2B99

Crystal Structure of an archaeal pentameric riboflavin synthase Complex with a Substrate analog inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of an Archaeal Pentameric Riboflavin Synthase in Complex with a Substrate Analog Inhibitor: stereochemical implications

Ramsperger, A.Augustin, M.Schott, A.K.Gerhardt, S.Krojer, T.Eisenreich, W.Illarionov, B.Cushman, M.Bacher, A.Huber, R.Fischer, M.

(2006) J Biol Chem 281: 1224-1232

  • DOI: 10.1074/jbc.M509440200
  • Primary Citation of Related Structures:  
    2B99, 2B98

  • PubMed Abstract: 
  • Whereas eubacterial and eukaryotic riboflavin synthases form homotrimers, archaeal riboflavin synthases from Methanocaldococcus jannaschii and Methanothermobacter thermoautrophicus are homopentamers with sequence similarity to the 6,7-dimethyl-8-ribityllumazine synthase catalyzing the penultimate step in riboflavin biosynthesis ...

    Whereas eubacterial and eukaryotic riboflavin synthases form homotrimers, archaeal riboflavin synthases from Methanocaldococcus jannaschii and Methanothermobacter thermoautrophicus are homopentamers with sequence similarity to the 6,7-dimethyl-8-ribityllumazine synthase catalyzing the penultimate step in riboflavin biosynthesis. Recently it could be shown that the complex dismutation reaction catalyzed by the pentameric M. jannaschii riboflavin synthase generates riboflavin with the same regiochemistry as observed for trimeric riboflavin synthases. Here we present crystal structures of the pentameric riboflavin synthase from M. jannaschii and its complex with the substrate analog inhibitor, 6,7-dioxo-8-ribityllumazine. The complex structure shows five active sites located between adjacent monomers of the pentamer. Each active site can accommodate two substrate analog molecules in anti-parallel orientation. The topology of the two bound ligands at the active site is well in line with the known stereochemistry of a pentacyclic adduct of 6,7-dimethyl-8-ribityllumazine that has been shown to serve as a kinetically competent intermediate. The pentacyclic intermediates of trimeric and pentameric riboflavin synthases are diastereomers.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung für Strukturforschung, Martinsried, Germany. ramsperg@biochem.mpg.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Riboflavin synthaseA, B, C, D, E156Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: ribC
EC: 2.5.1.9
Find proteins for Q58584 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58584 
Go to UniProtKB:  Q58584
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RDL
Query on RDL

Download CCD File 
A, B, C, D, E
6,7-DIOXO-5H-8-RIBITYLAMINOLUMAZINE
C11 H14 N4 O8
MIBROOURCUHKMD-RPDRRWSUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.94α = 68.5
b = 72.912β = 74.39
c = 72.782γ = 74.53
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance