4OVM

Crystal structure of SgcJ protein from Streptomyces carzinostaticus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027.

Huang, T.Chang, C.Y.Lohman, J.R.Rudolf, J.D.Kim, Y.Chang, C.Yang, D.Ma, M.Yan, X.Crnovcic, I.Bigelow, L.Clancy, S.Bingman, C.A.Yennamalli, R.M.Babnigg, G.Joachimiak, A.Phillips, G.N.Shen, B.

(2016) J Antibiot (Tokyo) 

  • DOI: https://doi.org/10.1038/ja.2016.88
  • Primary Citation of Related Structures:  
    4I4K, 4OVM

  • PubMed Abstract: 

    Comparative analysis of the enediyne biosynthetic gene clusters revealed sets of conserved genes serving as outstanding candidates for the enediyne core. Here we report the crystal structures of SgcJ and its homologue NCS-Orf16, together with gene inactivation and site-directed mutagenesis studies, to gain insight into enediyne core biosynthesis. Gene inactivation in vivo establishes that SgcJ is required for C-1027 production in Streptomyces globisporus. SgcJ and NCS-Orf16 share a common structure with the nuclear transport factor 2-like superfamily of proteins, featuring a putative substrate binding or catalytic active site. Site-directed mutagenesis of the conserved residues lining this site allowed us to propose that SgcJ and its homologues may play a catalytic role in transforming the linear polyene intermediate, along with other enediyne polyketide synthase-associated enzymes, into an enzyme-sequestered enediyne core intermediate. These findings will help formulate hypotheses and design experiments to ascertain the function of SgcJ and its homologues in nine-membered enediyne core biosynthesis.


  • Organizational Affiliation

    Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
uncharacterized protein SgcJ
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
144Streptomyces carzinostaticus subsp. neocarzinostaticusMutation(s): 0 
UniProt
Find proteins for Q84HC7 (Streptomyces carzinostaticus subsp. neocarzinostaticus)
Explore Q84HC7 
Go to UniProtKB:  Q84HC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84HC7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.318α = 90
b = 52.827β = 90.14
c = 131.796γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXrefinement
HKL-3000phasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Structure summary
  • Version 1.2: 2014-04-23
    Changes: Other, Structure summary
  • Version 1.3: 2014-08-06
    Changes: Database references, Structure summary
  • Version 1.4: 2015-02-25
    Changes: Derived calculations
  • Version 1.5: 2016-11-02
    Changes: Database references, Other, Structure summary
  • Version 1.6: 2017-09-27
    Changes: Derived calculations
  • Version 1.7: 2023-03-22
    Changes: Database references, Structure summary