Lysine carboxylation in proteins: OXA-10 β-lactamase

Jie Li, Jason B. Cross, Thom Vreven, Samy O. Meroueh, Shahriar Mobashery, H. Bernhard Schlegel

Research output: Contribution to journalArticle

36 Scopus citations

Abstract

An increasing number of proteins are being shown to have an N ζ-carboxylated lysine in their structures, a posttranslational modification of proteins that proceeds without the intervention of a specific enzyme. The role of the carboxylated lysine in these proteins is typically structural (hydrogen bonding or metal coordination). However, carboxylated lysines in the active sites of OXA-10 and OXA-1 β-lactamases and the sensor domain of BlaR signal-transducer protein serve in proton transfer events required for the functions of these proteins. These examples demonstrate the utility of this unusual amino acid in acid-base chemistry, in expansion of function beyond those of the 20 standard amino acids. In this study, the ONIOM quantum-mechanical/molecular-mechanical (QM/MM) method is used to study the carboxylation of lysine in the OXA-10 β-lactamase. Lys-70 and the active site of the OXA-10 β-lactamase were treated with B3LYP/6-31G(d,p) density functional calculations and the remainder of the enzyme with the AMBER molecular mechanics force field. The barriers for unassisted carboxylation of neutral lysine by carbon dioxide or bicarbonate are high. However, when the reaction with CO2 is catalyzed by a molecule of water in the active site, it is exothermic by about 13 kcal/mol, with a barrier of approximately 14 kcal/mol. The calculations show that the carboxylation and decarboxylation of Lys-70 are likely to be accompanied by deprotonation and protonation of the carbamate, respectively. The analysis may also be relevant for other proteins with carboxylated lysines, a feature that may be more common in nature than previously appreciated.

Original languageEnglish (US)
Pages (from-to)246-257
Number of pages12
JournalProteins: Structure, Function and Genetics
Volume61
Issue number2
DOIs
StatePublished - Nov 1 2005
Externally publishedYes

Keywords

  • Carboxylation mechanism
  • Class D β-lactamase
  • Density functional calculations
  • ONIOM QM/MM method
  • Penicillin-binding proteins

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Fingerprint Dive into the research topics of 'Lysine carboxylation in proteins: OXA-10 β-lactamase'. Together they form a unique fingerprint.

  • Cite this