Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.61 kDa 
• Atom Count: 2227 
• Modelled Residue Count: 282 
• Deposited Residue Count: 328 
• Unique protein chains: 1

4Y6N

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-1

• DOI: 10.2210/pdb4Y6N/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-02-13 Released: 2015-07-15 
• Deposition Author(s): Albesa-Jove, D., Rodrigo-Unzueta, A., Cifuente, J.O., Urresti, S., Comino, N., Sancho-Vaello, E., Guerin, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.200 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Literature

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

• PubMed: 26136334 
• DOI: 10.1002/anie.201504617
• Primary Citation of Related Structures:  
  4Y6U, 4Y9X, 4Y6N, 4Y7F, 4Y7G


• 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.

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Organizational Affiliation: 

IKERBASQUE, 48013 Bilbao (Spain). [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosyl-3-phosphoglycerate synthase	A	328	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: gpgS, Rv1208 EC: 2.4.1.266
Find proteins for P9WMW9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WMW9  Go to UniProtKB:  P9WMW9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UPG	D [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N
3PG	C [auth A]	3-PHOSPHOGLYCERIC ACID C3 H7 O7 P OSJPPGNTCRNQQC-UWTATZPHSA-N
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.200 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.73	α = 90
b = 98.73	β = 90
c = 127.57	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-02-13 
• Released Date: 2015-07-15 
Deposition Author(s): Albesa-Jove, D., Rodrigo-Unzueta, A., Cifuente, J.O., Urresti, S., Comino, N., Sancho-Vaello, E., Guerin, M.E.

Revision History  

• 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