 |
PDBsum entry 1md9
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Crystal structure of dhbe, An archetype for aryl acid activating domains of modular nonribosomal peptide synthetases.
|
|
|
Authors
|
|
J.J.May,
N.Kessler,
M.A.Marahiel,
M.T.Stubbs.
|
|
|
Ref.
|
|
Proc Natl Acad Sci U S A, 2002,
99,
12120-12125.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
The synthesis of the catecholic siderophore bacillibactin is accomplished by the
nonribosomal peptide synthetase (NRPS) encoded by the dhb operon. DhbE is
responsible for the initial step in bacillibactin synthesis, the activation of
the aryl acid 2,3-dihydroxybenzoate (DHB). The stand-alone adenylation (A)
domain DhbE, the structure of which is presented here, exhibits greatest
homology to other NRPS A-domains, acyl-CoA ligases and luciferases. It's
structure is solved in three different states, without the ligands ATP and DHB
(native state), with the product DHB-AMP (adenylate state) and with the
hydrolyzed product AMP and DHB (hydrolyzed state). The 59.9-kDa protein folds
into two domains, with the active site at the interface between them. In
contrast to previous proposals of a major reorientation of the large and small
domains on substrate binding, we observe only local structural rearrangements.
The structure of the phosphate binding loop could be determined, a motif common
to many adenylate-forming enzymes, as well as with bound DHB-adenylate and the
hydrolyzed product DHB*AMP. Based on the structure and amino acid sequence
alignments, an adapted specificity conferring code for aryl acid activating
domains is proposed, allowing assignment of substrate specificity to gene
products of previously unknown function.
|
|
|
|
|
|
|
|
Figure 1.
Fig 1. (A) Bacillibactin NRPS cluster from B. subtilis with
the corresponding domain organization of synthetase modules.
ICL, isochorismatase; C, condensation domain; T, thiolation
domain. (B) Structure of the trilactone Bacillibactin, with one
of the catecholic moiety activated by DhbE shaded in gray. (C)
The DhbE-dependent aryl acid adenylation in peptide synthesis is
an ATP-consuming process leading to a protein-bound adenylate.
|
|
Figure 5.
Fig 5. Determination of the specificity conferring code of
ca-activating domains. The primary sequence between core A4 and
A5 (see Fig. 3) of nine ca activating domains are aligned by
using the Clustal method. Based on the structural data of DhbE,
extraction of the 10 residues conferring the substrate
specificity leads to the identification of the signature
sequence of ca activating A domain. The asterisks define the
residues that allow discrimination between DHB and SAL.
|
|
|
|
|
|
|
|
|
|
