4PZP

Substrate-free structure of D-alanine carrier protein ligase DltA from Bacillus cereus

Summary for 4PZP

• Entry DOI: 10.2210/pdb4pzp/pdb
• Related: 3DHV 3FCC 3FCE
• Descriptor: D-alanine--poly(phosphoribitol) ligase subunit 1 (2 entities in total)
• Functional Keywords: homologous to acetyl-coa synthetase, ligase
• Biological source: Bacillus cereus
• Cellular location: Cytoplasm : Q81G39
• Total number of polymer chains: 1
• Total formula weight: 57565.59

Authors

Du, L.,Atila, M.,Luo, Y. (deposition date: 2014-03-31, release date: 2014-11-26, Last modification date: 2023-09-20)

Primary citation

Du, L.,Luo, Y.
Thiolation-enhanced substrate recognition by D-alanyl carrier protein ligase DltA from Bacillus cereus.
F1000Res, 3:106-106, 2014

PubMed Abstract: D-alanylation of the lipoteichoic acid on Gram-positive cell wall is dependent on dlt gene-encoded proteins DltA, DltB, DltC and DltD. The D-alanyl carrier protein ligase DltA, as a remote homolog of acyl-(coenzyme A) (CoA) synthetase, cycles through two active conformations for the catalysis of adenylation and subsequent thiolation of D-alanine (D-Ala). The crystal structure of DltA in the absence of any substrate was observed to have a noticeably more disordered pocket for ATP which would explain why DltA has relatively low affinity for ATP in the absence of any D-alanyl carrier. We have previously enabled the thiolation of D-alanine in the presence of CoA as the mimic of D-alanyl carrier protein DltC which carries a 4'-phosphopantetheine group on a serine residue. Here we show that the resulting Michaelis constants in the presence of saturating CoA for both ATP and D-alanine were reduced more than 10 fold as compared to the values obtained in the absence of CoA. The presence of CoA also made DltA ~100-fold more selective on D-alanine over L-alanine. The CoA-enhanced substrate recognition further implies that the ATP and D-alanine substrates of the adenylation reaction are incorporated when the DltA enzyme cycles through its thiolation conformation.

PubMed: 25285205
DOI: 10.12688/f1000research.4097.1

Experimental method

X-RAY DIFFRACTION (1.9 Å)