O-succinylbenzoate synthase

Last updated
o-succinylbenzoate synthase
MenC with ligand.png
The conformation of o-succinylbenzoate synthase when it is bound to the Mg cation and its product, OSB, is illustrated here. The cyan-colored R groups represent the R groups that interact with the Mg cation. The red- and cyan-colored R groups represent the R groups that interact with OSB. The single yellow-colored R group represents Lys 133, which has been shown to act as both the catalytic base and acid in the dehydration reaction.
Identifiers
EC no. 4.2.1.113
CAS no. 97089-83-3
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / QuickGO

o-Succinylbenzoate synthase (OSBS) (EC 4.2.1.113) is an enzyme encoded by the menC gene in E.coli , and catalyzes the dehydration of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to form 4-(2'-carboxyphenyl)-4-oxobutyrate, also called o-succinylbenzoate or OSB, hence the name of the enzyme. [1] [2] [3] [4] [5] This reaction is the fourth step in the menaquinone biosynthetic pathway, which is used by bacteria to synthesize menaquinone, also known as vitamin K2. [6]

Contents

Classification

OSBS belongs to the muconate lactonizing enzyme subgroup of the enolase superfamily. The systematic name of this enzyme is (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate hydrolyase (2-succinylbenzoate-forming).Other common names include: o-succinylbenzoic acid synthase and OSB synthase.

Menaquinone biosynthetic pathway

The menaquinone biosynthetic pathway consists of nine enzymatic reactions, ultimately resulting in the synthesis of vitamin K. This pathway is quite similar in both plants and bacteria, however the final product of the pathway varies slightly in the two organisms. The final product in plants and some cyanobacteria is phylloquinone, which functions as an electron transporter in photosynthesis. The final product in bacteria and archaea is menaquinone, which is involved in anaerobic respiration. [6] The structures of the two end-products are illustrated below.

Phylloquinone (vitamin K1).png
Menaquinone (vitamin K2).png

Phylloquinone is commonly called "vitamin K1." Menaquinone is commonly called "vitamin K2." Both fall under the common name "vitamin K." This pathway is not present in humans and other animals, however vitamin K is essential for blood coagulation and therefore must be consumed. Good sources of vitamin K include vegetables (kale, spinach, broccoli, Brussels sprouts, cauliflower, etc.), and fish, liver, meat, and eggs (though these contain smaller amounts of vitamin K than do vegetables.) [7]

Structure

OSBS is a monomeric protein consisting of two domains: the "capping domain" and the "barrel domain," both of which are characteristic of the enolase superfamily. The enzyme's active site is located at the interface of the two domains, with the acid-base chemistry occurring on the barrel domain. [8] OSBS requires the presence of Mg2+ to function. Mg2+ stabilizes the intermediate during the reaction. [1]

Activity

The reaction catalyzed by OSBS is shown below:

Chemical reaction catalyzed by OSBS.png

The reaction involves the dehydration of SHCHC to form OSB. OSBS has one substrate, SHCHC, and two products, water and OSB.

Homologues in other organisms

The binding of OSB to OSBS's active site consists mainly of indirect interactions via water molecules or hydrophobic interactions. This lack of strict specificity and catalysis could possibly simplify the evolution of the shape and volume of the active site, meaning that OSBS could serve as a starting point for the evolution of new enzymes with new functions in the enolase superfamily. These homologues could catalyze completely different reactions, but because they maintain an active site similar to that of OSBS, the substrate and intermediate of the new reaction would be structurally similar to that of OSBS. [3] [4] [5]

One such homologue has already been identified: OSBS from Amycolatopsis. OSBS from Amycolatopsis was first identified as N-acylamino acid racemase (NAAAR) because it was found to catalyze the racemization of N-acylamino acids. However, this ability was discovered for commercial reasons, and considering racemization of N-acylamino acids does not occur in Amycolatopsis, its actual job in the bacteria itself was unknown. In 1999, it was discovered that NAAAR's protein sequence was quite similar to another protein with an unknown function in Bacillus subtilis. Both proteins were found to efficiently catalyze the same reaction as OSBS in E.coli, and so this was deemed their "correct" function. "NAAAR" was properly renamed to OSBS. The hypothesis stated in the first paragraph of this section helps explain how the OSBS from Amycolatopsis can also catalyze the racemization of N-acylamino acids, as well as the diversity of catalytic differences among the enzymes of the enolase superfamily. [3] [4] [5]

Related Research Articles

Pyridoxal phosphate Active formof vitamin B6

Pyridoxal phosphate (PLP, pyridoxal 5'-phosphate, P5P), the active form of vitamin B6, is a coenzyme in a variety of enzymatic reactions. The International Union of Biochemistry and Molecular Biology has catalogued more than 140 PLP-dependent activities, corresponding to ~4% of all classified activities. The versatility of PLP arises from its ability to covalently bind the substrate, and then to act as an electrophilic catalyst, thereby stabilizing different types of carbanionic reaction intermediates.

Muconate lactonizing enzyme

Muconate lactonizing enzymes are involved in the breakdown of lignin-derived aromatics, catechol and protocatechuate, to citric acid cycle intermediates as a part of the β-ketoadipate pathway in soil microbes. Some bacterial species are also capable of dehalogenating chloroaromatic compounds by the action of chloromuconate lactonizing enzymes. MLEs consist of several strands which have variable reaction favorable parts therefore the configuration of the strands affect its ability to accept protons. The bacterial MLEs belong to the enolase superfamily, several structures from which are known. MLEs have an identifying structure made up of two proteins and two Magnesium ions as well as various classes depending on whether it is bacterial or eukaryotic. The reaction mechanism that MLEs undergo are the reverse of beta-elimination in which the enolate alpha-carbon is protonated. MLEs can undergo mutations caused by a deletion of catB structural genes which can cause some bacteria to lose its functions such as the ability to grow. Additional mutations to MLEs can cause its structure and function to alter and could cause the conformation to change therefore making it an inactive enzyme that is unable to bind its substrate. There is another enzyme called Mandelate Racemase that is very similar to MLEs in the structural way as well as them both being a part of the enolase superfamily. They both have the same end product even though they undergo different chemical reactions in order to reach the end product.

Orotidine 5-phosphate decarboxylase

Orotidine 5'-phosphate decarboxylase or orotidylate decarboxylase is an enzyme involved in pyrimidine biosynthesis. It catalyzes the decarboxylation of orotidine monophosphate (OMP) to form uridine monophosphate (UMP). The function of this enzyme is essential to the de novo biosynthesis of the pyrimidine nucleotides uridine triphosphate, cytidine triphosphate, and thymidine triphosphate. OMP decarboxylase has been a frequent target for scientific investigation because of its demonstrated extreme catalytic efficiency and its usefulness as a selection marker for yeast strain engineering.

The crotonase family comprises mechanistically diverse proteins that share a conserved trimeric quaternary structure, the core of which consists of 4 turns of a (beta/beta/alpha)n superhelix.

Isochorismate synthase

Isochorismate synthase ( EC 5.4.4.2) is an isomerase enzyme that catalyzes the first step in the biosynthesis of vitamin K2 (menaquinone) in Escherichia coli.

UDP-glucose 4-epimerase Class of enzymes

The enzyme UDP-glucose 4-epimerase, also known as UDP-galactose 4-epimerase or GALE, is a homodimeric epimerase found in bacterial, fungal, plant, and mammalian cells. This enzyme performs the final step in the Leloir pathway of galactose metabolism, catalyzing the reversible conversion of UDP-galactose to UDP-glucose. GALE tightly binds nicotinamide adenine dinucleotide (NAD+), a co-factor required for catalytic activity.

Chorismate lyase

The enzyme chorismate lyase catalyzes the chemical reaction

Naphthoate synthase

The enzyme 1,4-dihydroxy-2-naphthoyl-CoA synthase catalyzes the sixth step in the biosynthesis of phylloquinone and menaquinone, the two forms of vitamin K. In E. coli, 1,4-dihydroxy-2-naphthoyl-CoA synthase, formerly known as naphthoate synthase, is encoded by menB and uses O-succinylbenzoyl-CoA as a substrate and converts it to 1,4-dihydroxy-2-naphthoyl-CoA.

In enzymology, a 5-(carboxyamino)imidazole ribonucleotide synthase (EC 6.3.4.18) is an enzyme that catalyzes the chemical reaction

Aminodeoxychorismate synthase

In enzymology, an aminodeoxychorismate synthase is an enzyme that catalyzes the chemical reaction

O-succinylbenzoate—CoA ligase

o-Succinylbenzoate—CoA ligase, encoded from the menE gene in Escherichia coli, catalyzes the fifth reaction in the synthesis of menaquinone. This pathway is called 1, 4-dihydroxy-2-naphthoate biosynthesis I. Vitamin K is a quinone that serves as an electron transporter during anaerobic respiration. This process of anaerobic respiration allows the bacteria to generate the energy required to survive.

Phosphoribosylaminoimidazolesuccinocarboxamide synthase Class of enzymes

In molecular biology, the protein domain SAICAR synthase is an enzyme which catalyses a reaction to create SAICAR. In enzymology, this enzyme is also known as phosphoribosylaminoimidazolesuccinocarboxamide synthase. It is an enzyme that catalyzes the chemical reaction

Chorismate synthase

In enzymology, a chorismate synthase is an enzyme that catalyzes the chemical reaction

In enzymology, a [acyl-carrier-protein] S-malonyltransferase is an enzyme that catalyzes the chemical reaction

Malate synthase

In enzymology, a malate synthase (EC 2.3.3.9) is an enzyme that catalyzes the chemical reaction

2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase, also known as SHCHC synthase, is encoded by the menH gene in E.coli and functions in the synthesis of vitamin K. The specific step in the synthetic pathway that SHCHC synthase catalyzes is the conversion of 5-enolpyruvoyl-6-hydroxy-2-succinylcyclohex-3-ene-1-carboxylate to (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate and pyruvate.

Enzyme Function Initiative Collaborative project to determine enzyme function

The Enzyme Function Initiative (EFI) is a large-scale collaborative project aiming to develop and disseminate a robust strategy to determine enzyme function through an integrated sequence–structure-based approach. The project was funded in May 2010 by the National Institute of General Medical Sciences as a Glue Grant which supports the research of complex biological problems that cannot be solved by a single research group. The EFI was largely spurred by the need to develop methods to identify the functions of the enormous number proteins discovered through genomic sequencing projects.

Radical SAM is a designation for a superfamily of enzymes that use a [4Fe-4S]+ cluster to reductively cleave S-adenosyl-L-methionine (SAM) to generate a radical, usually a 5′-deoxyadenosyl radical, as a critical intermediate. These enzymes utilize this radical intermediate to perform diverse transformations, often to functionalize unactivated C-H bonds. Radical SAM enzymes are involved in cofactor biosynthesis, enzyme activation, peptide modification, post-transcriptional and post-translational modifications, metalloprotein cluster formation, tRNA modification, lipid metabolism, biosynthesis of antibiotics and natural products etc. The vast majority of known radical SAM enzymes belong to the radical SAM superfamily, and have a cysteine-rich motif that matches or resembles CxxxCxxC. rSAMs comprise the largest superfamily of metal-containing enzymes.

1-4-dihydroxy-2-napthoate (DHNA) polyprenyltransferase (EC 2.5.1.74)is an enzyme that catalyzes the chemical reaction: all-trans-nonaprenyl diphosphate + 1-4-dihydroxy-2-napthoate + H+ demethylmenaquinol-9 + diphosphate + carbon dioxide

Glycerate 2-kinase is an enzyme with systematic name ATP:D-glycerate 2-phosphotransferase. This enzyme catalyses the following chemical reaction

References

  1. 1 2 Klenchin VA, Taylor Ringia EA, Gerlt JA, Rayment I (December 2003). "Evolution of enzymatic activity in the enolase superfamily: structural and mutagenic studies of the mechanism of the reaction catalyzed by o-succinylbenzoate synthase from Escherichia coli". Biochemistry. 42 (49): 14427–33. doi:10.1021/bi035545v. PMID   14661953.
  2. ↑ Sharma V, Meganathan R, Hudspeth ME (August 1993). "Menaquinone (vitamin K2) biosynthesis: cloning, nucleotide sequence, and expression of the menC gene from Escherichia coli". Journal of Bacteriology. 175 (15): 4917–21. doi:10.1128/jb.175.15.4917-4921.1993. PMC   204947 . PMID   8335646.
  3. 1 2 3 Thompson TB, Garrett JB, Taylor EA, Meganathan R, Gerlt JA, Rayment I (September 2000). "Evolution of enzymatic activity in the enolase superfamily: structure of o-succinylbenzoate synthase from Escherichia coli in complex with Mg2+ and o-succinylbenzoate". Biochemistry. 39 (35): 10662–76. CiteSeerX   10.1.1.565.5855 . doi:10.1021/bi000855o. PMID   10978150.
  4. 1 2 3 Palmer DR, Garrett JB, Sharma V, Meganathan R, Babbitt PC, Gerlt JA (April 1999). "Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase". Biochemistry. 38 (14): 4252–8. doi:10.1021/bi990140p. PMID   10194342.
  5. 1 2 3 Taylor Ringia EA, Garrett JB, Thoden JB, Holden HM, Rayment I, Gerlt JA (January 2004). "Evolution of enzymatic activity in the enolase superfamily: functional studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis". Biochemistry. 43 (1): 224–9. doi:10.1021/bi035815+. PMID   14705949.
  6. 1 2 van Oostende C, Widhalm JR, Furt F, Ducluzeau AL, Basset GJ (2011). "Phylloquinone (Vitamin K1): function, enzymes and genes". Advances in Botanical Research.
  7. ↑ "Vitamin K". University of Maryland Medical Center. 2011-06-21.
  8. ↑ "Research Interests". Gerlt Lab - Molecular and Cellular Biology - University of Illinois.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.