2R0G

Chromopyrrolic acid-soaked RebC with bound 7-carboxy-K252c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallographic trapping in the rebeccamycin biosynthetic enzyme RebC

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

(2007) Proc.Natl.Acad.Sci.Usa 104: 15311-15316

  • DOI: 10.1073/pnas.0707190104
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The biosynthesis of rebeccamycin, an antitumor compound, involves the remarkable eight-electron oxidation of chlorinated chromopyrrolic acid. Although one rebeccamycin biosynthetic enzyme is capable of generating low levels of the eight-electron oxid ...

    The biosynthesis of rebeccamycin, an antitumor compound, involves the remarkable eight-electron oxidation of chlorinated chromopyrrolic acid. Although one rebeccamycin biosynthetic enzyme is capable of generating low levels of the eight-electron oxidation product on its own, a second protein, RebC, is required to accelerate product formation and eliminate side reactions. However, the mode of action of RebC was largely unknown. Using crystallography, we have determined a likely function for RebC as a flavin hydroxylase, captured two snapshots of its dynamic catalytic cycle, and trapped a reactive molecule, a putative substrate, in its binding pocket. These studies strongly suggest that the role of RebC is to sequester a reactive intermediate produced by its partner protein and to react with it enzymatically, preventing its conversion to a suite of degradation products that includes, at low levels, the desired product.


    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RebC
A, B
549Lechevalieria aerocolonigenesMutation(s): 0 
Gene Names: rbmD (rebC)
Find proteins for Q8KI25 (Lechevalieria aerocolonigenes)
Go to UniProtKB:  Q8KI25
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
7CK
Query on 7CK

Download SDF File 
Download CCD File 
A, B
7-carboxy-5-hydroxy-12,13-dihydro-6H-indolo[2,3-a]pyrrolo[3,4-c]carbazole
7-HYDROXY-12,13-DIHYDRO-6H-INDOLO[2,3-A]PYRROLO[3,4-C]CARBAZOLE-5-CARBOXYLIC ACID
C21 H13 N3 O3
LTOZELYBRTWMHC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.892α = 90.00
b = 78.437β = 99.61
c = 123.625γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
ADSCdata collection
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance