4QYR

Streptomyces platensis isomigrastatin ketosynthase domain MgsE KS3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.902 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and evolutionary relationships of "AT-less" type I polyketide synthase ketosynthases.

Lohman, J.R.Ma, M.Osipiuk, J.Nocek, B.Kim, Y.Chang, C.Cuff, M.Mack, J.Bigelow, L.Li, H.Endres, M.Babnigg, G.Joachimiak, A.Phillips, G.N.Shen, B.

(2015) Proc.Natl.Acad.Sci.USA 112: 12693-12698

  • DOI: 10.1073/pnas.1515460112
  • Primary Citation of Related Structures:  4OPF, 4OQJ, 4TKT, 4WKY, 4ZDN, 4OPE

  • PubMed Abstract: 
  • Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, ...

    Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representation of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. One set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs.


    Organizational Affiliation

    Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AT-less polyketide synthase
A
615Streptomyces platensis subsp. rosaceusN/A
Find proteins for D0U2E3 (Streptomyces platensis subsp. rosaceus)
Go to UniProtKB:  D0U2E3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.902 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.151 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 145.418α = 90.00
b = 145.418β = 90.00
c = 67.718γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-3000phasing
PHENIXmodel building
HKL-3000data collection
MOLREPphasing
PHENIXrefinement
HKL-3000data reduction
SBC-Collectdata collection
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-08-27
    Type: Structure summary
  • Version 1.2: 2016-11-16
    Type: Database references
  • Version 1.3: 2016-12-07
    Type: Structure summary