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 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    2QO3

  • 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 addition to the full-length ketosynthase (KS) and acyltransferase (AT) domains ...

    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 U S A 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EryAII Erythromycin polyketide synthase modules 3 and 4A, B915Saccharopolyspora erythraeaMutation(s): 0 
Gene Names: eryAII, eryA
EC: 2.3.1.94
UniProt
Find proteins for Q03132 (Saccharopolyspora erythraea)
Explore Q03132 
Go to UniProtKB:  Q03132
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03132
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CER
Query on CER
Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]		(2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE
C12 H19 N O3
QEPYZBPOTYDXNA-FECJWDPASA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 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 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.203α = 90
b = 139.005β = 106.14
c = 102.342γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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