Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 90.93 kDa 
• Atom Count: 6187 
• Residue Count: 734 
• Unique protein chains: 1

2B99

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

• DOI: 10.2210/pdb2B99/pdb

• Classification: TRANSFERASE
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-10-11 Released: 2005-11-08 
• Deposition Author(s): Ramsperger, A., Augustin, M., Schott, A.K., Gerhardt, S., Krojer, T., Eisenreich, W., Illarionov, B., Cushman, M., Bacher, A., Huber, R., Fischer, M.

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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 

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

• PubMed: 16272154 
• 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. 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.

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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, Abteilung für Strukturforschung, Martinsried, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Riboflavin synthase	A, B, C, D, E	156	Methanocaldococcus jannaschii	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RDL	A, B, C, D, E	6,7-DIOXO-5H-8-RIBITYLAMINOLUMAZINE C11 H14 N4 O8 MIBROOURCUHKMD-RPDRRWSUSA-N

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 = 41.94	α = 68.5
b = 72.912	β = 74.39
c = 72.782	γ = 74.53

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-11 
• Released Date: 2005-11-08 
Deposition Author(s): Ramsperger, A., Augustin, M., Schott, A.K., Gerhardt, S., Krojer, T., Eisenreich, W., Illarionov, B., Cushman, M., Bacher, A., Huber, R., Fischer, M.

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