2W04

Co-complex Structure of Achromobactin Synthetase Protein D (AcsD) with citrate in ATP binding site from Pectobacterium Chrysanthemi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 

Starting Model: other
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This is version 1.4 of the entry. See complete history


Literature

Acsd Catalyzes Enantioselective Citrate Desymmetrization in Siderophore Biosynthesis

Schmelz, S.Kadi, N.Mcmahon, S.A.Song, L.Oves-Costales, D.Oke, M.Liu, H.Johnson, K.A.Carter, L.Botting, C.H.White, M.F.Challis, G.L.Naismith, J.H.

(2009) Nat Chem Biol 5: 174

  • DOI: https://doi.org/10.1038/nchembio.145
  • Primary Citation of Related Structures:  
    2W02, 2W03, 2W04

  • PubMed Abstract: 

    Bacterial pathogens need to scavenge iron from their host for growth and proliferation during infection. They have evolved several strategies to do this, one being the biosynthesis and excretion of small, high-affinity iron chelators known as siderophores. The biosynthesis of siderophores is an important area of study, not only for potential therapeutic intervention but also to illuminate new enzyme chemistries. Two general pathways for siderophore biosynthesis exist: the well-characterized nonribosomal peptide synthetase (NRPS)-dependent pathway and the NRPS-independent siderophore (NIS) pathway, which relies on a different family of sparsely investigated synthetases. Here we report structural and biochemical studies of AcsD from Pectobacterium (formerly Erwinia) chrysanthemi, an NIS synthetase involved in achromobactin biosynthesis. The structures of ATP and citrate complexes provide a mechanistic rationale for stereospecific formation of an enzyme-bound (3R)-citryladenylate, which reacts with L-serine to form a likely achromobactin precursor. AcsD is a unique acyladenylate-forming enzyme with a new fold and chemical catalysis strategy.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACSD
A, B
620Dickeya chrysanthemiMutation(s): 0 
UniProt
Find proteins for Q93AT8 (Dickeya chrysanthemi)
Explore Q93AT8 
Go to UniProtKB:  Q93AT8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93AT8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download Ideal Coordinates CCD File 
C [auth B]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.371α = 90
b = 94.959β = 90
c = 160.261γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-29
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references, Other, Refinement description