4QYR

Streptomyces platensis isomigrastatin ketosynthase domain MgsE KS3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.6 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 U S A 112: 12693-12698

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

  • 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, 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AT-less polyketide synthase615Streptomyces platensis subsp. rosaceusMutation(s): 0 
UniProt
Find proteins for D0U2E3 (Streptomyces platensis subsp. rosaceus)
Explore D0U2E3 
Go to UniProtKB:  D0U2E3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0U2E3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.418α = 90
b = 145.418β = 90
c = 67.718γ = 120
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIXmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-08-27
    Changes: Structure summary
  • Version 1.2: 2016-11-16
    Changes: Database references
  • Version 1.3: 2016-12-07
    Changes: Structure summary
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2023-12-06
    Changes: Data collection
  • Version 1.6: 2024-11-27
    Changes: Structure summary