PDBsum entry: 2f59

Transferase

PDB id: 2f59

Contents

Protein chains

146 a.a. *

Ligands

INI ×5

Metals

_CA ×6

Waters ×219

* Residue conservation analysis

PDB id:

2f59

Name:

Transferase

Title:

Lumazine synthase ribh1 from brucella abortus (gene bruab1_0 swiss-prot entry q57dy1) complexed with inhibitor 5-nitro-6 ribitylamino)-2,4(1h,3h) pyrimidinedione

Structure:

6,7-dimethyl-8-ribityllumazine synthase 1. Chain: a, b, c, d, e. Synonym: dmrl synthase 1, lumazine synthase 1, riboflavin s beta chain. Engineered: yes

Source:

Brucella abortus. Organism_taxid: 235. Gene: ribh1, ribh, ribh-1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Pentamer (from PQS)

Resolution:

2.30Å R-factor: 0.217 R-free: 0.241

Authors:

S.Klinke,V.Zylberman,H.R.Bonomi,I.Haase,B.G.Guimaraes,B.C.Br A.Bacher,M.Fischer,F.A.Goldbaum

Key ref:

S.Klinke et al. (2007). Structural and kinetic properties of lumazine synthase isoenzymes in the order Rhizobiales. J Mol Biol, 373, 664-680. PubMed id: 17854827 DOI: 10.1016/j.jmb.2007.08.021

Date:

25-Nov-05 Release date: 28-Nov-06

Protein chains

Q57DY1  (RISB1_BRUAB) -  6,7-dimethyl-8-ribityllumazine synthase 1

Seq: 157 a.a.

Struc: 146 a.a.

Enzyme reactions

• Enzyme class: E.C.2.5.1.9 - Riboflavin synthase.
• Reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D- ribitylamino)-5-amino-2,6-dihydroxypyrimidine

2 × 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D- ribitylamino)-5-amino-2,6-dihydroxypyrimidine (Bound ligand (Het Group name = INI) matches with 90.48% similarity)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: riboflavin synthase complex (1 term)
• Biological process: riboflavin biosynthetic process (1 term)
• Biochemical function: transferase activity (2 terms)

Added reference

DOI no: 10.1016/j.jmb.2007.08.021

J Mol Biol 373:664-680 (2007)

PubMed id: 17854827

Structural and kinetic properties of lumazine synthase isoenzymes in the order Rhizobiales.

S.Klinke, V.Zylberman, H.R.Bonomi, I.Haase, B.G.Guimarães, B.C.Braden, A.Bacher, M.Fischer, F.A.Goldbaum.

ABSTRACT

6,7-Dimethyl-8-ribityllumazine synthase (lumazine synthase; LS) catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. This protein is known to exhibit different quaternary assemblies between species, existing as free pentamers, decamers (dimers of pentamers) and icosahedrally arranged dodecamers of pentamers. A phylogenetic analysis on eubacterial, fungal and plant LSs allowed us to classify them into two categories: Type I LSs (pentameric or icosahedral) and Type II LSs (decameric). The Rhizobiales represent an order of alpha-proteobacteria that includes, among others, the genera Mesorhizobium, Agrobacterium and Brucella. Here, we present structural and kinetic studies on several LSs from Rhizobiales. Interestingly, Mesorhizobium and Brucella encode both a Type-I LS and a Type-II LS called RibH1 and RibH2, respectively. We show that Type II LSs appear to be almost inactive, whereas Type I LSs present a highly variable catalytic activity according to the genus. Additionally, we have solved four RibH1/RibH2 crystallographic structures from the genera Mesorhizobium and Brucella. The relationship between the active-site architecture and catalytic properties in these isoenzymes is discussed, and a model that describes the enzymatic behavior is proposed. Furthermore, sequence alignment studies allowed us to extend our results to the genus Agrobacterium. Our results suggest that the selective pressure controlling the riboflavin pathway favored the evolution of catalysts with low reaction rates, since the excess of flavins in the intracellular pool in Rhizobiales could act as a negative factor when these bacteria are exposed to oxidative or nitrosative stress.

Selected figure(s)

Figure 1.
Fig. 1. Reactions involved in the riboflavin biosynthesis pathway. 1, 5-Amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione; 2, 3,4-dihydroxy-2-butanone 4-phosphate; 3, 6,7-dimethyl-8-ribityllumazine; 4, riboflavin; BPS, 3,4-dihydroxy-2-butanone 4-phosphate synthase; LS, 6,7-dimethyl-8-ribityllumazine synthase (reaction highlighted on gray background); RS, riboflavin synthase (dismutation reaction).

Figure 3.
Fig. 3. Schematic representation of the hydrophilic interactions between NRP and LS in the complex structures RibH2-Mlo-NRP (residue atoms in blue) and RibH1-Bab-NRP and RibH1-Bme-NRP (residue atoms in red). The contact with residue Lys137′ is only valid in RibH1-Bab-NRP. Numbers near the ligand atoms correspond to the nomenclature used in the Protein Data Bank structures.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 373, 664-680) copyright 2007.

Figures were selected by an automated process.