1SJW

Structure of polyketide cyclase SnoaL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation.

Sultana, A.Kallio, P.Jansson, A.Wang, J.S.Niemi, J.Schneider, G.

(2004) Embo J. 23: 1911-1921

  • DOI: 10.1038/sj.emboj.7600201

  • PubMed Abstract: 
  • SnoaL belongs to a family of small polyketide cyclases, which catalyse ring closure steps in the biosynthesis of polyketide antibiotics produced in Streptomyces. Several of these antibiotics are among the most used anti-cancer drugs currently in use. ...

    SnoaL belongs to a family of small polyketide cyclases, which catalyse ring closure steps in the biosynthesis of polyketide antibiotics produced in Streptomyces. Several of these antibiotics are among the most used anti-cancer drugs currently in use. The crystal structure of SnoaL, involved in nogalamycin biosynthesis, with a bound product, has been determined to 1.35 A resolution. The fold of the subunit can be described as a distorted alpha+beta barrel, and the ligand is bound in the hydrophobic interior of the barrel. The 3D structure and site-directed mutagenesis experiments reveal that the mechanism of the intramolecular aldol condensation catalysed by SnoaL is different from that of the classical aldolases, which employ covalent Schiff base formation or a metal ion cofactor. The invariant residue Asp121 acts as an acid/base catalyst during the reaction. Stabilisation of the enol(ate) intermediate is mainly achieved by the delocalisation of the electron pair over the extended pi system of the substrate. These polyketide cyclases thus form of family of enzymes with a unique catalytic strategy for aldol condensation.


    Related Citations: 
    • Crystallization and preliminary crystallographic data of SnoaL, a polyketide cyclase in nogalamycin biosynthesis
      Sultana, A.,Kallio, P.,Jansson, A.,Neimi, J.,Mantsala, P.,Schneider, G.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
nogalonic acid methyl ester cyclase
A
144Streptomyces nogalaterMutation(s): 0 
Gene Names: snoaL
Find proteins for Q9RN59 (Streptomyces nogalater)
Go to UniProtKB:  Q9RN59
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGV
Query on NGV

Download SDF File 
Download CCD File 
A
METHYL 5,7-DIHYDROXY-2-METHYL-4,6,11-TRIOXO-3,4,6,11-TETRAHYDROTETRACENE-1-CARBOXYLATE
NOGALAVIKETONE
C21 H14 O7
QHNJNOBWURJIEK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.143 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 69.100α = 90.00
b = 72.000β = 90.00
c = 65.400γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SHELXLrefinement
ARP/wARPmodel building
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Data collection, Refinement description