File Download
 
Links for fulltext
(May Require Subscription)
 
Supplementary

Article: Autocatalytic intramolecular isopeptide bond formation in Gram-positive bacterial pili: A QM/MM simulation
  • Basic View
  • Metadata View
  • XML View
TitleAutocatalytic intramolecular isopeptide bond formation in Gram-positive bacterial pili: A QM/MM simulation
 
AuthorsHu, X3
Hu, H2
Melvin, JA1
Clancy, KW3
McCafferty, DG3
Yang, W3
 
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
 
CitationJournal Of The American Chemical Society, 2011, v. 133 n. 3, p. 478-485 [How to Cite?]
DOI: http://dx.doi.org/10.1021/ja107513t
 
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.
 
ISSN0002-7863
2012 Impact Factor: 10.677
2012 SCImago Journal Rankings: 5.182
 
DOIhttp://dx.doi.org/10.1021/ja107513t
 
PubMed Central IDPMC3081525
 
ISI Accession Number IDWOS:000287553000018
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.

 
ReferencesReferences in Scopus
 
DC FieldValue
dc.contributor.authorHu, X
 
dc.contributor.authorHu, H
 
dc.contributor.authorMelvin, JA
 
dc.contributor.authorClancy, KW
 
dc.contributor.authorMcCafferty, DG
 
dc.contributor.authorYang, W
 
dc.date.accessioned2011-10-28T02:43:11Z
 
dc.date.available2011-10-28T02:43:11Z
 
dc.date.issued2011
 
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.
 
dc.description.naturelink_to_OA_fulltext
 
dc.identifier.citationJournal Of The American Chemical Society, 2011, v. 133 n. 3, p. 478-485 [How to Cite?]
DOI: http://dx.doi.org/10.1021/ja107513t
 
dc.identifier.doihttp://dx.doi.org/10.1021/ja107513t
 
dc.identifier.eissn1520-5126
 
dc.identifier.epage485
 
dc.identifier.hkuros184581
 
dc.identifier.isiWOS:000287553000018
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.

 
dc.identifier.issn0002-7863
2012 Impact Factor: 10.677
2012 SCImago Journal Rankings: 5.182
 
dc.identifier.issue3
 
dc.identifier.pmcidPMC3081525
 
dc.identifier.pmid21142157
 
dc.identifier.scopuseid_2-s2.0-79851474953
 
dc.identifier.spage478
 
dc.identifier.urihttp://hdl.handle.net/10722/142326
 
dc.identifier.volume133
 
dc.languageeng
 
dc.publisherAmerican Chemical Society. The Journal's web site is located at http://pubs.acs.org/journals/jacsat/index.html
 
dc.publisher.placeUnited States
 
dc.relation.ispartofJournal of the American Chemical Society
 
dc.relation.referencesReferences in Scopus
 
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 simulation
 
dc.typeArticle
 
<?xml encoding="utf-8" version="1.0"?>
<item><contributor.author>Hu, X</contributor.author>
<contributor.author>Hu, H</contributor.author>
<contributor.author>Melvin, JA</contributor.author>
<contributor.author>Clancy, KW</contributor.author>
<contributor.author>McCafferty, DG</contributor.author>
<contributor.author>Yang, W</contributor.author>
<date.accessioned>2011-10-28T02:43:11Z</date.accessioned>
<date.available>2011-10-28T02:43:11Z</date.available>
<date.issued>2011</date.issued>
<identifier.citation>Journal Of The American Chemical Society, 2011, v. 133 n. 3, p. 478-485</identifier.citation>
<identifier.issn>0002-7863</identifier.issn>
<identifier.uri>http://hdl.handle.net/10722/142326</identifier.uri>
<description.abstract>Many 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 C&#947; by nitrogen in the unprotonated Lys &#949;-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. &#169; 2011 American Chemical Society.</description.abstract>
<language>eng</language>
<publisher>American Chemical Society. The Journal&apos;s web site is located at http://pubs.acs.org/journals/jacsat/index.html</publisher>
<relation.ispartof>Journal of the American Chemical Society</relation.ispartof>
<subject>Amino group</subject>
<subject>Autocatalytic</subject>
<subject>Gram-positive bacterium</subject>
<subject>Hydrogen bonds</subject>
<subject>Pilin</subject>
<title>Autocatalytic intramolecular isopeptide bond formation in Gram-positive bacterial pili: A QM/MM simulation</title>
<type>Article</type>
<description.nature>link_to_OA_fulltext</description.nature>
<identifier.doi>10.1021/ja107513t</identifier.doi>
<identifier.pmid>21142157</identifier.pmid>
<identifier.pmcid>PMC3081525</identifier.pmcid>
<identifier.scopus>eid_2-s2.0-79851474953</identifier.scopus>
<identifier.hkuros>184581</identifier.hkuros>
<relation.references>http://www.scopus.com/mlt/select.url?eid=2-s2.0-79851474953&amp;selection=ref&amp;src=s&amp;origin=recordpage</relation.references>
<identifier.volume>133</identifier.volume>
<identifier.issue>3</identifier.issue>
<identifier.spage>478</identifier.spage>
<identifier.epage>485</identifier.epage>
<identifier.eissn>1520-5126</identifier.eissn>
<identifier.isi>WOS:000287553000018</identifier.isi>
<publisher.place>United States</publisher.place>
<bitstream.url>http://hub.hku.hk/bitstream/10722/142326/1/re01.htm</bitstream.url>
</item>
Author Affiliations
  1. Duke University School of Medicine
  2. The University of Hong Kong
  3. Duke University