5bpf | pdb_00005bpf

Crystal structure of ADP complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis

spinqualitylabelsall models 5bpf, resolution 2.28Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5bpf is a 4 chain structure with sequence from "bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ACT, ADP, GOL, NA Related: 5bph Gene: ddl, ddlB, YPO0557, y3624, YP_3627 ("Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900) Activity: D-alanine--D-alanine ligase, with EC number 6.3.2.4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [DDL_YERPE] cell wall formation {eco Publication Abstract from PubMed D-Alanyl-D-alanine is an essential precursor of bacterial peptidoglycan and is synthesized by D-alanine-D-alanine ligase (DDL) with hydrolysis of ATP; this reaction makes DDL an important drug target for the development of antibacterial agents. Five crystal structures of DDL from Yersinia pestis (YpDDL) were determined at 1.7-2.5 A resolution: apo, AMP-bound, ADP-bound, adenosine 5'-(beta,gamma-imido)triphosphate-bound, and D-alanyl-D-alanine- and ADP-bound structures. YpDDL consists of three domains, in which four loops, loop 1, loop 2 (the serine loop), loop 3 (the omega-loop) and loop 4, constitute the binding sites for two D-alanine molecules and one ATP molecule. Some of them, especially the serine loop and the omega-loop, show flexible conformations, and the serine loop is mainly responsible for the conformational change in substrate nucleotide phosphates. Enzyme-kinetics assays were carried out for both the D-alanine and ATP substrates and a substrate-binding mechanism was proposed for YpDDL involving conformational changes of the loops. Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.,Tran HT, Hong MK, Ngo HP, Huynh KH, Ahn YJ, Wang Z, Kang LW Acta Crystallogr D Struct Biol. 2016 Jan;72(Pt 1):12-21. doi:, 10.1107/S2059798315021671. Epub 2016 Jan 1. PMID:26894530 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also D-alanine-D-alanine ligase 3D structures

Proteopedia Page Contributors and Editors (what is this?)

OCA