2X3J

CO-COMPLEX STRUCTURE OF ACHROMOBACTIN SYNTHETASE PROTEIN D (ACSD) WITH ATP AND N-CITRYL-ETHYLENEDIAMINE FROM PECTOBACTERIUM CHRYSANTHEMI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural Basis for Acyl Acceptor Specificity in the Achromobactin Biosynthetic Enzyme Acsd.

Schmelz, S.Botting, C.H.Song, L.Kadi, N.F.Challis, G.L.Naismith, J.H.

(2011) J Mol Biol 412: 495

  • DOI: 10.1016/j.jmb.2011.07.059
  • Primary Citation of Related Structures:  
    2X3J

  • PubMed Abstract: 
  • Siderophores are known virulence factors, and their biosynthesis is a target for new antibacterial agents. A non-ribosomal peptide synthetase-independent siderophore biosynthetic pathway in Dickeya dadantii is responsible for production of the siderophore achromobactin ...

    Siderophores are known virulence factors, and their biosynthesis is a target for new antibacterial agents. A non-ribosomal peptide synthetase-independent siderophore biosynthetic pathway in Dickeya dadantii is responsible for production of the siderophore achromobactin. The D. dadantii achromobactin biosynthesis protein D (AcsD) enzyme has been shown to enantioselectively esterify citric acid with l-serine in the first committed step of achromobactin biosynthesis. The reaction occurs in two steps: stereospecific activation of citric acid by adenylation, followed by attack of the enzyme-bound citryl adenylate by l-serine to produce the homochiral ester. We now report a detailed characterization of the substrate profile and mechanism of the second (acyl transfer) step of AcsD enzyme. We demonstrate that the enzyme catalyzes formation of not only esters but also amides from the citryl-adenylate intermediate. We have rationalized the substrate utilization profile for the acylation reaction by determining the first X-ray crystal structure of a product complex for this enzyme class. We have identified the residues that are important for both recognition of l-serine and catalysis of ester formation. Our hypotheses were tested by biochemical analysis of various mutants, one of which shows a reversal of specificity from the wild type with respect to non-natural substrates. This change can be rationalized on the basis of our structural data. That this change in specificity is accompanied by no loss in activity suggests that AcsD and other members of the non-ribosomal peptide synthetase-independent siderophore superfamily may have biotransformation potential.


    Organizational Affiliation

    Scottish Structural Proteomics Facility and Centre for Biomolecular Sciences, The University of St Andrews, Scotland KY16 9ST, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ACSDA, B620Dickeya chrysanthemiMutation(s): 0 
Gene Names: acsD
Find proteins for Q93AT8 (Dickeya chrysanthemi)
Explore Q93AT8 
Go to UniProtKB:  Q93AT8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
C [auth A], H [auth B]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
X3J
Query on X3J

Download Ideal Coordinates CCD File 
L [auth B](2S)-2-{2-[(2-AMINOETHYL)AMINO]-2-OXOETHYL}-2-HYDROXYBUTANEDIOIC ACID
C8 H14 N2 O6
KQWWDTIPDRWKGZ-QMMMGPOBSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], J [auth B], K [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A], I [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.704α = 97.26
b = 71.521β = 101.97
c = 95.595γ = 91.01
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-08-10
    Changes: Database references, Other, Version format compliance
  • Version 1.2: 2011-09-14
    Changes: Database references
  • Version 1.3: 2017-07-12
    Changes: Refinement description
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2019-05-15
    Changes: Data collection, Experimental preparation