6MNU | pdb_00006mnu

Crystal structure of Yersinia pestis UDP-glucose pyrophosphorylase

• PDB DOI: https://doi.org/10.2210/pdb6MNU/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-03 Released: 2019-09-11 
• Deposition Author(s): Gibbs, M.E., Lountos, G.T., Gumpena, R., Waugh, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.241 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of UDP-glucose pyrophosphorylase from Yersinia pestis, a potential therapeutic target against plague.

Gibbs, M.E., Lountos, G.T., Gumpena, R., Waugh, D.S.

(2019) Acta Crystallogr F Struct Biol Commun 75: 608-615

• PubMed: 31475928 
• DOI: https://doi.org/10.1107/S2053230X19011154
• Primary Citation Related Structures: 
  6MNU


• PubMed Abstract: 
  

  Yersinia pestis, the causative agent of bubonic plague, is one of the most lethal pathogens in recorded human history. Today, the concern is the possible misuse of Y. pestis as an agent in bioweapons and bioterrorism. Current therapies for the treatment of plague include the use of a small number of antibiotics, but clinical cases of antibiotic resistance have been reported in some areas of the world. Therefore, the discovery of new drugs is required to combat potential Y. pestis infection. Here, the crystal structure of the Y. pestis UDP-glucose pyrophosphorylase (UGP), a metabolic enzyme implicated in the survival of Y. pestis in mouse macrophages, is described at 2.17 Å resolution. The structure provides a foundation that may enable the rational design of inhibitors and open new avenues for the development of antiplague therapeutics.

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Organizational Affiliation: 
• Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 129.36 kDa 
• Atom Count: 9,311 
• Modeled Residue Count: 1,156 
• Deposited Residue Count: 1,184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UTP--glucose-1-phosphate uridylyltransferase	A, B, C, D	296	Yersinia pestis	Mutation(s): 0  Gene Names: galU, galU1, y2631, YP_1428, DBB30_10560, EGT45_14485, NCTC144_03080 EC: 2.7.7.9
UniProt
Find proteins for A0A3N4B738 (Yersinia pestis) Explore A0A3N4B738  Go to UniProtKB:  A0A3N4B738

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth C], F [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.241 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.19	α = 90
b = 99.415	β = 90
c = 128.656	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Gibbs, M.E., Lountos, G.T., Gumpena, R., Waugh, D.S.

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description