Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate-glucose (UDP-Glc) and glycerol 3-phosphate (G3P) - GpgS Mn2+ UDP-Glc G3P

Experimental Data Snapshot

  • Resolution: 2.59 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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A Native Ternary Complex Trapped in a Crystal Reveals the Catalytic Mechanism of a Retaining Glycosyltransferase.

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.

(2015) Angew Chem Int Ed Engl 54: 9898-9902

  • DOI: https://doi.org/10.1002/anie.201504617
  • Primary Citation of Related Structures:  
    4Y6N, 4Y6U, 4Y7F, 4Y7G, 4Y9X

  • 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.

  • Organizational Affiliation

    Unidad de Biofísica, Consejo Superior de Investigaciones Científicas - Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC-UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia (Spain).

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucosyl-3-phosphoglycerate synthase328Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: gpgSRv1208
Find proteins for P9WMW9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WMW9 
Go to UniProtKB:  P9WMW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WMW9
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.59 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.18α = 90
b = 98.18β = 90
c = 127.34γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-08-19
    Changes: Database references
  • Version 1.2: 2016-01-27
    Changes: Structure summary
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description