5MJI | pdb_00005mji

Crystal Structure of RosB with bound intermediate OHC-RP (8-demethyl-8-formylriboflavin-5'-phosphate)

• PDB DOI: https://doi.org/10.2210/pdb5MJI/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Streptomyces davaonensis JCM 4913
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-01 Released: 2016-12-28 
• Deposition Author(s): Konjik, V., Bruenle, S., Demmer, U., Vanselow, A., Sandhoff, R., Mack, M., Ermler, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

The Crystal Structure of RosB: Insights into the Reaction Mechanism of the First Member of a Family of Flavodoxin-like Enzymes.

Konjik, V., Brunle, S., Demmer, U., Vanselow, A., Sandhoff, R., Ermler, U., Mack, M.

(2017) Angew Chem Int Ed Engl 56: 1146-1151

• PubMed: 27981706 
• DOI: https://doi.org/10.1002/anie.201610292
• Primary Citation Related Structures: 
  5MJI


• PubMed Abstract: 
  

  8-demethyl-8-aminoriboflavin-5'-phosphate (AFP) synthase (RosB) catalyzes the key reaction of roseoflavin biosynthesis by forming AFP from riboflavin-5'-phosphate (RP) and glutamate via the intermediates 8-demethyl-8-formylriboflavin-5'-phosphate (OHC-RP) and 8-demethyl-8-carboxylriboflavin-5'-phosphate (HO ₂ C-RP). To understand this reaction in which a methyl substituent of an aromatic ring is replaced by an amine we structurally characterized RosB in complex with OHC-RP (2.0 Å) and AFP (1.7 Å). RosB is composed of four flavodoxin-like subunits which have been upgraded with specific extensions and a unique C-terminal arm. It appears that RosB has evolved from an electron- or hydride-transferring flavoprotein to a sophisticated multi-step enzyme which uses RP as a substrate (and not as a cofactor). Structure-based active site analysis was complemented by mutational and isotope-based mass-spectrometric data to propose an enzymatic mechanism on an atomic basis.

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Organizational Affiliation: 
• Mannheim University of Applied Sciences, Paul-Wittsack-Strasse 10, 68163, Mannheim, Germany.
Max-Planck-Institute for Biophysics, Max-von-Laue-Strasse 3, 60438, Frankfurt am Main, Germany.
German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 29.37 kDa 
• Atom Count: 2,203 
• Modeled Residue Count: 252 
• Deposited Residue Count: 257 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BRAMP domain protein	A	257	Streptomyces davaonensis JCM 4913	Mutation(s): 0  Gene Names: BN159_7989 EC: 2.6.1.114
UniProt
Find proteins for K4REZ6 (Streptomyces davaonensis (strain DSM 101723 / JCM 4913 / KCC S-0913 / 768)) Explore K4REZ6  Go to UniProtKB:  K4REZ6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7O6	B [auth A]	[(2~{S},3~{R},4~{R})-5-[8-methanoyl-7-methyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-ium-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate C17 H20 N4 O10 P TZAPMZFMEMVUSE-MBNYWOFBSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.47	α = 90
b = 108.47	β = 90
c = 178.22	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-28 
Deposition Author(s): Konjik, V., Bruenle, S., Demmer, U., Vanselow, A., Sandhoff, R., Mack, M., Ermler, U.

Revision History  

• Version 1.0: 2016-12-28
  Type: Initial release
  
• Version 1.1: 2017-01-25
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references