PDBsum entry 2ccc

Flavoprotein

PDB id: 2ccc

Contents

Protein chain

64 a.a. *

Ligands

LFN

SO4

Metals

_MG ×2

_NA

_CL

Waters ×80

* Residue conservation analysis

PDB id:

2ccc

Name:

Flavoprotein

Title:

Complexes of dodecin with flavin and flavin-like ligands

Structure:

Vng1446h. Chain: a. Synonym: dodecin. Engineered: yes. Other_details: lumiflavin bound

Source:

Halobacterium salinarum. Organism_taxid: 478009. Strain: r1. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: german collection of microorganisms (dsm 671)

Biol. unit:

Dodecamer (from PDB file)

Resolution:

1.70Å R-factor: 0.185 R-free: 0.202

Authors:

M.Grininger,K.Zeth,D.Oesterhelt

Key ref:

M.Grininger et al. (2006). Dodecins: a family of lumichrome binding proteins. J Mol Biol, 357, 842-857. PubMed id: 16460756 DOI: 10.1016/j.jmb.2005.12.072

Date:

13-Jan-06 Release date: 31-Jan-06

Protein chain

B0R5M0  (DODEC_HALS3) -  Dodecin from Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1)

Seq: 68 a.a.

Struc: 64 a.a.

DOI no: 10.1016/j.jmb.2005.12.072

J Mol Biol 357:842-857 (2006)

PubMed id: 16460756

Dodecins: a family of lumichrome binding proteins.

M.Grininger, K.Zeth, D.Oesterhelt.

ABSTRACT

Dodecin is a small dodecameric flavoprotein from Halobacterium salinarum that contains two flavins stacked between two tryptophan residues to form an aromatic tetrade. The functional properties of heterologously expressed dodecin were investigated by fluorescence spectroscopy, which allowed the determination of dissociation constants for a number of protein-ligand complexes. The values obtained were in the nanomolar to micromolar range and correlate positively with the ligand size. These data were supplemented by X-ray crystal structures of the apododecin and holocomplexes with lumichrome, lumiflavin, riboflavin and FMN at resolutions between 1.55 to 1.95A to unravel a gating mechanism as the structural basis for the preferential binding of the small ligands lumichrome and lumiflavin. The detailed analysis of the dodecin manifold for preferential binding of lumichrome and lumiflavin provides insight on a subatom level into a protein's strategy to gain selectivity for low molecular mass compounds by steric restrictions rather than specific interactions. Investigations on the ligand composition of a wild-type dodecin crystal (1.32A resolution) support conclusions of functional and structural investigations on heterologously expressed dodecin, and strongly suggest that lumichrome, a molecule associated with the flavin metabolism, is a ligand of dodecin in vivo. Studies on mutant protein and a Halorhodospira halophila homologue spread the idea of a lumichrome binding system as a possible "waste"-trapping device, widely distributed in prokaryotes.

Selected figure(s)

Figure 1.
Figure 1. The riboflavin holocomplex. Surface representation of dodecin with the section through the holocomplex along a C2 axis uncovers the dodecin binding pocket. H-bonds are represented by red dotted lines. The residues (Trp36 and Gln55) mediate binding of the isoalloxazine ring; H-bonds between Glu45 and the ribityl chain (O2' and O3') as well as Val35 and O2' direct the aliphatic moiety towards the outer surface. Due to an intramolecular interaction (O4'-N1), the ribityl chain conformation is stabilized up to the O4' atom.

Figure 3.
Figure 3. Overall structure of H. salinarum dodecin. (a) View along the 3-fold axis. The monomer is highlighted through its corresponding molecular surface. Monomers of a trimer are held in red, green and blue, the ligand (riboflavin) is colored in gold. Heteroatoms of residues important for binding as well as of the ligand are colored red (O) and blue (N). b2-Strands of the monomers mediate the contacts in the trimer extending to a five-stranded antiparallel b-sheet. Four trimers are arranged in a dodecamer of 23-cubic symmetry. (b) and (c) View on the arrangement of two trimers along the 2-fold axis. In (b) one trimer is highlighted through its corresponding molecular surface. In the riboflavin holocomplex (H-RBF) a dimer of riboflavin is embedded between the indole groups of tryptophan (Trp36) with their ribityl chain pointing towards the outer surface. Monomers of a dodecameric assembly are marked by superscript alphabetic characters.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 357, 842-857) copyright 2006.

Figures were selected by an automated process.