2QO3

Crystal Structure of [KS3][AT3] didomain from module 3 of 6-deoxyerthronolide B synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and mechanistic analysis of protein interactions in module 3 of the 6-deoxyerythronolide B synthase

Tang, Y.Chen, Y.A.Kim, C.Y.Cane, E.D.Khosla, C.

(2007) Chem.Biol. 14: 931-943

  • DOI: 10.1016/j.chembiol.2007.07.012

  • PubMed Abstract: 
  • We report the 2.6 A X-ray crystal structure of a 190 kDa homodimeric fragment from module 3 of the 6-deoxyerthronolide B synthase covalently bound to the inhibitor cerulenin. The structure shows two well-organized interdomain linker regions in additi ...

    We report the 2.6 A X-ray crystal structure of a 190 kDa homodimeric fragment from module 3 of the 6-deoxyerthronolide B synthase covalently bound to the inhibitor cerulenin. The structure shows two well-organized interdomain linker regions in addition to the full-length ketosynthase (KS) and acyltransferase (AT) domains. Analysis of the substrate-binding site of the KS domain suggests that a loop region at the homodimer interface influences KS substrate specificity. We also describe a model for the interaction of the catalytic domains with the acyl carrier protein (ACP) domain. The ACP is proposed to dock within a deep cleft between the KS and AT domains, with interactions that span both the KS homodimer and AT domain. In conjunction with other recent data, our results provide atomic resolution pictures of several catalytically relevant protein interactions in this remarkable family of modular megasynthases.


    Related Citations: 
    • Structure-based dissociation of a type I polyketide synthase module
      Chen, Y.A.,Cane, E.D.,Khosla, C.
      (2007) Chem.Biol. 14: 784
    • The 2.7-Angstrom crystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase
      Tang, Y.,Kim, C.Y.,Mathews, I.I.,Cane, E.D.,Khosla, C.
      (2006) Proc.Natl.Acad.Sci.Usa 103: 11124
    • Reconstituting modular activity from separated domains of 6-deoxyerythronolide B synthase
      Kim, C.Y.,Alekseyev, V.Y.,Chen, Y.A.,Tang, Y.,Cane, E.D.,Khosla, C.
      (2004) Biochemistry 43: 13892


    Organizational Affiliation

    Department of Chemistry, Keck Building, Stanford University, Stanford, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EryAII Erythromycin polyketide synthase modules 3 and 4
A, B
915Saccharopolyspora erythraeaMutation(s): 0 
Gene Names: eryA
EC: 2.3.1.94
Find proteins for Q03132 (Saccharopolyspora erythraea)
Go to UniProtKB:  Q03132
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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

Download SDF File 
Download CCD File 
A, B
(2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE
CERULENIN
C12 H19 N O3
QEPYZBPOTYDXNA-FECJWDPASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 75.203α = 90.00
b = 139.005β = 106.14
c = 102.342γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance