4EIP | pdb_00004eip

Native and K252c bound RebC-10x


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 
    0.260 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view detailsBest fitted K2CClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

An Unusual Role for a Mobile Flavin in StaC-like Indolocarbazole Biosynthetic Enzymes.

Goldman, P.J.Ryan, K.S.Hamill, M.J.Howard-Jones, A.R.Walsh, C.T.Elliott, S.J.Drennan, C.L.

(2012) Chem Biol 19: 855-865

  • DOI: https://doi.org/10.1016/j.chembiol.2012.05.016
  • Primary Citation of Related Structures:  
    4EIP, 4EIQ

  • PubMed Abstract: 

    The indolocarbazole biosynthetic enzymes StaC, InkE, RebC, and AtmC mediate the degree of oxidation of chromopyrrolic acid on route to the natural products staurosporine, K252a, rebeccamycin, and AT2433-A1, respectively. Here, we show that StaC and InkE, which mediate a net 4-electron oxidation, bind FAD with a micromolar K(d), whereas RebC and AtmC, which mediate a net 8-electron oxidation, bind FAD with a nanomolar K(d) while displaying the same FAD redox properties. We further create RebC-10x, a RebC protein with ten StaC-like amino acid substitutions outside of previously characterized FAD-binding motifs and the complementary StaC-10x. We find that these mutations mediate both FAD affinity and product specificity, with RebC-10x displaying higher StaC activity than StaC itself. X-ray structures of this StaC catalyst identify the substrate of StaC as 7-carboxy-K252c and suggest a unique mechanism for this FAD-dependent enzyme.


  • Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative FAD-monooxygenase
A, B
549Lentzea aerocolonigenesMutation(s): 10 
Gene Names: rbmDrebC
UniProt
Find proteins for Q8KI25 (Lentzea aerocolonigenes)
Explore Q8KI25 
Go to UniProtKB:  Q8KI25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KI25
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free:  0.260 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.305α = 90
b = 78.593β = 99.87
c = 125.723γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
APEXdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view detailsBest fitted K2CClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations