Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate (UDP) and glucosyl-3-phosphoglycerate (GPG) - GpgS*GPG*UDP*Mn2+_2

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

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This is version 1.3 of the entry. See complete history


Structural Snapshots and Loop Dynamics along the Catalytic Cycle of Glycosyltransferase GpgS.

Albesa-Jove, D.Romero-Garcia, J.Sancho-Vaello, E.Contreras, F.X.Rodrigo-Unzueta, A.Comino, N.Carreras-Gonzalez, A.Arrasate, P.Urresti, S.Biarnes, X.Planas, A.Guerin, M.E.

(2017) Structure 25: 1034-1044.e3

  • DOI: https://doi.org/10.1016/j.str.2017.05.009
  • Primary Citation of Related Structures:  
    5JQX, 5JSX, 5JT0, 5JUC, 5JUD

  • PubMed Abstract: 

    Glycosyltransferases (GTs) play a central role in nature. They catalyze the transfer of a sugar moiety to a broad range of acceptor substrates. GTs are highly selective enzymes, allowing the recognition of subtle structural differences in the sequences and stereochemistry of their sugar and acceptor substrates. We report here a series of structural snapshots of the reaction center of the retaining glucosyl-3-phosphoglycerate synthase (GpgS). During this sequence of events, we visualize how the enzyme guides the substrates into the reaction center where the glycosyl transfer reaction takes place, and unveil the mechanism of product release, involving multiple conformational changes not only in the substrates/products but also in the enzyme. The structural data are further complemented by metadynamics free-energy calculations, revealing how the equilibrium of loop conformations is modulated along these itineraries. The information reported here represent an important contribution for the understanding of GT enzymes at the molecular level.

  • Organizational Affiliation

    Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Ed. 801A, 48160 Derio, Spain; Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas - Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC-UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain; Departamento de Bioquímica, Universidad del País Vasco, 48080 Bilbao, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, 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
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.434α = 90
b = 99.434β = 90
c = 126.785γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2018-12-05
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary