Crystal structure of periplasmic binding protein XoxJ from Methylobacterium extorquens AM1

Experimental Data Snapshot

  • Resolution: 2.27 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

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Biochemical and Structural Characterization of XoxG and XoxJ and Their Roles in Lanthanide-Dependent Methanol Dehydrogenase Activity.

Featherston, E.R.Rose, H.R.McBride, M.J.Taylor, E.M.Boal, A.K.Cotruvo Jr., J.A.

(2019) Chembiochem 20: 2360-2372

  • DOI: https://doi.org/10.1002/cbic.201900184
  • Primary Citation of Related Structures:  
    6ONP, 6ONQ

  • PubMed Abstract: 

    Lanthanide (Ln)-dependent methanol dehydrogenases (MDHs) have recently been shown to be widespread in methylotrophic bacteria. Along with the core MDH protein, XoxF, these systems contain two other proteins, XoxG (a c-type cytochrome) and XoxJ (a periplasmic binding protein of unknown function), about which little is known. In this work, we have biochemically and structurally characterized these proteins from the methyltroph Methylobacterium extorquens AM1. In contrast to results obtained in an artificial assay system, assays of XoxFs metallated with La III , Ce III , and Nd III using their physiological electron acceptor, XoxG, display Ln-independent activities, but the K m for XoxG markedly increases from La to Nd. This result suggests that XoxG's redox properties are tuned specifically for lighter Lns in XoxF, an interpretation supported by the unusually low reduction potential of XoxG (+172 mV). The X-ray crystal structure of XoxG provides a structural basis for this reduction potential and insight into the XoxG-XoxF interaction. Finally, the X-ray crystal structure of XoxJ reveals a large hydrophobic cleft and suggests a role in the activation of XoxF. These studies enrich our understanding of the underlying chemical principles that enable the activity of XoxF with multiple lanthanides in vitro and in vivo.

  • Organizational Affiliation

    Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
periplasmic binding protein XoxJ284Methylorubrum extorquens AM1Mutation(s): 0 
Gene Names: xoxJMexAM1_META1p1742
Find proteins for C5B122 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1))
Explore C5B122 
Go to UniProtKB:  C5B122
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC5B122
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.27 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.9α = 90
b = 51.759β = 98.237
c = 51.241γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.2: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.3: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence