3V91

Structure of T82M glycogenin mutant truncated at residue 270 complexed with UDP-glucose

• PDB DOI: https://doi.org/10.2210/pdb3V91/pdb

• Classification: TRANSFERASE
• Organism(s): Oryctolagus cuniculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-12-23 Released: 2012-01-25 
• Deposition Author(s): Carrizo, M.E., Romero, J.M., Issoglio, F.M., Curtino, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.236 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Structural and biochemical insight into glycogenin inactivation by the glycogenosis-causing T82M mutation.

Carrizo, M.E., Romero, J.M., Issoglio, F.M., Curtino, J.A.

(2012) FEBS Lett 586: 254-257

• PubMed: 22226635 
• DOI: https://doi.org/10.1016/j.febslet.2011.12.028
• Primary Citation of Related Structures:  
  3V8Y, 3V8Z, 3V90, 3V91


• PubMed Abstract: 
  

  The X-ray structure of rabbit glycogenin containing the T82M (T83M according to previous authors amino acid numbering) mutation causing glycogenosis showed the loss of Thr82 hydrogen bond to Asp162, the residue involved in the activation step of the glucose transfer reaction mechanism. Autoglucosylation, maltoside transglucosylation and UDP-glucose hydrolyzing activities were abolished even though affinity and interactions with UDP-glucose and positioning of Tyr194 acceptor were conserved. Substitution of Thr82 for serine but not for valine restored the maximum extent of autoglucosylation as well as transglucosylation and UDP-glucose hydrolysis rate. Results provided evidence sustaining the essential role of the lost single hydrogen bond for UDP-glucose activation leading to glycogenin-bound glycogen primer synthesis.

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Organizational Affiliation: 

Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, UNC-CONICET), Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.39 kDa 
• Atom Count: 2,170 
• Modelled Residue Count: 256 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogenin-1	A	291	Oryctolagus cuniculus	Mutation(s): 1  Gene Names: GYG, GYG1 EC: 2.4.1.186
UniProt
Find proteins for P13280 (Oryctolagus cuniculus) Explore P13280  Go to UniProtKB:  P13280

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UPG	E [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.236 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.21	α = 90
b = 103.51	β = 90
c = 119.87	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Carrizo, M.E., Romero, J.M., Issoglio, F.M., Curtino, J.A.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2012-02-15
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations