5A88

Crystal structure of the riboflavin kinase module of FAD synthetase from Corynebacterium ammoniagenes in complex with ADP

Summary for 5A88

• Entry DOI: 10.2210/pdb5a88/pdb
• Related: 5A89 5A8A
• Descriptor: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF, ADENOSINE-5'-DIPHOSPHATE, GLYCEROL, ... (5 entities in total)
• Functional Keywords: transferase, riboflavin kinase domain, atp-binding, nucleotide-binding
• Biological source: CORYNEBACTERIUM AMMONIAGENES
• Total number of polymer chains: 4
• Total formula weight: 70962.26

Authors

Herguedas, B.,Martinez-Julvez, M.,Hermoso, J.A.,Medina, M. (deposition date: 2015-07-13, release date: 2015-12-09, Last modification date: 2024-05-08)

Primary citation

Herguedas, B.,Lans, I.,Sebastian, M.,Hermoso, J.A.,Martinez-Julvez, M.,Medina, M.
Structural Insights Into the Synthesis of Fmn in Prokaryotic Organisms.
Acta Crystallogr.,Sect.D, 71:2526-, 2015

PubMed Abstract: Riboflavin kinases (RFKs) catalyse the phosphorylation of riboflavin to produce FMN. In most bacteria this activity is catalysed by the C-terminal module of a bifunctional enzyme, FAD synthetase (FADS), which also catalyses the transformation of FMN into FAD through its N-terminal FMN adenylyltransferase (FMNAT) module. The RFK module of FADS is a homologue of eukaryotic monofunctional RFKs, while the FMNAT module lacks homologyto eukaryotic enzymes involved in FAD production. Previously, the crystal structure of Corynebacterium ammoniagenes FADS (CaFADS) was determined in its apo form. This structure predicted a dimer-of-trimers organization with the catalytic sites of two modules of neighbouring protomers approaching each other, leading to a hypothesis about the possibility of FMN channelling in the oligomeric protein. Here, two crystal structures of the individually expressed RFK module of CaFADS in complex with the products of the reaction, FMN and ADP, are presented. Structures are complemented with computational simulations, binding studies and kinetic characterization. Binding of ligands triggers dramatic structural changes in the RFK module, which affect large portions of the protein. Substrate inhibition and molecular-dynamics simulations allowed the conformational changes that take place along the RFK catalytic cycle to be established. The influence of these conformational changes in the FMNAT module is also discussed in the context of the full-length CaFADS protomer and the quaternary organization.

PubMed: 26627660
DOI: 10.1107/S1399004715019641

Experimental method

X-RAY DIFFRACTION (2.08 Å)