PDBsum entry 2isl

Flavoprotein

PDB id: 2isl

Contents

Protein chains

(+ 2 more) 219 a.a. *

Ligands

FNR ×8

OXY ×8

Waters ×63

* Residue conservation analysis

PDB id:

2isl

Name:

Flavoprotein

Title:

Blub bound to reduced flavin (fmnh2) and molecular oxygen. (Clear crystal form)

Structure:

Blub. Chain: a, b, c, d, e, f, g, h. Engineered: yes

Source:

Sinorhizobium meliloti. Organism_taxid: 382. Gene: blub. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.90Å R-factor: 0.217 R-free: 0.285

Authors:

N.A.Larsen,M.E.Taga,A.R.Howard-Jones,C.T.Walsh,G.C.Walker

Key ref:

M.E.Taga et al. (2007). BluB cannibalizes flavin to form the lower ligand of vitamin B12. Nature, 446, 449-453. PubMed id: 17377583 DOI: 10.1038/nature05611

Date:

17-Oct-06 Release date: 27-Mar-07

Protein chains

Q92PC8  (BLUB_RHIME) -  5,6-dimethylbenzimidazole synthase from Rhizobium meliloti (strain 1021)

Seq: 227 a.a.

Struc: 219 a.a.

Enzyme reactions

• Enzyme class: E.C.1.13.11.79 - aerobic 5,6-dimethylbenzimidazole synthase.
• Reaction: FMNH2 + O2 = dialurate + 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + H⁺

FMNH2 (Bound ligand (Het Group name = FNR) corresponds exactly) + O2 (Bound ligand (Het Group name = OXY) corresponds exactly) = dialurate + 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nature05611

Nature 446:449-453 (2007)

PubMed id: 17377583

BluB cannibalizes flavin to form the lower ligand of vitamin B12.

M.E.Taga, N.A.Larsen, A.R.Howard-Jones, C.T.Walsh, G.C.Walker.

ABSTRACT

Vitamin B12 (cobalamin) is among the largest known non-polymeric natural products, and the only vitamin synthesized exclusively by microorganisms. The biosynthesis of the lower ligand of vitamin B(12), 5,6-dimethylbenzimidazole (DMB), is poorly understood. Recently, we discovered that a Sinorhizobium meliloti gene, bluB, is necessary for DMB biosynthesis. Here we show that BluB triggers the unprecedented fragmentation and contraction of the bound flavin mononucleotide cofactor and cleavage of the ribityl tail to form DMB and D-erythrose 4-phosphate. Our structural analysis shows that BluB resembles an NAD(P)H-flavin oxidoreductase, except that its unusually tight binding pocket accommodates flavin mononucleotide but not NAD(P)H. We characterize crystallographically an early intermediate along the reaction coordinate, revealing molecular oxygen poised over reduced flavin. Thus, BluB isolates and directs reduced flavin to activate molecular oxygen for its own cannibalization. This investigation of the biosynthesis of DMB provides clarification of an aspect of vitamin B12 that was otherwise incomplete, and may contribute to a better understanding of vitamin B12-related disease.

Selected figure(s)

Figure 2.
Figure 2: Structure of BluB. a, Ribbon diagram of BluB with FMN in the binding pocket (stick representation). The two-fold axis is perpendicular to the plane of the figure. b, E. coli nitroreductase NfsB (Protein Data Bank 1ICR)^21 with FMN and nicotinic acid (stick representation) in the binding pocket. c, Cross-section of BluB's molecular surface. The two-fold axis lies along the y axis such that the si-face of FMN is viewed on the left and re-face on the right. The surface is coloured according to electrostatic potential, where blue is electropositive, red is electronegative and k[B] is Boltzmann's constant. The back and front of the surface are cut away to reveal the FMN binding pocket buried in the dimer interface. The pocket wraps snugly around FMN, preventing interaction with other substrates. d, The BluB ribbon diagram has been coloured according to B-factor. Red represents flexible regions that may control or gate access to the active site.

Figure 3.
Figure 3: Active site of BluB. a, b, The active site with oxidized FMN (a) and reduced FMN (b), viewed from the re-face. H-bonds are represented as dashed lines. For clarity, water molecules are not rendered in this view. The rearrangement in H-bonds around N1 reflects the change in protonation in the reduced structure. Asp 32 may also form a close contact with C1' of the ribityl chain, suggesting a potential catalytic role for this residue. c, d, Side views of the active site in the oxidized (c) and reduced (d) structures. For clarity, Arg 34 has not been rendered in this view. The sigma-A weighted 2F[o]-F[c] electron density map is contoured at 1 and coloured grey (around protein side chains), blue (around FMN/FMNH[2]) and red (around water/oxygen) to enhance contrast.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 446, 449-453) copyright 2007.

Figures were selected by an automated process.