Crystal Structure of Phosphoglucomutase from Xanthomonas citri citri complexed with Glucose-1,6-biphosphate

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

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Structural and functional characterization of the phosphoglucomutase from Xanthomonas citri subsp. citri.

Goto, L.S.Vessoni Alexandrino, A.Malvessi Pereira, C.Silva Martins, C.D'Muniz Pereira, H.Brandao-Neto, J.Marques Novo-Mansur, M.T.

(2016) Biochim Biophys Acta 1864: 1658-1666

  • DOI: https://doi.org/10.1016/j.bbapap.2016.08.014
  • Primary Citation of Related Structures:  
    5BMN, 5BMP, 5KL0

  • PubMed Abstract: 

    Citrus canker, caused by bacteria Xanthomonas citri subsp. citri, can affect all economically important varieties of citrus. Studying Xanthomonas genes related to the invasive capacity may improve the knowledge on how this works and ultimately use the information to avoid the disease. Some annotated genes from Xanthomonas citri subsp. citri published genome are addressed to an interesting class of genes named "pathogenicity, virulence and adaptation". One of them is xanA, which encodes a predicted phosphoglucomutase. Phosphoglucomutases are ubiquitous enzymes among the living kingdoms that play roles in carbohydrate metabolism, catalyzing the reversible conversion of 1- to 6-phosphoglucose. In Xanthomonas, phosphoglucomutase activity is required to synthesize precursors of the pathogenesis-related polysaccharide xanthan. In this work, a characterization of this gene product is presented by structural and functional studies. Molecular cloning was used for heterologous expression and deletion of xanA. A Michaelis-Menten kinetics model was obtained using the recombinant protein. The protein structure was also determined by X-ray diffraction on the recombinant enzyme substrate-free, bound to glucose-1,6-biphosphate and to glucose-1-phosphate. Deletion of xanA was done with a suicide plasmid construct and the obtained mutant was tested for pathogenic capacity. This study is the first describing the properties of the Xanthomonas citri subsp. citri phosphoglucomutase.

  • Organizational Affiliation

    Laboratório de Bioquímica e Biologia Molecular Aplicada - LBBMA, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglucomutase467Xanthomonas citri pv. citri str. 306Mutation(s): 0 
Gene Names: xanAXAC3579
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on G16

Download Ideal Coordinates CCD File 
B [auth A]1,6-di-O-phosphono-alpha-D-glucopyranose
C6 H13 O12 P2
Query on MG

Download Ideal Coordinates CCD File 
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on SEP
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.98α = 90
b = 54.788β = 90
c = 173.495γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2007/50910-2

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references
  • Version 1.2: 2016-09-28
    Changes: Database references
  • Version 1.3: 2019-04-17
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary