Structure of the branched intermediate in protein splicing

Abstract

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 proteinengineering approaches to show that intein-succinimide formation is critically dependent on a backbone-to-side-chain hydrogenbond. 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.expressed | protein semisynthesis P rotein splicing is a posttranslational modification in which an internal domain, termed an intein, excises itself from a host protein with concomitant ligation of the flanking sequences (termed the N-and C-exteins) (1, 2). Inteins are found in unicellular organisms from all domains of life (3) and belong to the HINT (Hedgehog INTein) superfamily of autoprocessing domains (4), which includes the cholesterol ligase domain found in the eponymous hedgehog family of developmental proteins present in all bilaterian animals (5, 6). High-resolution structures of inteins reveal a characteristic horseshoe-like β-sheet fold (7), common to all HINT family members (8), which positions catalytic residues from four conserved sequence blocks (A, B, F, G) in proximity to N-and C-terminal splice junctions (Fig. 1A). This structural information has aided mechanistic studies into the protein splicing process, which we know to be a multistep cascade involving a series of acyl-transfer reactions (Fig. 1B) (1, 2). Although a biological role for protein splicing remains elusive, an ever-deepening understanding of the splicing mechanism has led to the development of a wide range of biotechnology and chemical biology approaches based on engineered inteins (9).The most intriguing chemical step in protein splicing is inteinsuccinimide formation. This acts as the rate-limiting step in the process and leads to the resolution of the so-called branched (thio) ester intermediate species (Fig. 1B, step 3). This step involves nucleophilic attack of the side-chain primary amide group of a conserved Asn residue (the block G Asn) on the adjacent peptide bond (+1 scissile amide), leading to cleavage of the intein from the Cextein. This is an extre...

Fast Amide Bond Cleavage Assisted by a Secondary Amino and a Carboxyl Group—A Model for yet Unknown Peptidases?

“…Details of the activation of the Asn side chain amide for the nucleophilic attack are not completely understood. This could involve its tautomerization with the formation of a more reactive imidate species [47] or, alternatively, twisting the amide bond, which is known to enhance its nucleophilicity [48]. Interestingly, a mechanism involving the twisted asparagine amide group was proposed for oligosaccharyltransferases, the membrane protein complexes which catalyze asparagine-linked glycosylation [49].…”

Xenoprotein engineering via synthetic libraries

“…X enoproteins-protein molecules composed of noncanonical amino acids-might exhibit function not readily achieved by the use of proteogenic amino acids alone (1)(2)(3)(4)(5)(6)(7)(8)(9) and other favorable properties such as protease stability or altered immunogenicity (10). Chemical protein synthesis is a powerful approach for incorporating a virtually unlimited variety of noncanonical amino acids into a protein molecule for biophysical and structure-function studies (11)(12)(13)(14)(15)(16)(17)(18)(19)(20). However, no experimental approach exists to differentiate beneficial versus deleterious mutations in a synthetic protein molecule with significant throughput.…”

Coordination of the third step of protein splicing in two cyanobacterial inteins

“…Conformational changes linked to the first and/or second steps of splicing may be required to properly align the active site to catalyze step three of splicing. For example, in a semisynthetic version of the Mycobacterium xenopi GyrA intein, formation of the branched ester accelerates the rate of succinimide formation, and a crystal structure suggests that this rate acceleration is due to optimal positioning of the Cterminal Asn side chain amide nucleophile due to a specific hydrogen bond not found in the structure of the linear precursor [23,24]. Branched ester formation also accelerates Asn cyclization for the split Nostoc punctiforme DnaE intein [25].…”