Angew.Chem.Int.Ed.Engl., 54:9898-9902, 2015

PubMed Abstract: Glycosyltransferases (GTs) comprise a prominent family of enzymes that play critical roles in a variety of cellular processes, including cell signaling, cell development, and host-pathogen interactions. Glycosyl transfer can proceed with either inversion or retention of the anomeric configuration with respect to the reaction substrates and products. The elucidation of the catalytic mechanism of retaining GTs remains a major challenge. A native ternary complex of a GT in a productive mode for catalysis is reported, that of the retaining glucosyl-3-phosphoglycerate synthase GpgS from M. tuberculosis in the presence of the sugar donor UDP-Glc, the acceptor substrate phosphoglycerate, and the divalent cation cofactor. Through a combination of structural, chemical, enzymatic, molecular dynamics, and quantum-mechanics/molecular-mechanics (QM/MM) calculations, the catalytic mechanism was unraveled, thereby providing a strong experimental support for a front-side substrate-assisted SN i-type reaction.

PubMed: 26136334
DOI: 10.1002/anie.201504617

Experimental method

X-RAY DIFFRACTION (2.637 Å)