6N1E | pdb_00006n1e

Crystal structure of X. citri phosphoglucomutase in complex with 1-methyl-glucose 6-phosphate

• PDB DOI: https://doi.org/10.2210/pdb6N1E/pdb

• Classification: ISOMERASE
• Organism(s): Xanthomonas citri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-11-08 Released: 2019-05-01 
• Deposition Author(s): Beamer, L.J., Stiers, K.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.202 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.164 (Depositor) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Synthesis, Derivatization, and Structural Analysis of Phosphorylated Mono-, Di-, and Trifluorinated d-Gluco-heptuloses by Glucokinase: Tunable Phosphoglucomutase Inhibition.

Zhu, J.S., Stiers, K.M., Winter, S.M., Garcia, A.D., Versini, A.F., Beamer, L.J., Jakeman, D.L.

(2019) ACS Omega 4: 7029-7037

• PubMed: 31179410 
• DOI: https://doi.org/10.1021/acsomega.9b00008
• Primary Citation Related Structures: 
  6N1E


• PubMed Abstract: 
  

  Glucokinase phosphorylated a series of C-1 fluorinated α-d-gluco-heptuloses. These phosphorylated products were discovered to be inhibitors of α-phosphomannomutase/phosphoglucomutase (αPMM/PGM) and β-phosphoglucomutase (βPGM). Inhibition potency with both mutases inversely correlated to the degree of fluorination. Structural analysis with αPMM demonstrated the inhibitor binding to the active site, with the phosphate in the phosphate binding site and the anomeric hydroxyl directed to the catalytic site.

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Organizational Affiliation: 
• College of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 4R2, Canada.
Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States.
Department of Chemistry, Hogeschool Leiden (UAS Leiden), Zernikedreef 11, CK Leiden 2333, The Netherlands.
École Nationale Supérieure de Chimie de Rennes, 11 Allée de Beaulieu, CS 50837, Rennes Cedex 7 35708, France.
École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris, 10 rue Vauquelin, Paris 75005, France.
Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 51.44 kDa 
• Atom Count: 4,045 
• Modeled Residue Count: 448 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphomannomutase/phosphoglucomutase	A	468	Xanthomonas citri	Mutation(s): 0  Gene Names: xavtCFBP7764_14885

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QIF (Subject of Investigation/LOI)	C [auth A]	1-deoxy-7-O-phosphono-alpha-D-gluco-hept-2-ulopyranose C7 H15 O9 P DFHDZDLZUMUBKN-ZFYZTMLRSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.202 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.164 (Depositor) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.705	α = 90
b = 54.745	β = 90
c = 172.432	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-01 
Deposition Author(s): Beamer, L.J., Stiers, K.M.

Revision History  

• Version 1.0: 2019-05-01
  Type: Initial release
  
• Version 1.1: 2019-11-13
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary