DNA polymerase

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ADN polymeraza
DNA polymerase.png
Cấu trúc không gian xoắn-cuộn-xoắn của enzim DNA polymerase beta ở người (dựa trên file PDB 7ICG)
Mã định danh(ID)
Mã EC 2.7.7.7
Mã CAS 9012-90-2
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IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc chu trình chuyển hóa
PRIAM profile
Các cấu trúc PDB RCSB PDB PDBe PDBsum
Bản thể gen AmiGO / EGO

Các enzim ADN polymeraza (DNA polymerases) tạo ra các phân tử ADN bằng cách lắp ráp các nucleotide, đơn phân của ADN. Các enzim này rất cần thiết để tái bản DNA và thường làm việc theo cặp để tạo ra hai phân tử ADN giống hệt nhau từ một phân tử ADN ban đầu. Trong quá trình này, ADN polymeraza “đọc” sợi ADN hiện có để tạo hai mạch khớp bổ sung với từng mạch cũ.[1][2][3][4][5][6]

Enzim này xúc tác phản ứng hóa học sau

deoxynucleoside triphotphat + ADNn \rightleftharpoons điphotphat + ADNn+1

Xúc tác mở rộng DNA-template-đạo của 3'- cuối của một sợi DNA của một nucleotide tại một thời điểm.

Mỗi khi một tế bào phân chia , DNA polymerase là cần thiết để giúp nhân DNA của tế bào, do đó, một bản sao của phân tử ADN ban đầu có thể được thông qua với mỗi tế bào con. Bằng cách này, thông tin di truyền được truyền từ thế hệ này sang thế hệ khác.

Trước khi nhân rộng có thể xảy ra, một loại enzyme gọi là helicase unwinds các phân tử DNA từ mẫu dệt chặt chẽ của nó. Điều này mở ra hoặc "unzips" DNA sợi kép để cung cấp cho hai sợi đơn của DNA có thể được sử dụng như là các mẫu để nhân rộng.

Lịch sử[sửa | sửa mã nguồn]

In 1956, Arthur Kornberg and colleagues discovered the enzyme ADN polymerase I, also known as Pol I, in Escherichia coli. They described the ADN replication process by which ADN polymerase copies the base sequence of a template ADN strand. Subsequently, in 1959, Kornberg was awarded the Nobel Prize in Physiology or Medicine for this work.[7] ADN polymerase II was also discovered by Kornberg and Malcolm E. Gefter in 1970 while further elucidating the role of Pol I in E. coli ADN replication.[8]

Chức năng[sửa | sửa mã nguồn]

ADN polymerase moves along the old strand in the 3'-5' direction, creating a new strand having a 5'-3' direction.
ADN polymerase with proofreading ability

The main function of ADN polymerase is to make ADN from nucleotides, the building blocks of ADN. The ADN copies are created by the pairing of nucleotides to bases present on each strand of the original ADN molecule. This pairing always occurs in specific combinations, with cytosine along with guanine, and thymine along with adenine, forming two separate pairs, respectively.

When creating ADN, ADN polymerase can add free nucleotides only to the 3' end of the newly forming strand. This results in elongation of the newly forming strand in a 5'-3' direction. No known ADN polymerase is able to begin a new chain (de novo); it can only add a nucleotide onto a pre-existing 3'-OH group, and therefore needs a primer at which it can add the first nucleotide. Primers consist of RNA or ADN bases (or both). In ADN replication, the first two bases are always RNA, and are synthesized by another enzyme called primase. Enzymes,helicasetopoisomerase II, are required to unwind ADN from a double-strand structure to a single-strand structure to facilitate replication of each strand consistent with the semiconservative model of ADN replication.

It is important to note that the directionality of the newly forming strand (the daughter strand) is opposite to the direction in which ADN polymerase moves along the template strand. Since ADN polymerase requires a free 3' OH group for initiation of synthesis, it can synthesize in only one direction by extending the 3' end of the preexisting nucleotide chain. Hence, ADN polymerase moves along the template strand in a 3'-5' direction, and the daughter strand is formed in a 5'-3' direction. This difference enables the resultant double-strand ADN formed to be composed of two ADN strands that are antiparallel to each other.

The function of ADN polymerase is not quite perfect, with the enzyme making about one mistake for every billion base pairs copied. Error correction is a property of some, but not all, ADN polymerases. This process corrects mistakes in newly synthesized ADN. When an incorrect base pair is recognized, ADN polymerase moves backwards by one base pair of ADN. The 3'-5' exonuclease activity of the enzyme allows the incorrect base pair to be excised (this activity is known as proofreading). Following base excision, the polymerase can re-insert the correct base and replication can continue forwards. This preserves the integrity of the original ADN strand that is passed onto the daughter cells.

Cấu trúc[sửa | sửa mã nguồn]

The known ADN polymerases have highly conserved structure, which means that their overall catalytic subunits vary very little from species to species, independent of their domain structures. Conserved structures usually indicate important, irreplaceable functions of the cell, the maintenance of which provides evolutionary advantages. The shape can be described as resembling a right hand with thumb, finger, and palm domains. The palm domain appears to function in catalyzing the transfer of phosphoryl groups in the phosphoryl transfer reaction. ADN is bound to the palm when the enzyme is active. This reaction is believed to be catalyzed by a two-metal-ion mechanism. The finger domain functions to bind the nucleotide triphosphate with the template base. The thumb domain plays a potential role in the processivity, translocation, and positioning of the ADN.[9]

Processivity[sửa | sửa mã nguồn]

ADN polymerase’s rapid catalysis is due to its processive nature. Processivity is a characteristic of enzymes that function on polymeric substrates. In the case of ADN polymerase, the degree of processivity refers to the average number of nucleotides added each time the enzyme binds a template. The average ADN polymerase requires about one second locating and binding a primer/template junction. Once it is bound, a nonprocessive ADN polymerase adds nucleotides at a rate of one nucleotide per second.[10]:207–208 Processive ADN polymerases, however, add multiple nucleotides per second, drastically increasing the rate of ADN synthesis. The degree of processivity is directly proportional to the rate of ADN synthesis. The rate of ADN synthesis in a living cell was first determined as the rate of phage T4 ADN elongation in phage infected E. coli. During the period of exponential ADN increase at 37 °C, the rate was 749 nucleotides per second.[11]

ADN polymerase’s ability to slide along the ADN template allows increased processivity. There is a dramatic increase in processivity at the replication fork. This increase is facilitated by the ADN polymerase’s association with proteins known as the sliding ADN clamp. The clamps are multiple protein subunits associated in the shape of a ring. Using the hydrolysis of ATP, a class of proteins known as the sliding clamp loading proteins open up the ring structure of the sliding ADN clamps allowing binding to and release from the ADN strand. Protein-protein interaction with the clamp prevents ADN polymerase from diffusing from the ADN template, thereby ensuring that the enzyme binds the same primer/template junction and continues replication.[10]:207–208 ADN polymerase changes conformation, increasing affinity to the clamp when associated with it and decreasing affinity when it completes the replication of a stretch of ADN to allow release from the clamp.

Variation across species[sửa | sửa mã nguồn]

DNA polymerase family A
PDB 2hht EBI.jpg
c:o6-methyl-guanine pair in the polymerase-2 basepair position
Danh pháp
Ký hiệu DNA_pol_A
Pfam PF00476
InterPro IPR001098
SMART -
PROSITE PDOC00412
SCOP 1dpi
DNA polymerase family B
PDB 2dy4 EBI.jpg
crystal structure of rb69 gp43 in complex with dna containing thymine glycol
Danh pháp
Ký hiệu DNA_pol_B
Pfam PF00136
Pfam clan CL0194
InterPro IPR006134
PROSITE PDOC00107
SCOP 1noy
DNA polymerase type B, organellar and viral
PDB 1xhz EBI.jpg
phi29 dna polymerase, orthorhombic crystal form, ssdna complex
Danh pháp
Ký hiệu DNA_pol_B_2
Pfam PF03175
Pfam clan CL0194
InterPro IPR004868

Based on sequence homology, ADN polymerases can be further subdivided into seven different families: A, B, C, D, X, Y, and RT.

Some viruses also encode special ADN polymerases, such as Hepatitis B virus ADN polymerase. These may selectively replicate viral ADN through a variety of mechanisms. Retroviruses encode an unusual ADN polymerase called reverse transcriptase, which is an RNA-dependent ADN polymerase (RdDp). It polymerizes ADN from a template of RNA.

Family Types of ADN polymerase Species Examples
A Replicative and Repair Polymerases Eukaryotic and Prokaryotic T7 ADN polymerase, Pol I, and ADN Polymerase γ
B Replicative and Repair Polymerases Eukaryotic and Prokaryotic Pol II, Pol B, Pol ζ, Pol α, δ, and ε
C Replicative Polymerases Prokaryotic Pol III
D Replicative Polymerases Euryarchaeota Not well-characterized
X Replicative and Repair Polymerases Eukaryotic Pol β, Pol σ, Pol λ, Pol μ, and Terminal deoxynucleotidyl transferase
Y Replicative and Repair Polymerases Eukaryotic and Prokaryotic Pol ι (iota), Pol κ (kappa), Pol IV, and Pol V
RT Replicative and Repair Polymerases Viruses, Retroviruses, and Eukaryotic Telomerase, Hepatitis B virus

Prokaryotic ADN polymerase[sửa | sửa mã nguồn]

Pol I[sửa | sửa mã nguồn]

Prokaryotic Family A polymerases include the ADN polymerase I (Pol I) enzyme, which is encoded by the polA gene and ubiquitous among prokaryotes. This repair polymerase is involved in excision repair with 3'-5' and 5'-3' exonuclease activity and processing of Okazaki fragments generated during lagging strand synthesis.[12] Pol I is the most abundant polymerase accounting for >95% of polymerase activity in E. coli, yet cells lacking Pol I have been found suggesting Pol I activity can be replaced by the other four polymerases. Pol I adds ~15-20 nucleotides per second, thus showing poor processivity. Instead, Pol I starts adding nucleotides at the RNA primer:template junction known as the origin of replication (ori). Approximately 400 bp downstream from the origin, the Pol III holoenzyme is assembled and takes over replication at a highly processive speed and nature.[13]

Pol II[sửa | sửa mã nguồn]

ADN polymerase II, a Family B polymerase, is a polB gene product also known as DinA. Pol II has 3'-5' exonuclease activity and participates in ADN repair, replication restart to bypass lesions, and its cell presence can jump from ~30-50 copies per cell to ~200-300 during SOS induction. Pol II is also thought to be a backup to Pol III as it can interact with holoenzyme proteins and assume a high level of processivity. The main role of Pol II is thought to be the ability to direct polymerase activity at the replication fork and helped stalled Pol III bypass terminal mismatches.[14]

Pol III[sửa | sửa mã nguồn]

ADN polymerase III holoenzyme is the primary enzyme involved in ADN replication in E. coli and belongs to Family C polymerases. It consists of three assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The core consists of three subunits - α, the polymerase activity hub, ɛ, exonucleolytic proofreader, and θ, which may act as a stabilizer for ɛ. The holoenzyme contains two cores, one for each strand, the lagging and leading.[15] The beta sliding clamp processivity factor is also present in duplicate, one for each core, to create a clamp that encloses ADN allowing for high processivity.[16] The third assembly is a seven-subunit (τ2γδδ′χψ) clamp loader complex. Recent research has classified Family C polymerases as a subcategory of Family X with no eukaryotic equivalents.[17]

Pol IV[sửa | sửa mã nguồn]

In E. coli, ADN polymerase IV (Pol 4) is an error-prone ADN polymerase involved in non-targeted mutagenesis.[18] Pol IV is a Family Y polymerase expressed by the dinB gene that is switched on via SOS induction caused by stalled polymerases at the replication fork. During SOS induction, Pol IV production is increased tenfold and one of the functions during this time is to interfere with Pol III holoenzyme processivity. This creates a checkpoint, stops replication, and allows time to repair ADN lesions via the appropriate repair pathway.[19] Another function of Pol IV is to perform translesion synthesis at the stalled replication fork like, for example, bypassing N2-deoxyguanine adducts at a faster rate than transversing undamaged ADN. Cells lacking dinB gene have a higher rate of mutagenesis caused by ADN damaging agents.[20]

Pol V[sửa | sửa mã nguồn]

ADN polymerase V (Pol V) is a Y-family ADN polymerase that is involved in SOS responsetranslesion synthesis ADN repair mechanisms.[21] Transcription of Pol V via the umuDC genes is highly regulated to produce only Pol V when damaged ADN is present in the cell generating an SOS response. Stalled polymerases causes RecA to bind to the ssADN, which causes the LexA protein to autodigest. LexA then loses its ability to repress the transcription of the umuDC operon. The same RecA-ssADN nucleoprotein posttranslationally modifies the UmuD protein into UmuD' protein. UmuD and UmuD' form a heterodimer that interacts with UmuC, which in turn activates umuC's polymerase catalytic activity on damaged ADN.[22]

Eukaryotic ADN polymerase[sửa | sửa mã nguồn]

Polymerases β, λ, σ and μ (beta, lambda, sigma, and mu)[sửa | sửa mã nguồn]

Family X polymerases contain the well-known eukaryotic polymerase pol β (beta), as well as other eukaryotic polymerases such as Pol σ (sigma), Pol λ (lambda), Pol μ (mu), and Terminal deoxynucleotidyl transferase (TdT). Family X polymerases are found mainly in vertebrates, and a few are found in plants and fungi. These polymerases have highly conserved regions that include two helix-hairpin-helix motifs that are imperative in the ADN-polymerase interactions. One motif is located in the 8 kDa domain that interacts with downstream ADN and one motif is located in the thumb domain that interacts with the primer strand. Pol β, encoded by POLB gene, is required for short-patch base excision repair, a ADN repair pathway that is essential for repairing alkylated or oxidized bases as well as abasic sites. Pol λ and Pol μ, encoded by the POLLPOLM genes respectively, are involved in non-homologous end-joining, a mechanism for rejoining ADN double-strand breaks due to hydrogen peroxide and ionizing radiation, respectively. TdT is expressed only in lymphoid tissue, and adds "n nucleotides" to double-strand breaks formed during V(D)J recombination to promote immunological diversity.[23]

Polymerases α, δ and ε (alpha, delta, and epsilon)[sửa | sửa mã nguồn]

Pol α (alpha), Pol δ (delta), and Pol ε (epsilon) are members of Family B Polymerases and are the main polymerases involved with nuclear ADN replication. Pol α complex (pol α-ADN primase complex) consists of four subunits: the catalytic subunit POLA1, the regulatory subunit POLA2, and the small and the large primase subunits PRIM1PRIM2 respectively. Once primase has created the RNA primer, Pol α starts replication elongating the primer with ~20 nucleotides.[24] Due to its high processivity, Pol δ takes over the leading and lagging strand synthesis from Pol α.[10]:218–219 Pol δ is expressed by genes POLD1, creating the catalytic subunit, POLD2, POLD3, and POLD4 creating the other subunits that interact with Proliferating Cell Nuclear Antigen (PCNA), which is a ADN clamp that allows Pol δ to possess processivity.[25] Pol ε is encoded by the POLE1, the catalytic subunit, POLE2, and POLE3 genes. It was previously thought that Pol ε's main function was to extend the leading strand during replication; however, recent evidence suggests that Pol δ alone replicates the leading and lagging strands of ADN, and Pol ε participates in repairing errors made in the leading strand during Pol δ replication in conjunction with ADN mismatch repair machinery.[26] Pol ε's C-terminus region is thought to be essential to cell vitality as well. The C-terminus region is thought to provide a checkpoint before entering anaphase, provide stability to the holoenzyme, and add proteins to the holoenzyme necessary for initiation of replication.[27]

Polymerases η, ι and κ (eta, iota, and kappa)[sửa | sửa mã nguồn]

Pol η (eta), Pol ι (iota), and Pol κ (kappa), are Family Y ADN polymerases involved in the ADN repair by translesion synthesis and encoded by genes POLH, POLI, and POLK respectively. Members of Family Y have five common motifs to aid in binding the substrate and primer terminus and they all include the typical right hand thumb, palm and finger domains with added domains like little finger (LF), polymerase-associated domain (PAD), or wrist. The active site, however, differs between family members due to the different lesions being repaired. Polymerases in Family Y are low-fidelity polymerases, but have been proven to do more good than harm as mutations that affect the polymerase can cause various diseases, such as skin cancerXeroderma Pigmentosum Variant (XPS). The importance of these polymerases is evidenced by the fact that gene encoding ADN polymerase η is referred as XPV, because loss of this gene results in the disease Xeroderma Pigmentosum Variant. Pol η is particularly important for allowing accurate translesion synthesis of ADN damage resulting from ultraviolet radiation. The functionality of Pol κ is not completely understood, but researchers have found two probable functions. Pol κ is thought to act as an extender or an inserter of a specific base at certain ADN lesions. All three translesion synthesis polymerases, along with Rev1, are recruited to damaged lesions via stalled replicative ADN polymerases. There are two pathways of damage repair leading researchers to conclude that the chosen pathway depends on which strand contains the damage, the leading or lagging strand.[28]

Polymerases Rev1 and ζ (zeta)[sửa | sửa mã nguồn]

Pol ζ another B family polymerase, is made of two subunits Rev3, the catalytic subunit, and Rev7, which increases the catalytic function of the polymerase, and is involved in translesion synthesis. Pol ζ lacks 3' to 5' exonuclease activity, is unique in that it can extend primers with terminal mismatches. Rev1 has three regions of interest in the BRCT domain, ubiquitin-binding domain, and C-terminal domain and has dCMP transferase ability, which adds deoxycytidine opposite lesions that would stall replicative polymerases Pol δ and Pol ε. These stalled polymerases activate ubiquitin complexes that in turn disassociate replication polymerases and recruit Pol ζ and Rev1. Together Pol ζ and Rev1 add deoxycytidine and Pol ζ extends past the lesion. Through a yet undetermined process, Pol ζ disassociates and replication polymerases reassociate and continue replication. Pol ζ and Rev1 are not required for replication, but loss of REV3 gene in budding yeast can cause increased sensitivity to ADN-damaging agents due to collapse of replication forks where replication polymerases have stalled.[29]

Telomerase[sửa | sửa mã nguồn]

Telomerase is a ribonucleoprotein recruited to replicate ends of linear chromosomes because normal ADN polymerase cannot replicate the ends, or telomere. The single-strand 3’ overhang of the double-strand chromosome with the sequence 5’-TTAGGG-3’ recruits telomerase. Telomerase acts like other ADN polymerases by extending the 3’ end, but, unlike other ADN polymerases, telomerase does not require a template. The TERT subunit, an example of a reverse transcriptase, uses the RNA subunit to form the primer–template junction that allows telomerase to extend the 3’ end of chromosome ends. The gradual decrease in size of telomeres as the result of many replications over a lifetime are thought to be associated with the effects of aging.[10]:248–249

Polymerases γ and θ (gamma and theta)[sửa | sửa mã nguồn]

Pol γ (gamma) and Pol θ (theta) are Family A polymerases. Pol γ, encoded by the POLG gene, is the only mtADN polymerase and therefore replicates, repairs, and has proofreading 3'-5' exonuclease and 5' dRP lyase activities. Any mutation that leads to limited or non-functioning Pol γ has a significant effect on mtADN and is the most common cause of autosomal inherited mitochondrial disorders.[30] Pol γ contains a C-terminus polymerase domain and an N-terminus 3'-5' exonuclease domain that are connected via the linker region, which binds the accessory subunit. The accessory subunit binds ADN and is required for processivity of Pol γ. Point mutation A467T in the linker region is responsible for more than one-third of all Pol γ-associated mitochondrial disorders.[31] While many homologs of Pol θ, encoded by the POLQ gene, are found in eukaryotes, its function is not clearly understood. The sequence of amino acids in the C-terminus is what classifies Pol θ as Family A polymerase, although the error rate for Pol θ is more closely related to Family Y polymerases. Pol θ extends mismatched primer termini and can bypass abasic sites by adding a nucleotide. It also has Deoxyribophosphodiesterase (dRPase) activity in the polymerase domain and can show ATPase activity in close proximity to ssADN.[32]

Polymerase ν (nu)[sửa | sửa mã nguồn]

Xem thêm thông tin: DNA polymerase nu

Reverse transcriptase[sửa | sửa mã nguồn]

Retroviruses encode an unusual ADN polymerase called reverse transcriptase, which is an RNA-dependent ADN polymerase (RdDp) that synthesizes ADN from a template of RNA. The reverse transcriptase family contain both ADN polymerase functionality and RNase H functionality, which degrades RNA base-paired to ADN. Some retrovirus examples include Hepatitis B virus and HIV.[10]:

Xem thêm[sửa | sửa mã nguồn]

Tham khảo[sửa | sửa mã nguồn]

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Đọc thêm[sửa | sửa mã nguồn]

  • Burgers PM, Koonin EV, Bruford E, Blanco L, Burtis KC, Christman MF, Copeland WC, Friedberg EC, Hanaoka F, Hinkle DC, Lawrence CW, Nakanishi M, Ohmori H, Prakash L, Prakash S, Reynaud CA, Sugino A, Todo T, Wang Z, Weill JC, Woodgate R (tháng 11 năm 2001). “Eukaryotic DNA polymerases: proposal for a revised nomenclature”. J. Biol. Chem. 276 (47): 43487–90. doi:10.1074/jbc.R100056200. PMID 11579108. 

External links[sửa | sửa mã nguồn]

Bản mẫu:DNA replication Bản mẫu:Kinases Bản mẫu:Enzymes