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2yzn, resolution 2.60Å ()
Activity: D-alanine--D-alanine ligase, with EC number
Related: 2yzg
Resources: FirstGlance, OCA, RCSB, PDBsum, TOPSAN
Coordinates: save as pdb, mmCIF, xml

Crystal structure of D-alanine:D-Alanine Ligase with AMPPNP from Thermus thermophilus HB8.

Publication Abstract from PubMed

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 A resolution), TtDdl-adenylyl imidodiphosphate (2.6 A), TtDdl-ADP (2.2 A), TtDdl-ADP-D-Ala (1.9 A) and TtDdl-ATP-D-Ala-D-Ala (2.3 A). 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.

Structure of D-alanine-D-alanine ligase from Thermus thermophilus HB8: cumulative conformational change and enzyme-ligand interactions., Kitamura Y, Ebihara A, Agari Y, Shinkai A, Hirotsu K, Kuramitsu S, Acta Crystallogr D Biol Crystallogr. 2009 Oct;65(Pt 10):1098-106. Epub, 2009 Sep 16. PMID:019770507

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

2yzn is a 3 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA.

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