2Q6L

SalL double mutant Y70T/G131S with CLDA and L-MET


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery and characterization of a marine bacterial SAM-dependent chlorinase

Eustaquio, A.S.Pojer, F.Noel, J.P.Moore, B.S.

(2008) Nat Chem Biol 4: 69-74

  • DOI: https://doi.org/10.1038/nchembio.2007.56
  • Primary Citation of Related Structures:  
    2Q6I, 2Q6K, 2Q6L, 2Q6O

  • PubMed Abstract: 

    Halogen atom incorporation into a scaffold of bioactive compounds often amplifies biological activity, as is the case for the anticancer agent salinosporamide A (1), a chlorinated natural product from the marine bacterium Salinispora tropica. Significant effort in understanding enzymatic chlorination shows that oxidative routes predominate to form reactive electrophilic or radical chlorine species. Here we report the genetic, biochemical and structural characterization of the chlorinase SalL, which halogenates S-adenosyl-L-methionine (2) with chloride to generate 5'-chloro-5'-deoxyadenosine (3) and L-methionine (4) in a rarely observed nucleophilic substitution strategy analogous to that of Streptomyces cattleya fluorinase. Further metabolic tailoring produces a halogenated polyketide synthase substrate specific for salinosporamide A biosynthesis. SalL also accepts bromide and iodide as substrates, but not fluoride. High-resolution crystal structures of SalL and active site mutants complexed with substrates and products support the S(N)2 nucleophilic substitution mechanism and further illuminate halide specificity in this newly discovered halogenase family.


  • Organizational Affiliation

    Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. bsmoore@ucsd.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical protein285Salinispora tropica CNB-440Mutation(s): 2 
Gene Names: salL
UniProt
Find proteins for A4X3Q0 (Salinispora tropica (strain ATCC BAA-916 / DSM 44818 / JCM 13857 / NBRC 105044 / CNB-440))
Explore A4X3Q0 
Go to UniProtKB:  A4X3Q0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4X3Q0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5CD
Query on 5CD

Download Ideal Coordinates CCD File 
B [auth A]5'-CHLORO-5'-DEOXYADENOSINE
C10 H12 Cl N5 O3
IYSNPOMTKFZDHZ-KQYNXXCUSA-N
MET
Query on MET

Download Ideal Coordinates CCD File 
C [auth A]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.08α = 90
b = 111.08β = 90
c = 93.36γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description