4L1K image
Entry Detail
PDB ID:
4L1K
Keywords:
Title:
Crystal structure of D-alanine-D-alnine ligase from Xanthomonas oryzae pv. oryzae with AMPPNP
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2013-06-03
Release Date:
2014-02-19
Method Details:
Experimental Method:
Resolution:
2.30 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 43 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:D-alanine--D-alanine ligase
Mutations:M327V
Chain IDs:A
Chain Length:384
Number of Molecules:1
Biological Source:Xanthomonas oryzae pv. oryzae
Primary Citation
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)
PMID: 24440607 DOI: 10.1016/j.abb.2014.01.009

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures