Poly ADP ribose polymerase
Encyclopedia
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s involved in a number of cell
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....
ular processes involving mainly DNA repair
DNA repair
DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many as 1...
and programmed cell death
Programmed cell death
Programmed cell-death is death of a cell in any form, mediated by an intracellular program. PCD is carried out in a regulated process which generally confers advantage during an organism's life-cycle...
.
Members of PARP family
The PARP family comprises 17 members (10 putative). They have all very different structures and functions in the cell.- PARP1PARP1Poly [ADP-ribose] polymerase 1 also known as NAD+ ADP-ribosyltransferase 1 or poly[ADP-ribose] synthase 1 is an enzyme that in humans is encoded by the PARP1 gene.- Function :PARP1 works:...
, PARP2PARP2Poly [ADP-ribose] polymerase 2 is an enzyme that in humans is encoded by the PARP2 gene.-Further reading:...
, VPARP (PARP4PARP4Poly [ADP-ribose] polymerase 4 is an enzyme that in humans is encoded by the PARP4 gene.-Interactions:PARP4 has been shown to interact with Major vault protein.-Further reading:...
), Tankyrase-1 and -2 (PARP-5a or TNKSTNKSTankyrase-1 is an enzyme that in humans is encoded by the TNKS gene.-Interactions:TNKS has been shown to interact with MCL1, TNKS1BP1, FNBP1 and TERF1.-Further reading:...
, and PARP-5b or TNKS2TNKS2Tankyrase-2 is an enzyme that in humans is encoded by the TNKS2 gene.-Interactions:TNKS2 has been shown to interact with GRB14, TERF1 and Cystinyl aminopeptidase.-Further reading:...
) have a confirmed PARP activity.
- Others include PARP3PARP3Poly [ADP-ribose] polymerase 3 is an enzyme that in humans is encoded by the PARP3 gene.-Further reading:...
, , (or "PARP7"), PARP8PARP8Poly [ADP-ribose] polymerase 8 is an enzyme that in humans is encoded by the PARP8 gene.-Further reading:...
, , PARP10PARP10Poly [ADP-ribose] polymerase 10 is an enzyme that in humans is encoded by the PARP10 gene.-Further reading:...
, , PARP12PARP12Poly [ADP-ribose] polymerase 12 is an enzyme that in humans is encoded by the PARP12 gene.-Further reading:...
, , , and .
PARP Structure
PARP is composed of four domains of interest: a DNA-binding domainDNA-binding domain
A DNA-binding domain is an independently folded protein domain that contains at least one motif that recognizes double- or single-stranded DNA. A DBD can recognize a specific DNA sequence or have a general affinity to DNA...
, a caspase-cleaved domain(see below), an auto-modification domain, and a catalytic domain.
The DNA-binding domain is composed of two zinc finger
Zinc finger
Zinc fingers are small protein structural motifs that can coordinate one or more zinc ions to help stabilize their folds. They can be classified into several different structural families and typically function as interaction modules that bind DNA, RNA, proteins, or small molecules...
motif
Structural motif
In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a supersecondary structure, which appears also in a variety of other molecules...
s. In the presence of damaged DNA (base pair-excised), the DNA-binding domain will bind the DNA and induce a conformational shift
Allosteric regulation
In biochemistry, allosteric regulation is the regulation of an enzyme or other protein by binding an effector molecule at the protein's allosteric site . Effectors that enhance the protein's activity are referred to as allosteric activators, whereas those that decrease the protein's activity are...
. It has been shown that this binding occurs independent of the other domains. This is integral in a programmed cell death model based on Caspase
Caspase
Caspases, or cysteine-aspartic proteases or cysteine-dependent aspartate-directed proteases are a family of cysteine proteases that play essential roles in apoptosis , necrosis, and inflammation....
cleavage
Cleavage
Cleavage may refer to:*Cleavage , partial exposure of the separation between a woman's breasts.**Cleavage enhancement, methods of making a person's breast cleavage look more substantial than it really is....
inhibition of PARP. The auto-modification domain is responsible for releasing the protein from the DNA after catalysis. Also, it plays an integral role in cleavage-induced inactivation.
Functions
PARP is found in the cell’s nucleus, the main role is to detect and signal single strand DNA breaks (SSB) to the enzymatic machinery involved in the SSB repair. PARP activation is an immediate cellular response to metabolic, chemical, or radiation-induced DNA SSB damage. Once PARP detects a SSB it binds to the DNA, and, after a structural change, begin the synthesis of a poly(ADP-ribose)chain (PAR)as a signal for the other DNA repairing enzymes such as DNA ligase III (LigIII), DNA polymerase beta (polβ) and scaffolding proteins such as x-ray cross complementing gene 1 (XRCC1). After repairing, the PAR chains are degraded via PAR glycohydrolase (PARG).Interestingly, NAD+ is required as substrate for generating ADP-ribose monomers. The overactivation of PARP may deplete the stores of cellular NAD+ and induce a progressive ATP depletion, since glucose oxidation is inhibited, and necrotic cell death. In this regard, PARP is inactivated by caspase-3 cleavage (in a specific domain of the enzyme) during programmed cell death.
PARP enzymes are essential in a number of cellular functions
, including expression of inflammatory genes: PARP1 is required for the induction of ICAM-1 gene expression by smooth muscle cells, in response to TNF.
Activity
The catalytic domain is responsible for Poly (ADP-ribose) polymerizationPolymerization
In polymer chemistry, polymerization is a process of reacting monomer molecules together in a chemical reaction to form three-dimensional networks or polymer chains...
. This domain has a highly conserved motif
Structural motif
In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a supersecondary structure, which appears also in a variety of other molecules...
that is common to all members of the PARP family. PAR polymer can reach lengths up to 200 bp before inducing apoptotic processes. The formation of PAR polymer is similar to the formation of DNA polymer from nucleoside triphosphates. Normal DNA synthesis requires that a pyrophosphate
Pyrophosphate
In chemistry, the anion, the salts, and the esters of pyrophosphoric acid are called pyrophosphates. Any salt or ester containing two phosphate groups is called a diphosphate. As a food additive, diphosphates are known as E450.- Chemistry :...
act as the leaving group, leaving a single phosphate group linking ribose sugars
Ribose
Ribose is an organic compound with the formula C5H10O5; specifically, a monosaccharide with linear form H––4–H, which has all the hydroxyl groups on the same side in the Fischer projection....
. PAR is synthesized using nicotinamide
Nicotinamide
Nicotinamide, also known as niacinamide and nicotinic acid amide, is the amide of nicotinic acid . Nicotinamide is a water-soluble vitamin and is part of the vitamin B group...
(NAM) as the leaving group. This leaves a pyrophosphate as the linking group between ribose sugars rather than single phosphate groups. This creates some special bulk to a PAR bridge, which may have an additional role in cell signaling.
Role in repairing DNA nicks
One important function of PARP is assisting in the repair of single-strand DNA nicks. It binds sites with single-strand breaks through its N-terminal zinc fingerZinc finger
Zinc fingers are small protein structural motifs that can coordinate one or more zinc ions to help stabilize their folds. They can be classified into several different structural families and typically function as interaction modules that bind DNA, RNA, proteins, or small molecules...
s and will recruit XRCC1
XRCC1
XRCC1 is a DNA repair protein.It complexes with DNA ligase III.-Interactions:XRCC1 has been shown to interact with PARP2, DNA polymerase beta, Aprataxin, Oxoguanine glycosylase, PCNA, APEX1, PNKP and PARP1.-Further reading:-External links:...
, DNA ligase
DNA ligase
In molecular biology, DNA ligase is a specific type of enzyme, a ligase, that repairs single-stranded discontinuities in double stranded DNA molecules, in simple words strands that have double-strand break . Purified DNA ligase is used in gene cloning to join DNA molecules together...
III, DNA polymerase
DNA polymerase
A DNA polymerase is an enzyme that helps catalyze in the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best known for their feedback role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand....
beta, and a kinase to the nick. This is called base excision repair
Base excision repair
In biochemistry and genetics, base excision repair is a cellular mechanism that repairs damaged DNA throughout the cell cycle. It is responsible primarily for removing small, non-helix-distorting base lesions from the genome. The related nucleotide excision repair pathway repairs bulky...
(BER). PARP-2 has been shown to oligomerize with PARP-1 and, therefore, is also implicated in BER. The oligomerization has also been shown to stimulate PARP catalytic activity. PARP-1 is also known for its role in transcription through remodeling of chromatin
Chromatin
Chromatin is the combination of DNA and proteins that make up the contents of the nucleus of a cell. The primary functions of chromatin are; to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, and to control gene...
by PARylating histones and relaxing chromatin structure, thus allowing transcription complex to access genes.
Role of tankyrases
The tankyrases are PARPs that comprise ankyrin repeatAnkyrin repeat
The ankyrin repeat is a 33-residue motif in proteins consisting of two alpha helices separated by loops, first discovered in signaling proteins in yeast Cdc10 and Drosophila Notch. Ankyrin repeats mediate protein–protein interactions and are among the most common structural motifs in known proteins...
s, oligomerization domain (SAM), and a PARP catalytic domain (PCD). Tankyrases are also known as PARP-5a and PARP-5b. They were named for their interaction with the telomere-associated TRF1 proteins and ankyrin repeats. They may allow the removal of telomerase-inhibiting complexes from chromosome ends to allow for telomere maintenance. Through their SAM domain and ANKs they can oligomerize and interact with many other proteins, such as TRF1, TAB182 (TNKS1BP1
TNKS1BP1
182 kDa tankyrase-1-binding protein is an enzyme that in humans is encoded by the TNKS1BP1 gene.-Further reading:...
), GRB14
GRB14
Growth factor receptor-bound protein 14 is a protein that in humans is encoded by the GRB14 gene.-Interactions:GRB14 has been shown to interact with Epidermal growth factor receptor, Fibroblast growth factor receptor 1 and TNKS2.-Further reading:...
, IRAP, NuMa, EBNA-1, and Mcl-1. They have multiple roles in the cell, vesicular trafficking through its interaction in GLUT4 vesicle (GSVs) with insulin-responsive amino peptidase (IRAP). It also plays a role in spindle assembly through its interaction with nuclear mitotic apparatus (NuMa), therefore allowing bipolarity. In the absence of TNKs mitosis arrest is observed in pre-anaphase through Mad2
MAD2
MAD2 is an essential spindle checkpoint protein. The spindle checkpoint system is a regulatory system that restrains progression through the metaphase-to-anaphase transition. The Mad2 gene was first identified in the yeast S. cerevisiae in a screen for genes which when mutated would confer...
kinetochore checkpoint
Spindle checkpoint
In order to preserve one cell's identity and its proper functioning, it is necessary to maintain constant the appropriate number of chromosomes after each cell division...
. TNKs can also PARsylate Mcl-1L and Mcl-1S and inhibit both their pro- and anti-apoptotic function. Relevance of this is not yet known. However this could cause extreme pain.
Role in cell death
Upon DNA cleavage by enzymes involved in cell death (such as caspases), PARP can deplete the ATP of a cell in an attempt to repair the damaged DNA. ATP depletion in a cell leads to lysis and cell death. PARP also has the ability to directly induce apoptosis, via the production of PAR, which stimulates mitochondria to release AIFApoptosis-inducing factor
Apoptosis inducing factor is a flavoprotein.Apoptosis inducing factor is involved in initiating a caspase-independent pathway of apoptosis by causing DNA fragmentation and chromatin condensation. It also acts as an NADH oxidase. Another AIF function is to regulate the permeability of the...
. This mechanism appears to be caspase-independent.
Role in Epigenetic DNA modification
PARP-mediated post-translational modification of proteins such as CTCF can affect the amount of DNA methylation at CpG dinucleotides. This regulates the insulator features of CTCF can differentially mark the copy of DNA inherited from either the maternal or the paternal DNA through the process known as genomic imprinting. PARP has also been proposed to affect the amount of DNA methylation by directly binding to the DNA methyltransferase DNMT-1 after attaching poly ADP-ribose chains to itself after interaction with CTCF and affecting DNMT1's enzymatic activity .PARP Inactivation
PARP is inactivated by caspaseCaspase
Caspases, or cysteine-aspartic proteases or cysteine-dependent aspartate-directed proteases are a family of cysteine proteases that play essential roles in apoptosis , necrosis, and inflammation....
cleavage. It is believed that normal inactivation occurs in systems where DNA damage is extensive. In these cases, more energy would be invested in repairing damage than is feasible, so that energy is instead retrieved for other cells in the tissue through programmed cell death.
While in vitro
In vitro
In vitro refers to studies in experimental biology that are conducted using components of an organism that have been isolated from their usual biological context in order to permit a more detailed or more convenient analysis than can be done with whole organisms. Colloquially, these experiments...
cleavage by caspase occurs throughout the caspase family, preliminary data suggest that caspase-3 and caspase-7 are responsible for in vivo
In vivo
In vivo is experimentation using a whole, living organism as opposed to a partial or dead organism, or an in vitro controlled environment. Animal testing and clinical trials are two forms of in vivo research...
cleavage.
Cleavage occurs at aspartic acid
Aspartic acid
Aspartic acid is an α-amino acid with the chemical formula HOOCCHCH2COOH. The carboxylate anion, salt, or ester of aspartic acid is known as aspartate. The L-isomer of aspartate is one of the 20 proteinogenic amino acids, i.e., the building blocks of proteins...
214 and glycine
Glycine
Glycine is an organic compound with the formula NH2CH2COOH. Having a hydrogen substituent as its 'side chain', glycine is the smallest of the 20 amino acids commonly found in proteins. Its codons are GGU, GGC, GGA, GGG cf. the genetic code.Glycine is a colourless, sweet-tasting crystalline solid...
215, separating PARP into a 24kDA and 89kDA segment. The smaller moiety includes the zinc finger motif requisite in DNA binding. The 89 kDa fragment includes the auto-modification domain and catalytic domain.
The putative mechanism of PCD activation via PARP inactivation relies on the separation of the DNA-binding region and the auto-modification domain. The DNA-binding region is capable of doing so independent of the rest of the protein, cleaved or not. It is unable, however, to dissociate without the auto-modification domain. In this way, the DNA-binding domain will attach to a damaged site and be unable to effect repair, as it no longer has the catalytic domain. The DNA-binding domain prevents other, non-cleaved PARP from accessing the damaged site and initiating repairs. This model suggests that this “sugar plug” can also begin the signal for apoptosis.
External links
- Entry for a PARP immunoassay at bioreagents.com
- PARP - Poly (ADP-ribose) polymerase at inotekcorp.com
- The PARP Link Homepage at parplink.u-strasbg.fr
- Parp Inhibitors Information Site
- PARP Activity and Inhibition Assays at trevigen.com