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Article: Autocatalytic intramolecular isopeptide bond formation in Gram-positive bacterial pili: A QM/MM simulation

TitleAutocatalytic intramolecular isopeptide bond formation in Gram-positive bacterial pili: A QM/MM simulation
Authors
KeywordsAmino group
Autocatalytic
Gram-positive bacterium
Hydrogen bonds
Pilin
Issue Date2011
PublisherAmerican Chemical Society. The Journal's web site is located at http://pubs.acs.org/journals/jacsat/index.html
Citation
Journal Of The American Chemical Society, 2011, v. 133 n. 3, p. 478-485 How to Cite?
AbstractMany Gram-positive pathogens possess external pili or fimbriae with which they adhere to host cells during the infection process. Unusual dual intramolecular isopeptide bonds between Asn and Lys side chains within the N-terminal and C-terminal domains of the pilus subunits have been observed initially in the Streptococcus pyogenes pilin subunit Spy0128 and subsequently in GBS52 from Streptococcus agalactiae, in the BcpA major pilin of Bacillus cereus and in the RrgB pilin of Streptococcus pneumoniae, among others. Within each pilin subunit, intramolecular isopeptide bonds serve to stabilize the protein. These bonds provide a means to withstand large external mechanical forces, as well as possibly assisting in supporting a conformation favored for pilin subunit polymerization via sortase transpeptidases. Genomewide analyses of pili-containing Gram-positive bacteria are known or suspected to contain isopeptide bonds in pilin subunits. For the autocatalytic formation of isopeptide cross-links, a conservation of three amino acids including Asn, Lys, and a catalytically important acidic Glu (or Asp) residue are responsible. However, the chemical mechanism of how isopeptide bonds form within pilin remains poorly understood. Although it is possible that several mechanistic paths could lead to isopeptide bond formation in pili, the requirement of a conserved glutamate and highly organized positioning of residues within the hydrophobic environment of the active site were found in numerous pilin crystal structures such as Spy0128 and RrgB. This suggests a mechanism involving direct coupling of lysine side chain amine to the asparagine carboxamide mediated by critical acid/base or hydrogen bonding interactions with the catalytic glutamate residue. From this mechanistic perspective, we used the QM/MM minimum free-energy path method to examine the reaction details of forming the isopeptide bonds with Spy0128 as a model pilin, specifically focusing on the role of the glutamate in catalysis. It was determined that the reaction mechanism likely consists of two major steps: the nucleophilic attack on Cγ by nitrogen in the unprotonated Lys ε-amino group and, then two concerted proton transfers occur during the formation of the intramolecular isopeptide bond to subsequently release ammonia. More importantly, within the dual active sites of Spy0128, Glu 117, and Glu 258 residues function as crucial catalysts for each isopeptide bond formation, respectively, by relaying two proton transfers. This work also suggests that domain-domain interactions within Spy0128 may modulate the reactivity of residues within each active site. Our results may hopefully shed light on the molecular mechanisms of pilin biogenesis in Gram-positive bacteria. © 2011 American Chemical Society.
Persistent Identifierhttp://hdl.handle.net/10722/142326
ISSN
2014 Impact Factor: 12.113
2014 SCImago Journal Rankings: 5.567
PubMed Central ID
ISI Accession Number ID
Funding AgencyGrant Number
National Institutes of Health (NIH)R01-A146611
R01-GM061870
Funding Information:

Support from the National Institutes of Health (NIH R01-A146611 to D.G.M., R01-GM061870 to WY.) is greatly appreciated.

References

 

DC FieldValueLanguage
dc.contributor.authorHu, Xen_HK
dc.contributor.authorHu, Hen_HK
dc.contributor.authorMelvin, JAen_HK
dc.contributor.authorClancy, KWen_HK
dc.contributor.authorMcCafferty, DGen_HK
dc.contributor.authorYang, Wen_HK
dc.date.accessioned2011-10-28T02:43:11Z-
dc.date.available2011-10-28T02:43:11Z-
dc.date.issued2011en_HK
dc.identifier.citationJournal Of The American Chemical Society, 2011, v. 133 n. 3, p. 478-485en_HK
dc.identifier.issn0002-7863en_HK
dc.identifier.urihttp://hdl.handle.net/10722/142326-
dc.description.abstractMany Gram-positive pathogens possess external pili or fimbriae with which they adhere to host cells during the infection process. Unusual dual intramolecular isopeptide bonds between Asn and Lys side chains within the N-terminal and C-terminal domains of the pilus subunits have been observed initially in the Streptococcus pyogenes pilin subunit Spy0128 and subsequently in GBS52 from Streptococcus agalactiae, in the BcpA major pilin of Bacillus cereus and in the RrgB pilin of Streptococcus pneumoniae, among others. Within each pilin subunit, intramolecular isopeptide bonds serve to stabilize the protein. These bonds provide a means to withstand large external mechanical forces, as well as possibly assisting in supporting a conformation favored for pilin subunit polymerization via sortase transpeptidases. Genomewide analyses of pili-containing Gram-positive bacteria are known or suspected to contain isopeptide bonds in pilin subunits. For the autocatalytic formation of isopeptide cross-links, a conservation of three amino acids including Asn, Lys, and a catalytically important acidic Glu (or Asp) residue are responsible. However, the chemical mechanism of how isopeptide bonds form within pilin remains poorly understood. Although it is possible that several mechanistic paths could lead to isopeptide bond formation in pili, the requirement of a conserved glutamate and highly organized positioning of residues within the hydrophobic environment of the active site were found in numerous pilin crystal structures such as Spy0128 and RrgB. This suggests a mechanism involving direct coupling of lysine side chain amine to the asparagine carboxamide mediated by critical acid/base or hydrogen bonding interactions with the catalytic glutamate residue. From this mechanistic perspective, we used the QM/MM minimum free-energy path method to examine the reaction details of forming the isopeptide bonds with Spy0128 as a model pilin, specifically focusing on the role of the glutamate in catalysis. It was determined that the reaction mechanism likely consists of two major steps: the nucleophilic attack on Cγ by nitrogen in the unprotonated Lys ε-amino group and, then two concerted proton transfers occur during the formation of the intramolecular isopeptide bond to subsequently release ammonia. More importantly, within the dual active sites of Spy0128, Glu 117, and Glu 258 residues function as crucial catalysts for each isopeptide bond formation, respectively, by relaying two proton transfers. This work also suggests that domain-domain interactions within Spy0128 may modulate the reactivity of residues within each active site. Our results may hopefully shed light on the molecular mechanisms of pilin biogenesis in Gram-positive bacteria. © 2011 American Chemical Society.en_HK
dc.languageengen_US
dc.publisherAmerican Chemical Society. The Journal's web site is located at http://pubs.acs.org/journals/jacsat/index.htmlen_HK
dc.relation.ispartofJournal of the American Chemical Societyen_HK
dc.subjectAmino group-
dc.subjectAutocatalytic-
dc.subjectGram-positive bacterium-
dc.subjectHydrogen bonds-
dc.subjectPilin-
dc.titleAutocatalytic intramolecular isopeptide bond formation in Gram-positive bacterial pili: A QM/MM simulationen_HK
dc.typeArticleen_HK
dc.identifier.emailHu, H:haohu@hku.hken_HK
dc.identifier.authorityHu, H=rp00707en_HK
dc.description.naturelink_to_OA_fulltext-
dc.identifier.doi10.1021/ja107513ten_HK
dc.identifier.pmid21142157-
dc.identifier.pmcidPMC3081525-
dc.identifier.scopuseid_2-s2.0-79851474953en_HK
dc.identifier.hkuros184581en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-79851474953&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume133en_HK
dc.identifier.issue3en_HK
dc.identifier.spage478en_HK
dc.identifier.epage485en_HK
dc.identifier.eissn1520-5126-
dc.identifier.isiWOS:000287553000018-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridHu, X=12782008400en_HK
dc.identifier.scopusauthoridHu, H=7404097564en_HK
dc.identifier.scopusauthoridMelvin, JA=26534759400en_HK
dc.identifier.scopusauthoridClancy, KW=36491131500en_HK
dc.identifier.scopusauthoridMcCafferty, DG=7005594982en_HK
dc.identifier.scopusauthoridYang, W=35265650900en_HK

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