4oz6

Structure of the Branched Intermediate in Protein Splicing

spinqualitylabelsall models 4oz6, resolution 2.79Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4oz6 is a 2 chain structure with sequence from "mycobacterium_xenopei"_(sic)_schwabacher_1959 "mycobacterium xenopei" (sic) schwabacher 1959. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: MG NonStd Res: TIH Gene: gyrA ("Mycobacterium xenopei" (sic) Schwabacher 1959) Activity: DNA topoisomerase (ATP-hydrolyzing), with EC number 5.99.1.3 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [GYRA_MYCXE] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings (By similarity). Publication Abstract from PubMed Inteins are autoprocessing domains that cut themselves out of host proteins in a traceless manner. This process, known as protein splicing, involves multiple chemical steps that must be coordinated to ensure fidelity in the process. The committed step in splicing involves attack of a conserved Asn side-chain amide on the adjacent backbone amide, leading to an intein-succinimide product and scission of that peptide bond. This cleavage reaction is stimulated by formation of a branched intermediate in the splicing process. The mechanism by which the Asn side-chain becomes activated as a nucleophile is not understood. Here we solve the crystal structure of an intein trapped in the branched intermediate step in protein splicing. Guided by this structure, we use protein-engineering approaches to show that intein-succinimide formation is critically dependent on a backbone-to-side-chain hydrogen-bond. We propose that this interaction serves to both position the side-chain amide for attack and to activate its nitrogen as a nucleophile. Collectively, these data provide an unprecedented view of an intein poised to carry out the rate-limiting step in protein splicing, shedding light on how a nominally nonnucleophilic group, a primary amide, can become activated in a protein active site. Structure of the branched intermediate in protein splicing.,Liu Z, Frutos S, Bick MJ, Vila-Perello M, Debelouchina GT, Darst SA, Muir TW Proc Natl Acad Sci U S A. 2014 Apr 28. PMID:24778214 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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