Prokaryotic riboflavin biosynthesis protein

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FAD synthetase
PDB 1s4m EBI.jpg
crystal structure of flavin binding to fad synthetase from thermotoga maritina
Identifiers
SymbolFAD_syn
Pfam PF06574
Pfam clan CL0119
InterPro IPR015864
SCOP2 1n05 / SCOPe / SUPFAM
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary

The prokaryotic riboflavin biosynthesis protein is a bifunctional enzyme found in bacteria that catalyzes the phosphorylation of riboflavin into flavin mononucleotide (FMN) and the adenylylation of FMN into flavin adenine dinucleotide (FAD). It consists of a C-terminal riboflavin kinase and an N-terminal FMN-adenylyltransferase. This bacterial protein is functionally similar to the monofunctional riboflavin kinases and FMN-adenylyltransferases of eukaryotic organisms, but only the riboflavin kinases are structurally homologous.

Contents

Structure

Prokaryotic riboflavin biosynthesis proteins are also known as the prokaryotic type-I FAD synthetases, which consist of a C-terminal riboflavin kinase (RFK) and an N-terminal FMN-adenylyltransferase (FMNAT). The globular RFK consists of six antiparallel β-sheets that form a β-barrel, and an α-helix adjacent to this structure. The barrel and helix are held together by 7 independent loops. [1] The FMNAT module contains an α/β dinucleotide binding domain within the active site, which it uses to bind to the substrate. The overall structure is held together by 5 parallel β-sheets that are adjacent to 4 α-helices, with 2 being long and 2 being short. A subdomain, containing 2 smaller α-helices, encompasses the area that connects to the C-terminal RFK module. [2]

Mechanism

Riboflavin is converted into catalytically active cofactors FAD and FMN by the actions of riboflavin kinase EC 2.7.1.26, which converts it into FMN, and FAD synthetase EC 2.7.7.2, which adenylates FMN to FAD. The RFK module phosphorylates the riboflavin substrate and converts it into FMN, which is then released from the module. This reaction is dependent on an ATP molecule stabilized by an Mg2+ ion, which causes only a single phosphate group to leave the ATP and bond to riboflavin. The released FMN then joins to the N-terminal FMNAT module and is adenylated, with the adenylyl group of ATP attaching to the phosphate group on FMN and the diphosphate group leaving. [1]

ATP + riboflavin ⇌ ADP + FMN

ATP + FMN ⇌ diphosphate + FAD

Phylogenetic Domain Comparison

Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional RFK is orthologous to the bifunctional prokaryotic RFK module, the monofunctional FMNAT differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family. [3] [4] The bacterial FMNAT module of the bifunctional enzyme has remote similarity to eukaryotic nucleotidyltransferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases. [5]

Related Research Articles

<span class="mw-page-title-main">Riboflavin</span> Vitamin and supplement

Riboflavin, also known as vitamin B2, is a vitamin found in food and sold as a dietary supplement. It is essential to the formation of two major coenzymes, flavin mononucleotide and flavin adenine dinucleotide. These coenzymes are involved in energy metabolism, cellular respiration, and antibody production, as well as normal growth and development. The coenzymes are also required for the metabolism of niacin, vitamin B6, and folate. Riboflavin is prescribed to treat corneal thinning, and taken orally, may reduce the incidence of migraine headaches in adults.

<span class="mw-page-title-main">Kinase</span> Enzyme catalyzing transfer of phosphate groups onto specific substrates

In biochemistry, a kinase is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates. This process is known as phosphorylation, where the high-energy ATP molecule donates a phosphate group to the substrate molecule. This transesterification produces a phosphorylated substrate and ADP. Conversely, it is referred to as dephosphorylation when the phosphorylated substrate donates a phosphate group and ADP gains a phosphate group. These two processes, phosphorylation and dephosphorylation, occur four times during glycolysis.

<span class="mw-page-title-main">Flavin group</span> Group of chemical compounds

Flavins refers generally to the class of organic compounds containing the tricyclic heterocycle isoalloxazine or its isomer alloxazine, and derivatives thereof. The biochemical source of flavin is the vitamin riboflavin. The flavin moiety is often attached with an adenosine diphosphate to form flavin adenine dinucleotide (FAD), and, in other circumstances, is found as flavin mononucleotide, a phosphorylated form of riboflavin. It is in one or the other of these forms that flavin is present as a prosthetic group in flavoproteins.

<span class="mw-page-title-main">Adenylate kinase</span> Class of enzymes

Adenylate kinase is a phosphotransferase enzyme that catalyzes the interconversion of the various adenosine phosphates. By constantly monitoring phosphate nucleotide levels inside the cell, ADK plays an important role in cellular energy homeostasis.

<span class="mw-page-title-main">Flavin adenine dinucleotide</span> Redox-active coenzyme

In biochemistry, flavin adenine dinucleotide (FAD) is a redox-active coenzyme associated with various proteins, which is involved with several enzymatic reactions in metabolism. A flavoprotein is a protein that contains a flavin group, which may be in the form of FAD or flavin mononucleotide (FMN). Many flavoproteins are known: components of the succinate dehydrogenase complex, α-ketoglutarate dehydrogenase, and a component of the pyruvate dehydrogenase complex.

<span class="mw-page-title-main">Flavin mononucleotide</span> Chemical compound

Flavin mononucleotide (FMN), or riboflavin-5′-phosphate, is a biomolecule produced from riboflavin (vitamin B2) by the enzyme riboflavin kinase and functions as the prosthetic group of various oxidoreductases, including NADH dehydrogenase, as well as cofactor in biological blue-light photo receptors. During the catalytic cycle, a reversible interconversion of the oxidized (FMN), semiquinone (FMNH), and reduced (FMNH2) forms occurs in the various oxidoreductases. FMN is a stronger oxidizing agent than NAD and is particularly useful because it can take part in both one- and two-electron transfers. In its role as blue-light photo receptor, (oxidized) FMN stands out from the 'conventional' photo receptors as the signaling state and not an E/Z isomerization.

<span class="mw-page-title-main">Glutamine synthetase</span> Class of enzymes

Glutamine synthetase (GS) is an enzyme that plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine:

<span class="mw-page-title-main">Flavoprotein</span> Protein family

Flavoproteins are proteins that contain a nucleic acid derivative of riboflavin. These proteins are involved in a wide array of biological processes, including removal of radicals contributing to oxidative stress, photosynthesis, and DNA repair. The flavoproteins are some of the most-studied families of enzymes.

<span class="mw-page-title-main">Amino acid synthesis</span> The set of biochemical processes by which amino acids are produced

Amino acid synthesis is the set of biochemical processes by which the amino acids are produced. The substrates for these processes are various compounds in the organism's diet or growth media. Not all organisms are able to synthesize all amino acids. For example, humans can synthesize 11 of the 20 standard amino acids. These 11 are called the non-essential amino acids).

<span class="mw-page-title-main">Long-chain-fatty-acid—CoA ligase</span> Class of enzymes

The long chain fatty acyl-CoA ligase is an enzyme of the ligase family that activates the oxidation of complex fatty acids. Long chain fatty acyl-CoA synthetase catalyzes the formation of fatty acyl-CoA by a two-step process proceeding through an adenylated intermediate. The enzyme catalyzes the following reaction,

<span class="mw-page-title-main">Adenylylation</span> Biological process

Adenylylation, more commonly known as AMPylation, is a process in which an adenosine monophosphate (AMP) molecule is covalently attached to the amino acid side chain of a protein. This covalent addition of AMP to a hydroxyl side chain of the protein is a post-translational modification. Adenylylation involves a phosphodiester bond between a hydroxyl group of the molecule undergoing adenylylation, and the phosphate group of the adenosine monophosphate nucleotide. Enzymes that are capable of catalyzing this process are called AMPylators.

In enzymology, a FAD diphosphatase (EC 3.6.1.18) is an enzyme that catalyzes the chemical reaction

In enzymology, a FMN adenylyltransferase is an enzyme that catalyzes the chemical reaction

In enzymology, a nucleoside-phosphate kinase is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Phosphoribulokinase</span>

Phosphoribulokinase (PRK) (EC 2.7.1.19) is an essential photosynthetic enzyme that catalyzes the ATP-dependent phosphorylation of ribulose 5-phosphate (RuP) into ribulose 1,5-bisphosphate (RuBP), both intermediates in the Calvin Cycle. Its main function is to regenerate RuBP, which is the initial substrate and CO2-acceptor molecule of the Calvin Cycle. PRK belongs to the family of transferase enzymes, specifically those transferring phosphorus-containing groups (phosphotransferases) to an alcohol group acceptor. Along with ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo), phosphoribulokinase is unique to the Calvin Cycle. Therefore, PRK activity often determines the metabolic rate in organisms for which carbon fixation is key to survival. Much initial work on PRK was done with spinach leaf extracts in the 1950s; subsequent studies of PRK in other photosynthetic prokaryotic and eukaryotic organisms have followed. The possibility that PRK might exist was first recognized by Weissbach et al. in 1954; for example, the group noted that carbon dioxide fixation in crude spinach extracts was enhanced by the addition of ATP. The first purification of PRK was conducted by Hurwitz and colleagues in 1956.

ATP + Mg2+ - D-ribulose 5-phosphate  ADP + D-ribulose 1,5-bisphosphate
<span class="mw-page-title-main">Riboflavin kinase</span>

In enzymology, a riboflavin kinase is an enzyme that catalyzes the chemical reaction

In enzymology, a streptomycin 3"-adenylyltransferase is an enzyme that catalyzes the chemical reaction:

<span class="mw-page-title-main">Sulfate adenylyltransferase</span>

In enzymology, a sulfate adenylyltransferase is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">DAK (gene)</span> Protein-coding gene in the species Homo sapiens

Triokinase/FMN cyclase is an enzyme that in humans is encoded by the DAK gene.

References

  1. 1 2 Sebastián M, Serrano A, Velázquez-Campoy A, Medina M (August 2017). "Kinetics and thermodynamics of the protein-ligand interactions in the riboflavin kinase activity of the FAD synthetase from Corynebacterium ammoniagenes". Scientific Reports. 7 (1): 7281. Bibcode:2017NatSR...7.7281S. doi:10.1038/s41598-017-07875-5. PMC   5544777 . PMID   28779158.
  2. Frago S, Martínez-Júlvez M, Serrano A, Medina M (September 2008). "Structural analysis of FAD synthetase from Corynebacterium ammoniagenes". BMC Microbiology. 8 (1): 160. doi: 10.1186/1471-2180-8-160 . PMC   2573891 . PMID   18811972.
  3. Karthikeyan S, Zhou Q, Osterman AL, Zhang H (November 2003). "Ligand binding-induced conformational changes in riboflavin kinase: structural basis for the ordered mechanism". Biochemistry. 42 (43): 12532–8. doi:10.1021/bi035450t. PMID   14580199.
  4. Galluccio M, Brizio C, Torchetti EM, Ferranti P, Gianazza E, Indiveri C, Barile M (March 2007). "Over-expression in Escherichia coli, purification and characterization of isoform 2 of human FAD synthetase". Protein Expression and Purification. 52 (1): 175–81. doi:10.1016/j.pep.2006.09.002. PMID   17049878.
  5. Krupa A, Sandhya K, Srinivasan N, Jonnalagadda S (January 2003). "A conserved domain in prokaryotic bifunctional FAD synthetases can potentially catalyze nucleotide transfer". Trends in Biochemical Sciences. 28 (1): 9–12. doi:10.1016/S0968-0004(02)00009-9. PMID   12517446.
This article incorporates text from the public domain Pfam and InterPro: IPR015864