5YHH

Crystal structure of YiiM from Geobacillus stearothermophilus

Summary for 5YHH

• Entry DOI: 10.2210/pdb5yhh/pdb
• Descriptor: Uncharacterized conserved protein YiiM (2 entities in total)
• Functional Keywords: enzyme, mosc, oxidoreductase
• Biological source: Geobacillus stearothermophilus (Bacillus stearothermophilus)
• Total number of polymer chains: 1
• Total formula weight: 24194.43

Authors

Namgung, B.,Kim, J.H.,Song, W.S.,Yoon, S.I. (deposition date: 2017-09-28, release date: 2018-03-07, Last modification date: 2023-11-22)

Primary citation

Namgung, B.,Kim, J.H.,Song, W.S.,Yoon, S.I.
Crystal structure of the hydroxylaminopurine resistance protein, YiiM, and its putative molybdenum cofactor-binding catalytic site.
Sci Rep, 8:3304-3304, 2018

PubMed Abstract: The molybdenum cofactor (Moco) is a molybdenum-conjugated prosthetic group that is ubiquitously found in plants, animals, and bacteria. Moco is required for the nitrogen-reducing reaction of the Moco sulfurase C-terminal domain (MOSC) family. Despite the biological significance of MOSC proteins in the conversion of prodrugs and resistance against mutagens, their structural features and Moco-mediated catalysis mechanism have not been described in detail. YiiM is a MOSC protein that is involved in reducing mutagenic 6-N-hydroxylaminopurine to nontoxic adenine in bacteria. Here, we report two crystal structures of YiiM: one from Gram-positive Geobacillus stearothermophilus (gsYiiM) and the other from Gram-negative Escherichia coli (ecYiiM). Although gsYiiM and ecYiiM differ in oligomerization state and protein stability, both consist of three structural modules (a β-barrel and two α-helix bundles) and feature a cavity surrounded by the three modules. The cavity is characterized by positive electrostatic potentials and high sequence conservation. Moreover, the ecYiiM cavity houses a phosphate group, which emulates a part of Moco, and contains a highly reactive invariant cysteine residue. We thus propose that the cavity is the catalytic site where Moco binds and the substrate is reduced. Moreover, our comparative structural analysis highlights the common but distinct structural features of MOSC proteins.

PubMed: 29459651
DOI: 10.1038/s41598-018-21660-y

Experimental method

X-RAY DIFFRACTION (2 Å)