3F5H

Crystal structure of fused docking domains from PikAIII and PikAIV of the pikromycin polyketide synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for binding specificity between subclasses of modular polyketide synthase docking domains.

Buchholz, T.J.Geders, T.W.Bartley, F.E.Reynolds, K.A.Smith, J.L.Sherman, D.H.

(2009) Acs Chem.Biol. 4: 41-52

  • DOI: 10.1021/cb8002607

  • PubMed Abstract: 
  • Bacterial type I polyketide synthases (PKSs) assemble structurally diverse natural products of significant clinical value from simple metabolic building blocks. The synthesis of these compounds occurs in a processive fashion along a large multiprotei ...

    Bacterial type I polyketide synthases (PKSs) assemble structurally diverse natural products of significant clinical value from simple metabolic building blocks. The synthesis of these compounds occurs in a processive fashion along a large multiprotein complex. Transfer of the acyl intermediate across interpolypeptide junctions is mediated, at least in large part, by N- and C-terminal docking domains. We report here a comprehensive analysis of the binding affinity and selectivity for the complete set of discrete docking domain pairs in the pikromycin and erythromycin PKS systems. Despite disconnection from their parent module, each cognate pair of docking domains retained exquisite binding selectivity. Further insights were obtained by X-ray crystallographic analysis of the PikAIII/PikAIV docking domain interface. This new information revealed a series of key interacting residues that enabled development of a structural model for the recently proposed H2-T2 class of polypeptides involved in PKS intermodular molecular recognition.


    Organizational Affiliation

    Life Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type I polyketide synthase PikAIII, Type I polyketide synthase PikAIV fusion protein
A, B
68Streptomyces venezuelaeMutation(s): 0 
Gene Names: pikAIII, pikAIV
EC: 2.3.1.239, 2.3.1.240 2.3.1.239, 2.3.1.240
Find proteins for Q9ZGI3 (Streptomyces venezuelae)
Go to UniProtKB:  Q9ZGI3
Find proteins for Q9ZGI2 (Streptomyces venezuelae)
Go to UniProtKB:  Q9ZGI2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 59.016α = 90.00
b = 117.944β = 90.00
c = 41.773γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
HKL-2000data collection
PDB_EXTRACTdata extraction
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-08-02
    Type: Refinement description, Source and taxonomy
  • Version 1.3: 2017-10-25
    Type: Refinement description