title: Evidence-based docking of the urease activation complex.
abstract: Ureases require accessory proteins for their activation and proper function. In Klebsiella aerogenes, UreD, UreF, UreG, and UreE are sequentially complexed to UreABC as required for its activation. Until now, only low-resolution structures are available for this activation complex. To circumvent such limitation, our work intends to provide an atomic-level model for the (UreABC-UreDFG)₃ complex from K. aerogenes, by employing comparative modeling associated to sequential macromolecular dockings, validated through small-angle X-ray scattering profiles and comparison with results from cross-linking, mutagenesis, and pull-down experiments. Additionally, normal mode analyses of the obtained complex supported the characterization of the elevated flexibility of both UreD-UreF dimer and (UreABC-UreDFG)₃ oligomer, explaining the previously observed diffuse binding of UreD to the apoenzyme. The model shown here is the first atomic-level depiction of this complex, a required step for the unraveling of the urease activation process. (1)Both authors share senior authorship. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:6.
authors.affiliation: Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, RS, Brazil.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Ligabue-Braun
authors.forename: Rafael
authors.initials: R
authors.lastname: Real-Guerra
authors.forename: Célia Regina
authors.initials: CR
authors.lastname: Carlini
authors.forename: Hugo
authors.initials: H
authors.lastname: Verli
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D004789:Enzyme Activation; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011487:Protein Conformation; D014510:Urease / Q000737:chemistry* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D014510:Urease