Open AccessStructure of d ‐alanine‐ d ‐alanine ligase from Thermus thermophilus HB8: cumulative conformational change and enzyme–ligand interactions
Author(s) -
Kitamura Yoshiaki,
Ebihara Akio,
Agari Yoshihiro,
Shinkai Akeo,
Hirotsu Ken,
Kuramitsu Seiki
Publication year - 2009
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444909029710
Subject(s) - thermus thermophilus , dna ligase , peptidoglycan , stereochemistry , conformational change , chemistry , alanine scanning , enzyme , alanine , protein structure , biochemistry , amino acid , mutagenesis , escherichia coli , mutation , gene
d ‐Alanine‐ d ‐alanine ligase (Ddl) is one of the key enzymes in peptidoglycan biosynthesis and is an important target for drug discovery. The enzyme catalyzes the condensation of two d ‐Ala molecules using ATP to produce d ‐Ala‐ d ‐Ala, which is the terminal peptide of a peptidoglycan monomer. The structures of five forms of the enzyme from Thermus thermophilus HB8 (TtDdl) were determined: unliganded TtDdl (2.3 Å resolution), TtDdl–adenylyl imidodiphosphate (2.6 Å), TtDdl–ADP (2.2 Å), TtDdl–ADP– d ‐Ala (1.9 Å) and TtDdl–ATP– d ‐Ala‐ d ‐Ala (2.3 Å). The central domain rotates as a rigid body towards the active site in a cumulative manner in concert with the local conformational change of three flexible loops depending upon substrate or product binding, resulting in an overall structural change from the open to the closed form through semi‐open and semi‐closed forms. Reaction‐intermediate models were simulated using TtDdl‐complex structures and other Ddl structures previously determined by X‐ray methods. The catalytic process accompanied by the cumulative conformational change has been elucidated based on the intermediate models in order to provide new insights regarding the details of the catalytic mechanism.