5JUC

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1016/j.str.2017.05.009
  • Primary Citation of Related Structures:  

  • 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 sequenc ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucosyl-3-phosphoglycerate synthase
A
328Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: gpgS
EC: 2.4.1.266
Find proteins for P9WMW9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WMW9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
XDX
Query on XDX

Download SDF File 
Download CCD File 
A
(2R)-2-(alpha-D-glucopyranosyloxy)-3-(phosphonooxy)propanoic acid
C9 H17 O12 P
RJDBNSZFZDWPFL-CECBSOHTSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 99.434α = 90.00
b = 99.434β = 90.00
c = 126.785γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2018-12-05
    Type: Data collection, Database references