3E7W

Crystal structure of DLTA: Implications for the reaction mechanism of non-ribosomal peptide synthetase (NRPS) adenylation domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of DltA. Implications for the reaction mechanism of non-ribosomal peptide synthetase adenylation domains

Yonus, H.Neumann, P.Zimmermann, S.May, J.J.Marahiel, M.A.Stubbs, M.T.

(2008) J Biol Chem 283: 32484-32491

  • DOI: https://doi.org/10.1074/jbc.M800557200
  • Primary Citation of Related Structures:  
    3E7W, 3E7X

  • PubMed Abstract: 

    DltA, the D-alanine:D-alanyl carrier protein ligase responsible for the initial step of lipoteichoic acid D-alanylation in Gram-positive bacteria, belongs to the adenylation domain superfamily, which also includes acetyl-CoA synthetase and the adenylation domains of non-ribosomal synthetases. The two-step reaction catalyzed by these enzymes (substrate adenylation followed by transfer to the reactive thiol group of CoA or the phosphopantheinyl prosthetic group of peptidyl carrier proteins) has been suggested to proceed via large scale rearrangements of structural domains within the enzyme. The structures of DltA reported here reveal the determinants for D-Ala substrate specificity and confirm that the peptidyl carrier protein-activating domains are able to adopt multiple conformational states, in this case corresponding to the thiolation reaction. Comparisons of available structures allow us to propose a mechanism whereby small perturbations of finely balanced metastable structural states would be able to direct an ordered formation of non-ribosomal synthetase products.


  • Organizational Affiliation

    Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-alanine--poly(phosphoribitol) ligase subunit 1511Bacillus subtilisMutation(s): 0 
Gene Names: dltA
EC: 6.1.1.13
UniProt
Find proteins for P39581 (Bacillus subtilis (strain 168))
Explore P39581 
Go to UniProtKB:  P39581
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39581
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.205 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.564α = 90
b = 94.99β = 90
c = 132.547γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
SHELXphasing
CNSrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations