Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.57 kDa 
• Atom Count: 3922 
• Modelled Residue Count: 464 
• Deposited Residue Count: 512 
• Unique protein chains: 1

4PZP

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

• PDB DOI: 10.2210/pdb4PZP/pdb

• Classification: LIGASE
• Organism(s): Bacillus cereus ATCC 14579
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-03-31 Released: 2014-11-26 
• Deposition Author(s): Du, L., Atila, M., Luo, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.261 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Literature

Thiolation-enhanced substrate recognition by D-alanyl carrier protein ligase DltA from Bacillus cereus.

Du, L., Luo, Y.

(2014) F1000res 3: 106-106

• PubMed: 25285205 
• DOI: 10.12688/f1000research.4097.1
• Primary Citation of Related Structures:  
  4PZP


• 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.

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Organizational Affiliation: 

Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanine--poly(phosphoribitol) ligase subunit 1	A	512	Bacillus cereus ATCC 14579	Mutation(s): 0  Gene Names: BC_1372, dltA EC: 6.1.1.13 (PDB Primary Data), 6.2.1.54 (UniProt)
UniProt
Find proteins for Q81G39 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q81G39  Go to UniProtKB:  Q81G39

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.261 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.9	α = 90
b = 81.9	β = 108.3
c = 59.3	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
CNS	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-03-31 
• Released Date: 2014-11-26 
Deposition Author(s): Du, L., Atila, M., Luo, Y.

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release