6ONP image
Deposition Date 2019-04-22
Release Date 2019-05-08
Last Version Date 2024-10-23
Entry Detail
PDB ID:
6ONP
Title:
Crystal structure of periplasmic binding protein XoxJ from Methylobacterium extorquens AM1
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.27 Å
R-Value Free:
0.27
R-Value Work:
0.23
R-Value Observed:
0.24
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:periplasmic binding protein XoxJ
Gene (Uniprot):xoxJ
Chain IDs:A
Chain Length:284
Number of Molecules:1
Biological Source:Methylobacterium extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)
Ligand Molecules
Primary Citation
Biochemical and Structural Characterization of XoxG and XoxJ and Their Roles in Lanthanide-Dependent Methanol Dehydrogenase Activity.
Chembiochem 20 2360 2372 (2019)
PMID: 31017712 DOI: 10.1002/cbic.201900184

Abstact

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 LaIII , CeIII , and NdIII using their physiological electron acceptor, XoxG, display Ln-independent activities, but the Km 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.

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