3JRT

Structure from the mobile metagenome of V. paracholerae: Integron cassette protein Vpc_cass2

Summary for 3JRT

• Entry DOI: 10.2210/pdb3jrt/pdb
• Descriptor: Integron cassette protein Vpc_cass2 (2 entities in total)
• Functional Keywords: integron cassette protein, vibrio paracholerae, mobile metagenome, structural genomics, psi-2 protein structure initiative, midwest center for structural genomics, mcsg, unknown function
• Biological source: Vibrio paracholerae
• Total number of polymer chains: 1
• Total formula weight: 22282.03

Authors

Harrop, S.J.,Deshpande, C.,Sureshan, V.,Boucher, Y.,Xu, X.,Cui, H.,Cuff, M.,Edwards, A.,Savchenko, A.,Joachimiak, A.,Stokes, H.W.,Curmi, P.M.G.,Mabbutt, B.C.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2009-09-08, release date: 2009-09-22, Last modification date: 2013-02-06)

Primary citation

Sureshan, V.,Deshpande, C.N.,Boucher, Y.,Koenig, J.E.,Stokes, H.W.,Harrop, S.J.,Curmi, P.M.,Mabbutt, B.C.
Integron gene cassettes: a repository of novel protein folds with distinct interaction sites.
Plos One, 8:e52934-e52934, 2013

PubMed Abstract: Mobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. In most cases, functional annotation of gene cassettes directly recovered by cassette-PCR is obscured by their characteristically high sequence novelty. This inhibits identification of those specific functions or biological features that might constitute preferential factors for lateral gene transfer via the integron system. A structural genomics approach incorporating x-ray crystallography has been utilised on a selection of cassettes to investigate evolutionary relationships hidden at the sequence level. Gene cassettes were accessed from marine sediments (pristine and contaminated sites), as well as a range of Vibrio spp. We present six crystal structures, a remarkably high proportion of our survey of soluble proteins, which were found to possess novel folds. These entirely new structures are diverse, encompassing all-α, α+β and α/β fold classes, and many contain clear binding pocket features for small molecule substrates. The new structures emphasise the large repertoire of protein families encoded within the integron cassette metagenome and which remain to be characterised. Oligomeric association is a notable recurring property common to these new integron-derived proteins. In some cases, the protein-protein contact sites utilised in homomeric assembly could instead form suitable contact points for heterogeneous regulator/activator proteins or domains. Such functional features are ideal for a flexible molecular componentry needed to ensure responsive and adaptive bacterial functions.

PubMed: 23349695
DOI: 10.1371/journal.pone.0052934

Experimental method

X-RAY DIFFRACTION (2.3 Å)