3PQB

The crystal structure of pregilvocarcin in complex with GilR, an oxidoreductase that catalyzes the terminal step of gilvocarcin biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.324 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Crystal Structure and Mechanism of an Unusual Oxidoreductase, GilR, Involved in Gilvocarcin V Biosynthesis.

Noinaj, N.Bosserman, M.A.Schickli, M.A.Piszczek, G.Kharel, M.K.Pahari, P.Buchanan, S.K.Rohr, J.

(2011) J.Biol.Chem. 286: 23533-23543

  • DOI: 10.1074/jbc.M111.247833
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • GilR is a recently identified oxidoreductase that catalyzes the terminal step of gilvocarcin V biosynthesis and is a unique enzyme that establishes the lactone core of the polyketide-derived gilvocarcin chromophore. Gilvocarcin-type compounds form a ...

    GilR is a recently identified oxidoreductase that catalyzes the terminal step of gilvocarcin V biosynthesis and is a unique enzyme that establishes the lactone core of the polyketide-derived gilvocarcin chromophore. Gilvocarcin-type compounds form a small distinct family of anticancer agents that are involved in both photo-activated DNA-alkylation and histone H3 cross-linking. High resolution crystal structures of apoGilR and GilR in complex with its substrate pregilvocarcin V reveals that GilR belongs to the small group of a relatively new type of the vanillyl-alcohol oxidase flavoprotein family characterized by bicovalently tethered cofactors. GilR was found as a dimer, with the bicovalently attached FAD cofactor mediated through His-65 and Cys-125. Subsequent mutagenesis and functional assays indicate that Tyr-445 may be involved in reaction catalysis and in mediating the covalent attachment of FAD, whereas Tyr-448 serves as an essential residue initiating the catalysis by swinging away from the active site to accommodate binding of the 6R-configured substrate and consequently abstracting the proton of the hydroxyl residue of the substrate hemiacetal 6-OH group. These studies lay the groundwork for future enzyme engineering to broaden the substrate specificity of this bottleneck enzyme of the gilvocarcin biosynthetic pathway for the development of novel anti-cancer therapeutics.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative oxidoreductase
A, B, C, D
501Streptomyces griseoflavusMutation(s): 0 
Gene Names: gilR
Find proteins for Q7X2G7 (Streptomyces griseoflavus)
Go to UniProtKB:  Q7X2G7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VGP
Query on VGP

Download SDF File 
Download CCD File 
A, B, C, D
(1R)-1,4-anhydro-6-deoxy-1-[(6R)-8-ethenyl-1,6-dihydroxy-10,12-dimethoxy-6H-dibenzo[c,h]chromen-4-yl]-D-galactitol
pregilvocarcin V
C27 H28 O9
YVGUIYUDGGDTSX-ZDRXMRRKSA-N
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.324 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.003α = 90.00
b = 115.973β = 90.00
c = 291.405γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-03
    Type: Database references