4ZDN

Streptomyces platensis isomigrastatin ketosynthase domain MgsF KS4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1073/pnas.1515460112
  • Structures With Same Primary Citation

  • 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; Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458; Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL 33458 shenb@scripps.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AT-less polyketide synthaseA639Streptomyces platensis subsp. rosaceusMutation(s): 0 
Find proteins for D0U2E4 (Streptomyces platensis subsp. rosaceus)
Explore D0U2E4 
Go to UniProtKB:  D0U2E4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.685α = 90
b = 126.685β = 90
c = 143.681γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-3000data reduction
HKL-3000phasing
SBC-Collectdata collection

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Derived calculations, Structure summary