Porphobilinogen synthase

Last updated

porphobilinogen synthase
1e51.jpg
DALA dehydratase
Identifiers
EC number 4.2.1.24
CAS number 9036-37-7
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
Delta-aminolevulinic acid dehydratase
Identifiers
Symbol ALAD
NCBI gene 210
HGNC 395
OMIM 125270
RefSeq NM_001003945
UniProt P13716
Other data
EC number 4.2.1.24
Locus Chr. 9 q32
ALAD
PDB 1b4k EBI.jpg
high resolution crystal structure of a mg2-dependent 5-aminolevulinic acid dehydratase
Identifiers
SymbolALAD
Pfam PF00490
Pfam clan CL0036
InterPro IPR001731
PROSITE PDOC00153
SCOPe 1aw5 / SUPFAM

Porphobilinogen synthase (or ALA dehydratase, or aminolevulinate dehydratase) synthesizes porphobilinogen through the asymmetric condensation of two molecules of aminolevulinic acid. All natural tetrapyrroles, including hemes, chlorophylls and vitamin B12, share porphobilinogen as a common precursor.

Porphobilinogen chemical compound

Porphobilinogen is an organic compound that occurs in living organisms as an intermediate in the biosynthesis of porphyrins, which include critical substances like hemoglobin and chlorophyll. The name is often abbreviated PBG.

Condensation Change of the physical state of matter from gas phase into liquid phase; reverse of evaporation

Condensation is the change of the physical state of matter from the gas phase into the liquid phase, and is the reverse of vaporization. The word most often refers to the water cycle. It can also be defined as the change in the state of water vapor to liquid water when in contact with a liquid or solid surface or cloud condensation nuclei within the atmosphere. When the transition happens from the gaseous phase into the solid phase directly, the change is called deposition.

Aminolevulinic acid chemical compound

δ-Aminolevulinic acid, an endogenous non-proteinogenic amino acid, is the first compound in the porphyrin synthesis pathway, the pathway that leads to heme in mammals and chlorophyll in plants.

Contents

It catalyzes the second step of the biosynthesis of porphyrin:

Porphyrin group of compounds containing four pyrrole rings connected by methine bridges in a cyclic configuration

Porphyrins are a group of heterocyclic macrocycle organic compounds, composed of four modified pyrrole subunits interconnected at their α carbon atoms via methine bridges (=CH−). The parent porphyrin is porphine, a rare chemical compound of exclusively theoretical interest. Substituted porphines are called porphyrins. With a total of 26 π-electrons, of which 18 π-electrons form a planar, continuous cycle, the porphyrin ring structure is often described as aromatic. One result of the large conjugated system is that porphyrins typically absorb strongly in the visible region of the electromagnetic spectrum, i.e. they are deeply colored. The name "porphyrin" derives from the Greek word πορφύρα (porphyra), meaning purple.

2 δ-aminolevulinic acid porphobilinogen + 2 H2O

The porphobilinogen synthase catalyzed reaction is the first common step in the biosynthesis of all biological tetrapyrroles.

Porphobilinogen synthase is the prototype morpheein. [1]

Morpheein

Morpheeins are proteins that can form two or more different homo-oligomers, but must come apart and change shape to convert between forms. The alternate shape may reassemble to a different oligomer. The shape of the subunit dictates which oligomer is formed. Each oligomer has a finite number of subunits (stoichiometry). Morpheeins can interconvert between forms under physiological conditions and can exist as an equilibrium of different oligomers. These oligomers are physiologically relevant and are not misfolded protein; this distinguishes morpheeins from prions and amyloid. The different oligomers have distinct functionality. Interconversion of morpheein forms can be a structural basis for allosteric regulation. A mutation that shifts the normal equilibrium of morpheein forms can serve as the basis for a conformational disease. Features of morpheeins can be exploited for drug discovery. The dice image represents a morpheein equilibrium containing two different monomeric shapes that dictate assembly to a tetramer or a pentamer. The one protein that is established to function as a morpheein is porphobilinogen synthase, though there are suggestions throughout the literature that other proteins may function as morpheeins.

Structure

The structural basis for allosteric regulation of Porphobilinogen synthase (PBGS) is modulation of a quaternary structure equilibrium between octamer and hexamer (via dimers), which is represented schematically as 6mer* ↔ 2mer* ↔ 2mer ↔ 8mer. The * represents a reorientation between two domains of each subunit that occurs in the dissociated state because it is sterically forbidden in the larger multimers. [1]

Allosteric regulation regulation of enzyme activity

In biochemistry, allosteric regulation is the regulation of an enzyme by binding an effector molecule at a site other than the enzyme's active site.

Quaternary is the current and most recent of the three periods of the Cenozoic Era in the geologic time scale of the International Commission on Stratigraphy (ICS). It follows the Neogene Period and spans from 2.588 ± 0.005 million years ago to the present. The Quaternary Period is divided into two epochs: the Pleistocene and the Holocene. The informal term "Late Quaternary" refers to the past 0.5–1.0 million years.

The PBGS quaternary structure equilibrium includes an inactive hexamer (PDB id 1PV8) that does not have subunit interactions necessary for an ordered active site lid. Dissociation to the pro-hexamer dimer can be followed by a conformational change that reorients the two ab-barrel domains to form the pro-octamer dimer. Association of pro-octamer dimer to octamer (PDB id 1E51) includes formation of subunit interfaces that support order in the active site lid. PBGS Quaternary Structure Equlibrium.jpg
The PBGS quaternary structure equilibrium includes an inactive hexamer (PDB id 1PV8) that does not have subunit interactions necessary for an ordered active site lid. Dissociation to the pro-hexamer dimer can be followed by a conformational change that reorients the two αβ-barrel domains to form the pro-octamer dimer. Association of pro-octamer dimer to octamer (PDB id 1E51) includes formation of subunit interfaces that support order in the active site lid.

PBGS is encoded by a single gene and each PBGS multimer is composed of multiple copies of the same protein. Each PBGS subunit consists of a ~300 residue αβ-barrel domain, which houses the enzyme's active site in its center, and a >25 residue N-terminal arm domain. Allosteric regulation of PBGS can be described in terms of the orientation of the αβ-barrel domain with respect to the N-terminal arm domain.

Gene Basic physical and functional unit of heredity

In biology, a gene is a sequence of nucleotides in DNA or RNA that codes for a molecule that has a function. During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic trait. These genes make up different DNA sequences called genotypes. Genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes as well as gene–environment interactions. Some genetic traits are instantly visible, such as eye color or number of limbs, and some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that constitute life.

Amino acid Organic compounds containing amine and carboxylic groups

Amino acids are organic compounds that contain amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid. The key elements of an amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), although other elements are found in the side chains of certain amino acids. About 500 naturally occurring amino acids are known (though only 20 appear in the genetic code) and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid residues form the second-largest component (water is the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis.

Each N-terminal arm has up to two interactions with other subunits in a PBGS multimer. One of these interactions helps to stabilize a "closed" conformation of the active site lid. The other interaction restricts solvent access from the other end of the αβ-barrel.

In the inactive multimeric state, the N-terminal arm domain is not involved in the lid-stabilizing interaction, and in the crystal structure of the inactive assembly, the active site lid is disordered.

Allosteric regulators

As a nearly universal enzyme with a highly conserved active site, PBGS would not be a prime target for the development of antimicrobials and/or herbicides. To the contrary, allosteric sites can be much more phylogenetically variable than active sites, thus presenting more drug development opportunities. [1]

Phylogenetic variation in PBGS allostery leads to the framing of discussion of PBGS allosteric regulation in terms of intrinsic and extrinsic factors.

Intrinsic allosteric regulators

Magnesium

The allosteric magnesium ion lies at the highly hydrated interface of two pro-octamer dimers. It appears to be easily dissociable, and it has been shown that hexamers accumulate when magnesium is removed in vitro . [2]

pH

Though it is not common to consider hydronium ions as allosteric regulators, in the case of PBGS, side chain protonation at locations other than the active site has been shown to affect the quaternary structure equilibrium, and thus to affect the rate of its catalyzed reaction as well.

Extrinsic allosteric regulators

Small molecule hexamer stabilization

Inspection of the PBGS 6mer* reveals a surface cavity that is not present in the 8mer. Small molecule binding to this phylogenetically variable cavity has been proposed to stabilize 6mer* of the targeted PBGS and consequently inhibit activity.

Such allosteric regulators are known as morphlocks because they lock PBGS in a specific morpheein form (6mer*). [3]

Deficiency

A deficiency of porphobilinogen synthase is usually acquired (rather than hereditary) and can be caused by heavy metal poisoning, especially lead poisoning, as the enzyme is very susceptible to inhibition by heavy metals. [4]

Hereditary insufficiency of porphobilinogen synthase is called porphobilinogen synthase (or ALA dehydratase) deficiency poprhyria. It is an extremely rare cause of porphyria, [5] with less than 10 cases ever reported. [6] All disease associated protein variants favor hexamer formation relative to the wild type human enzyme. [5]

Heme synthesis--note that some reactions occur in the cytoplasm and some in the mitochondrion (yellow) Heme synthesis.png
Heme synthesis—note that some reactions occur in the cytoplasm and some in the mitochondrion (yellow)

Lead poisoning works on the cellular level by binding to this enzyme, rendering it useless.

PBGS as the prototype morpheein

The morpheein model of allostery exemplified by PBGS adds an additional layer of understanding to potential mechanisms for regulation of protein function and complements the increased focus that the protein science community is placing on protein structure dynamics. [1]

This model illustrates how the dynamics of phenomena such as alternate protein conformations, alternate oligomeric states, and transient protein-protein interactions can be harnessed for allosteric regulation of catalytic activity.

Related Research Articles

Phenylalanine hydroxylase protein-coding gene in the species Homo sapiens

Phenylalanine hydroxylase (PAH) (EC 1.14.16.1) is an enzyme that catalyzes the hydroxylation of the aromatic side-chain of phenylalanine to generate tyrosine. PAH is one of three members of the biopterin-dependent aromatic amino acid hydroxylases, a class of monooxygenase that uses tetrahydrobiopterin (BH4, a pteridine cofactor) and a non-heme iron for catalysis. During the reaction, molecular oxygen is heterolytically cleaved with sequential incorporation of one oxygen atom into BH4 and phenylalanine substrate.

Aminolevulinic acid synthase class of enzymes

Aminolevulinic acid synthase (ALA synthase, ALAS, or delta-aminolevulinic acid synthase) is an enzyme (EC 2.3.1.37) that catalyzes the synthesis of D-aminolevulinic acid (ALA) the first common precursor in the biosynthesis of all tetrapyrroles such as hemes, cobalamins and chlorophylls. The reaction is as follows:

Glutamate dehydrogenase 1 protein-coding gene in the species Homo sapiens

GLUD1 is a mitochondrial matrix enzyme, one of the family of glutamate dehydrogenases that are ubiquitous in life, with a key role in nitrogen and glutamate (Glu) metabolism and energy homeostasis. This dehydrogenase is expressed at high levels in liver, brain, pancreas and kidney, but not in muscle. In the pancreatic cells, GLUD1 is thought to be involved in insulin secretion mechanisms. In nervous tissue, where glutamate is present in concentrations higher than in the other tissues, GLUD1 appears to function in both the synthesis and the catabolism of glutamate and perhaps in ammonia detoxification.

Citrate synthase protein-coding gene in the species Homo sapiens

The enzyme citrate synthase E.C. 2.3.3.1 ] exists in nearly all living cells and stands as a pace-making enzyme in the first step of the citric acid cycle. Citrate synthase is localized within eukaryotic cells in the mitochondrial matrix, but is encoded by nuclear DNA rather than mitochondrial. It is synthesized using cytoplasmic ribosomes, then transported into the mitochondrial matrix.

Porphobilinogen deaminase protein-coding gene in the species Homo sapiens

Porphobilinogen deaminase (hydroxymethylbilane synthase, or uroporphyrinogen I synthase) is an enzyme (EC 2.5.1.61) that in humans is encoded by the HMBS gene. Porphobilinogen deaminase is involved in the third step of the heme biosynthetic pathway. It catalyzes the head to tail condensation of four porphobilinogen molecules into the linear hydroxymethylbilane while releasing four ammonia molecules:

Uroporphyrinogen III synthase class of enzymes

Uroporphyrinogen III synthase EC 4.2.1.75 is an enzyme involved in the metabolism of the cyclic tetrapyrrole compound porphyrin. It is involved in the conversion of hydroxymethyl bilane into uroporphyrinogen III. This enzyme catalyses the inversion of the final pyrrole unit of the linear tetrapyrrole molecule, linking it to the first pyrrole unit, thereby generating a large macrocyclic structure, uroporphyrinogen III. The enzyme folds into two alpha/beta domains connected by a beta-ladder, the active site being located between the two domains.

Allosteric enzymes are enzymes that change their conformational ensemble upon binding of an effector, which results in an apparent change in binding affinity at a different ligand binding site. This "action at a distance" through binding of one ligand affecting the binding of another at a distinctly different site, is the essence of the allosteric concept. Allostery plays a crucial role in many fundamental biological processes, including but not limited to cell signaling and the regulation of metabolism. Allosteric enzymes need not be oligomers as previously thought, and in fact many systems have demonstrated allostery within single enzymes. In biochemistry, allosteric regulation is the regulation of a protein by binding an effector molecule at a site other than the enzyme's active site.

Aspartate kinase is an enzyme that catalyzes the phosphorylation of the amino acid aspartate. This reaction is the first step in the biosynthesis of three essential amino acids: methionine, lysine, and threonine, known as the "aspartate family". The gene for aspartokinase is present only in microorganisms and plants; it is not present in animals, which must obtain aspartate-family amino acids in their diet.

Cystathionine beta synthase protein-coding gene in the species Homo sapiens

Cystathionine-β-synthase, also known as CBS, is an enzyme (EC 4.2.1.22) that in humans is encoded by the CBS gene. It catalyzes the first step of the transsulfuration pathway, from homocysteine to cystathionine:

Uracil phosphoribosyltransferase is an enzyme which creates UMP from uracil and phosphoribosylpyrophosphate. This protein may use the morpheein model of allosteric regulation.

Delta-aminolevulinic acid dehydratase protein-coding gene in the species Homo sapiens

Delta-aminolevulinic acid dehydratase is an enzyme (EC 4.2.1.24) that in humans is encoded by the ALAD gene. It catalyzes the following reaction:

Chorismate mutase class of enzymes

In enzymology, chorismate mutase is an enzyme that catalyzes the chemical reaction for the conversion of chorismate to prephenate in the pathway to the production of phenylalanine and tyrosine, also known as the shikimate pathway. Hence, this enzyme has one substrate, chorismate, and one product, prephenate. Chorismate mutase is found at a branch point in the pathway. The enzyme channels the substrate, chorismate to the biosynthesis of tyrosine and phenylalanine and away from tryptophan. Its role in maintaining the balance of these aromatic amino acids in the cell is vital. This is the single known example of a naturally occurring enzyme catalyzing a pericyclic reaction. Chorismate mutase is only found in fungi, bacteria, and higher plants. Some varieties of this protein may use the morpheein model of allosteric regulation.

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

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

Aminolevulinic acid dehydratase deficiency porphyria porphyria that has symptom abdominal pain, has symptom neuropathy, has symptom autonomic instability and has symptom psychosis

Aminolevulinic acid dehydratase deficiency porphyria is a neuropsychiatric condition, disease can present during early childhood with acute neurologic symptoms that resemble those encountered in acute intermittent porphyria.

6-Deoxyerythronolide B Synthase or DEBS has been identified as a Type 1 polyketide synthase. DEBS is found in Saccharopolyspora erythraea and responsible for the synthesis of the macrolide ring which is the precursor of the antibiotic erythromycin. There have been three categories of polyketide synthases identified to date, type 1, 2 and 3. Type one synthases involve large multidomain proteins containing all the sites necessary for polyketide synthesis. Type two synthases contain active sites distributed among several smaller polypeptides, and type three synthases are large multi-protein complexes containing modules which have a single active site for each and every step of polyketide synthesis. In the case of DEBS, there are three large multi-functional proteins, DEBS 1,2, and 3, that each exist as a dimer of two modules. Each module consists of a minimum of a Ketosynthase (KS), Acyl carrier protein (ACP) site, and acyltransferase (AT), but may also contain a Ketoreductase (KR), Dehydrotase (DH), and Enol Reductase (ER) for additional reduction reactions. The DEBS complex also contains a Loading Domain on module 1 consisting of an acyl carrier protein and an acyltransferase. The terminal Thioesterase acts solely to terminate DEBS polyketide synthesis and cyclize the macrolide ring.

References

  1. 1 2 3 4 Jaffe EK, Lawrence SH (March 2012). "Allostery and the dynamic oligomerization of porphobilinogen synthase". Arch. Biochem. Biophys. 519 (2): 144–53. doi:10.1016/j.abb.2011.10.010. PMC   3291741 . PMID   22037356.
  2. ↑ Breinig S, Kervinen J, Stith L, Wasson AS, Fairman R, Wlodawer A, Zdanov A, Jaffe EK (September 2003). "Control of tetrapyrrole biosynthesis by alternate quaternary forms of porphobilinogen synthase". Nat. Struct. Biol. 10 (9): 757–63. doi:10.1038/nsb963. PMID   12897770.
  3. ↑ Lawrence SH, Jaffe EK (2008). "Expanding the Concepts in Protein Structure-Function Relationships and Enzyme Kinetics: Teaching using Morpheeins". Biochem Mol Biol Educ. 36 (4): 274–283. doi:10.1002/bmb.20211. PMC   2575429 . PMID   19578473.
  4. ↑ ALA dehydratase reaction, from NetBiochem at the University of Utah. Last modified 1/5/95
  5. 1 2 Jaffe EK, Stith L (February 2007). "ALAD porphyria is a conformational disease". Am. J. Hum. Genet. 80 (2): 329–37. doi:10.1086/511444. PMC   1785348 . PMID   17236137.
  6. ↑ Overview of the Porphyrias Archived 2011-07-22 at the Wayback Machine at The Porphyrias Consortium (a part of NIH Rare Diseases Clinical Research Network (RDCRN)) Retrieved June 2011
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.