2WKA

Structure of Plp_Thr_decanoyl-CoA aldimine form of Vibrio cholerae CqsA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Insights Into the Biosynthesis of the Vibrio Cholerae Major Autoinducer Cai-1 from the Crystal Structure of the Plp-Dependent Enzyme Cqsa.

Jahan, N.Potter, J.A.Sheikh, M.A.Botting, C.H.Shirran, S.L.Westwood, N.J.Taylor, G.L.

(2009) J Mol Biol 392: 763

  • DOI: 10.1016/j.jmb.2009.07.042
  • Primary Citation of Related Structures:  
    2WK7, 2WK8, 2WK9, 2WKA

  • PubMed Abstract: 
  • CqsA is an enzyme involved in the biosynthesis of cholerae autoinducer-1 (CAI-1), the major Vibrio cholerae autoinducer engaged in quorum sensing. The amino acid sequence of CqsA suggests that it belongs to the family of alpha-oxoamine synthases that catalyse the condensation of an amino acid to an acyl-CoA substrate ...

    CqsA is an enzyme involved in the biosynthesis of cholerae autoinducer-1 (CAI-1), the major Vibrio cholerae autoinducer engaged in quorum sensing. The amino acid sequence of CqsA suggests that it belongs to the family of alpha-oxoamine synthases that catalyse the condensation of an amino acid to an acyl-CoA substrate. Here we present the apo- and PLP-bound crystal structures of CqsA and confirm that it shares structural homology with the dimeric alpha-oxoamine synthases, including a conserved PLP-binding site. The chemical structure of CAI-1 suggests that decanoyl-CoA may be one substrate of CqsA and that another substrate may be l-threonine or l-2-aminobutyric acid. A crystal structure of CqsA at 1.9-A resolution obtained in the presence of PLP and l-threonine reveals an external aldimine that has lost the l-threonine side chain. Similarly, a 1.9-A-resolution crystal structure of CqsA in the presence of PLP, l-threonine, and decanoyl-CoA shows a trapped external aldimine intermediate, suggesting that the condensation and decarboxylation steps have occurred, again with loss of the l-threonine side chain. It is suggested that this side-chain loss, an observation supported by mass spectrometry, is due to a retro-aldol reaction. Although no structural data have been obtained on CqsA using l-2-aminobutyric acid and decanoyl-CoA as substrates, mass spectrometry confirms the expected product of the enzyme reaction. It is proposed that a region of structure that is disordered in the apo structure is involved in the release of product. While not confirming if CqsA alone is able to synthesize CAI-1, these results suggest possible synthetic routes.


    Organizational Affiliation

    Centre for Biomolecular Sciences, University of St. Andrews, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CAI-1 AUTOINDUCER SYNTHASEA, B389Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: cqsAVC_A0523
EC: 2.3
UniProt
Find proteins for Q9KM65 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KM65 
Go to UniProtKB:  Q9KM65
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P89 (Subject of Investigation/LOI)
Query on P89

Download Ideal Coordinates CCD File 
C [auth A], E [auth B][6-methyl-5-oxidanyl-4-[(~{E})-2-oxidanylideneundecyliminomethyl]pyridin-3-yl]methyl dihydrogen phosphate
C19 H31 N2 O6 P
NFGPSQDCIMWBHR-DEDYPNTBSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.03α = 90
b = 70.57β = 90
c = 70.67γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Source and taxonomy
  • Version 2.0: 2018-10-03
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary