4ME6

Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP

Summary for 4ME6

• Entry DOI: 10.2210/pdb4me6/pdb
• Related: 3E5N 3R5F 4L1K
• Descriptor: D-alanine--D-alanine ligase, MAGNESIUM ION, ADENOSINE-5'-DIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: adp-depending enzyme, d-alanine-d-alanine ligase, nucleotide binding, ligase
• Biological source: Xanthomonas oryzae pv. oryzae
• Cellular location: Cytoplasm (By similarity): Q5H614
• Total number of polymer chains: 1
• Total formula weight: 42397.28

Authors

Doan, T.T.N.,Kim, J.K.,Ahn, Y.J.,Lee, B.M.,Kang, L.W. (deposition date: 2013-08-25, release date: 2014-02-19, Last modification date: 2023-11-08)

Primary citation

Doan, T.N.N.,Kim, J.K.,Ngo, H.P.T.,Tran, H.T.,Cha, S.S.,Chung, K.M.,Huynh, K.H.,Ahn, Y.J.,Kang, L.W.
Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides
Arch.Biochem.Biophys., 545C:92-99, 2014

PubMed Abstract: D-Alanine-D-alanine ligase (DDL) catalyzes the biosynthesis of d-alanyl-d-alanine, an essential bacterial peptidoglycan precursor, and is an important drug target for the development of antibacterials. We determined four different crystal structures of DDL from Xanthomonas oryzae pv. oryzae (Xoo) causing Bacteria Blight (BB), which include apo, ADP-bound, ATP-bound, and AMPPNP-bound structures at the resolution between 2.3 and 2.0 Å. Similarly with other DDLs, the active site of XoDDL is formed by three loops from three domains at the center of enzyme. Compared with d-alanyl-d-alanine and ATP-bound TtDDL structure, the γ-phosphate of ATP in XoDDL structure was shifted outside toward solution. We swapped the ω-loop (loop3) of XoDDL with those of Escherichia coli and Helicobacter pylori DDLs, and measured the enzymatic kinetics of wild-type XoDDL and two mutant XoDDLs with the swapped ω-loops. Results showed that the direct interactions between ω-loop and other two loops are essential for the active ATP conformation for D-ala-phosphate formation.

PubMed: 24440607
DOI: 10.1016/j.abb.2014.01.009

Experimental method

X-RAY DIFFRACTION (2.1 Å)