6DAM
Crystal structure of lanthanide-dependent methanol dehydrogenase XoxF from Methylomicrobium buryatense 5G
Summary for 6DAM
| Entry DOI | 10.2210/pdb6dam/pdb |
| Descriptor | Lanthanide-dependent methanol dehydrogenase XoxF, LANTHANUM (III) ION, PYRROLOQUINOLINE QUINONE, ... (5 entities in total) |
| Functional Keywords | dehydrogenase, pqq, methanol, xoxf, lanthanide, lanthanum, methanotroph, oxidoreductase |
| Biological source | Methylomicrobium buryatense 5G |
| Total number of polymer chains | 1 |
| Total formula weight | 67770.81 |
| Authors | Deng, Y.,Ro, S.Y.,Rosenzweig, A.C. (deposition date: 2018-05-01, release date: 2018-09-05, Last modification date: 2023-10-04) |
| Primary citation | Deng, Y.W.,Ro, S.Y.,Rosenzweig, A.C. Structure and function of the lanthanide-dependent methanol dehydrogenase XoxF from the methanotroph Methylomicrobium buryatense 5GB1C. J. Biol. Inorg. Chem., 23:1037-1047, 2018 Cited by PubMed Abstract: In methylotrophic bacteria, which use one-carbon (C1) compounds as a carbon source, methanol is oxidized by pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH) enzymes. Methylotrophic genomes generally encode two distinct MDHs, MxaF and XoxF. MxaF is a well-studied, calcium-dependent heterotetrameric enzyme whereas XoxF is a lanthanide-dependent homodimer. Recent studies suggest that XoxFs are likely the functional MDHs in many environments. In methanotrophs, methylotrophs that utilize methane, interactions between particulate methane monooxygenase (pMMO) and MxaF have been detected. To investigate the possibility of interactions between pMMO and XoxF, XoxF was isolated from the methanotroph Methylomicrobium buryatense 5GB1C (5G-XoxF). Purified 5G-XoxF exhibits a specific activity of 0.16 μmol DCPIP reduced min mg. The 1.85 Å resolution crystal structure reveals a La(III) ion in the active site, in contrast to the calcium ion in MxaF. The overall fold is similar to other MDH structures, but 5G-XoxF is a monomer in solution. An interaction between 5G-XoxF and its cognate pMMO was detected by biolayer interferometry, with a K value of 50 ± 17 μM. These results suggest an alternative model of MDH-pMMO association, in which a XoxF monomer may bind to pMMO, and underscore the potential importance of lanthanide-dependent MDHs in biological methane oxidation. PubMed: 30132076DOI: 10.1007/s00775-018-1604-2 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.85 Å) |
Structure validation
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