DNA polymerase: Difference between revisions
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[[Image:1taq.png|left|200px|thumb|Crystal Structure of DNA polymerase [[1taq]]]] | [[Image:1taq.png|left|200px|thumb|Crystal Structure of DNA polymerase [[1taq]]]] | ||
{{STRUCTURE_1taq| PDB=1taq | SIZE= | {{STRUCTURE_1taq| PDB=1taq | SIZE=400| SCENE=DNA_polymerase/Cv/1 |right|CAPTION=DNA polymerase complex with octylglucoside [[1taq]] }} | ||
[[DNA polymerase]] '''(Dpo)''' reads a [[DNA|DNA strand]] and catalyzes the synthesis of its complementary strand. Dpo sliding clamp is made of the complex of Dpo and [[Proliferating Cell Nuclear Antigen]] (PCNA) which encircles it. The BRCT domain in Dpo is the C-terminal domain of breast [[cancer]] susceptibility protein. The Klenow fragment is a large Dpo fragment produced upon cleavage of Dpo by [[Subtilisin|subtilisin]]. In the ''E. coli'', the EcDpo III subunits γ, δ, δ' are named clamp loader. This complex assembles the β subunit sliding clamp unto the DNA. '''Rev1''' is a '''Dpo''' involved in replication over DNA lesions. '''Terminal deoxynucleotidyl transferase (TdT)''' is a Dpo expressed in immature lymphoid cells. TdT adds nucleotides to exons during antibody gene recombination. The images at the left and at the right correspond to one representative Dpo, ''i.e.'' the crystal structure of DNA polymerase I from ''Thermus aquaticus'' ([[1taq]]). | [[DNA polymerase]] '''(Dpo)''' reads a [[DNA|DNA strand]] and catalyzes the synthesis of its complementary strand. Dpo sliding clamp is made of the complex of Dpo and [[Proliferating Cell Nuclear Antigen]] (PCNA) which encircles it. The BRCT domain in Dpo is the C-terminal domain of breast [[cancer]] susceptibility protein. The Klenow fragment is a large Dpo fragment produced upon cleavage of Dpo by [[Subtilisin|subtilisin]]. In the ''E. coli'', the EcDpo III subunits γ, δ, δ' are named clamp loader. This complex assembles the β subunit sliding clamp unto the DNA. '''Rev1''' is a '''Dpo''' involved in replication over DNA lesions. '''Terminal deoxynucleotidyl transferase (TdT)''' is a Dpo expressed in immature lymphoid cells. TdT adds nucleotides to exons during antibody gene recombination. The images at the left and at the right correspond to one representative Dpo, ''i.e.'' the crystal structure of DNA polymerase I from ''Thermus aquaticus'' ([[1taq]]). For more details see [[DNA Polymerase I]]. | ||
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Revision as of 23:53, 10 January 2012
DNA polymerase (Dpo) reads a DNA strand and catalyzes the synthesis of its complementary strand. Dpo sliding clamp is made of the complex of Dpo and Proliferating Cell Nuclear Antigen (PCNA) which encircles it. The BRCT domain in Dpo is the C-terminal domain of breast cancer susceptibility protein. The Klenow fragment is a large Dpo fragment produced upon cleavage of Dpo by subtilisin. In the E. coli, the EcDpo III subunits γ, δ, δ' are named clamp loader. This complex assembles the β subunit sliding clamp unto the DNA. Rev1 is a Dpo involved in replication over DNA lesions. Terminal deoxynucleotidyl transferase (TdT) is a Dpo expressed in immature lymphoid cells. TdT adds nucleotides to exons during antibody gene recombination. The images at the left and at the right correspond to one representative Dpo, i.e. the crystal structure of DNA polymerase I from Thermus aquaticus (1taq). For more details see DNA Polymerase I.
3D Structures of DNA polymerase3D Structures of DNA polymerase
Updated November 2011
Family A – replicative and repair DpoFamily A – replicative and repair Dpo
2ajq – T7Dpo (mutant) + thioredoxin (mutant) + DNA - Enterobacteria phage T7
1t7p - T7Dpo (mutant) + thioredoxin + DNA
1zyq, 1x9m, 1x9s, 1x9w, 1tk0, 1skr, 1sks, 1skw, 1sl0, 1sl1, 1sl2, 1t7p - T7Dpo (mutant) + thioredoxin + DNA + nucleotide
1t8e, 1tk5, 1tk8, 1tkd - T7Dpo + thioredoxin + DNA + nucleotide
2gv9 – Dpo – Herpes simplex virus
2kzz, 1d8y, 2kzm – EcDpo I klenow fragment - Escherichia coli
1qsl - EcDpo I klenow fragment + DNA
1kfs, 1krp, 1ksp, 1kln - EcDpo I klenow fragment (mutant) + DNA
1kfd, 1dpi - EcDpo I klenow fragment + nucleotide
1d9d, 1d9f, 2kfn - EcDpo I klenow fragment + DNA + nucleotide
2kfz - EcDpo I klenow fragment (mutant) + DNA + nucleotide
1taq – TaDpo I - Thermus aquaticus
1jxe – TaDpo I Stoffel fragment
1ktq - TaDpo I klenow fragment
5ktq – TaDpo I + nucleotide
3ojs, 3oju, 1tau - TaDpo I + DNA
3po4, 3po5 - TaDpo I klenow fragment + DNA
3py8 - TaDpo I klenow fragment (mutant) + DNA
3m8r, 3m8s, 3lwl, 3lwm, 1qss, 1qsy, 1qtm, 2ktq, 3ktq, 4ktq - TaDpo I klenow fragment + DNA + nucleotide
1xwl - GsDpo I fragment - Geobacillus stearothermophilus
2xo7, 3hp6, 3hpo, 2hhq, 2hhs, 2hht, 2hhu, 2hhv, 2hhw, 2hhx, 2hvh, 2hvi, 2hw3, 1xc9, 1ua0, 1ua1, 1njw, 1njx, 1njy, 1njz, 1nk0, 1nk4, 1nk5, 1nk6, 1nk7, 1nk8, 1nk9, 1nkb, 1nkc, 1nke, 1l3s, 2bdp, 4bdp, 2xy5, 2xy6, 2xy7, 2y1i, 2y1j, 3tan, 3tap, 3taq, 3tar, 3thv - GsDpo I fragment + DNA
3ht3, 1u45, 1u47, 1u48, 1u49, 1u4b, 1l3t, 1l3u, 1l3v, 1l5u, 1lv5, 3bdp - GsDpo I fragment + DNA + nucleotide
3ikm - hDpo γ1+γ2 - human
3ikl, 2g4c - hDpo γ2
3g6v, 3g6x, 3g6y - hDpo ι + DNA
3gdx, 3rh4, 3rh5, 3rh6 - hDpo β + DNA
3si8 - hDpo η + DNA
Family B – 3’-5’ exonuclease activityFamily B – 3’-5’ exonuclease activity
1ih7 – EpDpo - Enterobacteria phage RB69
3cfo – EpDpo (mutant)
1waf, 1waj - EpDpo + nucleotide
3nci, 3lds, 3l8b, 3cq8,3cfp, 3cfr, 3kd1, 3kd5 - EpDpo (mutant) + DNA
3ndk, 3ne6, 3ngi, 3nhg, 3nae, 3lzj, 3lzi, 2ozs, 2p5g, 2dy4, 1q9x, 1q9y, 1ig9, 3qep, 3rma, 3rmb, 3rmc, 3rmd, 3rwu, 3s9h, 3scx, 3si6, 3sjj, 3snn, 3spy, 3spz, 3sq0, 3sq1, 3sq2, 3sq4, 3sun, 3suo, 3sup, 3suq, 3tab, 3tae, 3taf, 3tag- EpDpo (mutant) + DNA + nucleotide
1clq - EpDpo + DNA + nucleotide
2oyq, 2ozm, 2p5o, 2dtu - EpDpo (mutant) + DNA + nucleotide analog
2atq – EpDpo + GP32
1noy – T4Dpo + DNA - Enterobacteria phage T4
1noz – T4Dpo residues 1-388
2ex3 – Dpo (mutant) + DNA terminal protein – Bacillus phage φ29
2py5, 2pzs, 1xhz, 1xi1 – BpDpo (mutant) + DNA
2pyj, 2pyl - BpDpo (mutant) + DNA + nucleotide
1xhx - BpDpo (mutant)
2keb - hDpo αB - NMR
1n5g, 1k0p, 1k18 - hDpo α zinc finger domain- NMR
1zqj – hDpo β + DNA
3e0j - hDpo δ2+δ3
3mr4, 3mr2, 3mr3, 3mr5, 3mr6 - hDpo ε catalytic core + DNA + nucleotide
3oiq - yDpo α + cell division control protein 13 – yeast
3flo, 3lgb - yDpo α subunits A,B
3iay - yDpo δ catalytic subunit + DNA
3oha, 3ohb, 3mfh - yDpo ε (mutant) + DNA
3mfi - yDpo ε (mutant) + DNA + nucleotide
2r8j, 2r8k - yDpo ε catalytic domain + DNA + nucleotide
2xgp, 2xgq, 2wtf - yDpo ε + DNA
3maq, 3k57, 3k58, 3k59, 3k5l, 3k5m - EcDpo II (mutant) + DNA + nucleotide
3k5n - EcDpo II (mutant) + DNA
3k5o, 1q8i - EcDpo II (mutant)
3a2f - PfDpo + PCNA - Pyrococcus furiosus
2jgu - PfDpo
1tgo - TgDpo – Thermococcus gorgonarius
2vwj – TgDpo (mutant) + DNA
2vwk - TgDpo (mutant)
2xhb - Dpo (mutant) + DNA + Thermococcus gorgonarius
1wn7, 1wns – Dpo B - Thermococcus kodakarensis
1qht - Dpo (mutant) – Thermococcus
1d5a – DeDpo – Desulfurococcus
Family C – bacterial chromosomal replicative DpoFamily C – bacterial chromosomal replicative Dpo
2hnh, 2hqa - EcDpo III subunit α catalytic fragment
2gui – EcDpo III subunit ε N-terminal
1j53, 1j54 - EcDpo III subunit ε N-terminal exonuclease domain
2ido - EcDpo III subunit ε + HOT protein
1ok7 - EcDpo III + EcDpo IV C-terminal
1mmi, 2pol - EcDpo III subunit β
2xur, 3f1v, 3pwe - EcDpo III subunit β (mutant)
3d1e - EcDpo III subunit β + EcDpo II C-terminal
1unn - EcDpo III subunit β + EcDpo IV little finger
3d1g, 3qsb - EcDpo III subunit β + inhibitor
3bep - EcDpo III subunit β + DNA
3d1f - EcDpo III β subunit + polypeptide
1njf, 1njg - EcDpo III subunit γ N-terminal domains 1-2
1jqj, 1jql - EcDpo III subunit β, δ(mutant)
1a5t - EcDpo III subunit δ’
1xxh, 1jr3 - EcDpo III subunit γ, δ, δ'
1xxi - EcDpo III subunit γ, δ, δ' + nucleotide
3glh - EcDpo III subunit δ, δ', τ
3glf - EcDpo III subunit δ, δ', τ DNA
3gli - EcDpo III subunit δ, δ', τ, ξ DNA
3glg - EcDpo III subunit δ, δ', τ mutant DNA
2xy8 - EcDpo III subunit ε,θ
2axd, 2ae9, 1du2 - EcDpo III subunit θ - NMR
2aya - EcDpo III subunit τ
1em8 - EcDpo III subunit φ, χ
3sxu - EcDpo III subunit ϕ,χ + peptide
1bgx – TaDpo + TP7 MAB
Family X – eukaryotic Dpo involved in base excision repair, non-homologous end-joining and V(D)J recombination.Family X – eukaryotic Dpo involved in base excision repair, non-homologous end-joining and V(D)J recombination.
3q8p, 3q8q, 3lk9, 3mby, 3isb, 3isc, 1zjm, 1tv9, 1tva, 1bpx, 1bpz, 1zqa, 1zqb, 1zqc, 1zqd, 1zqf, 1zqg, 1zqh, 1zqi, 1zaj, 1zqk, 1zql, 1zqm, 1zqn, 1zqo, 1zqp, 1zqq, 1zqr, 1zqs, 1zqt, 1zqu, 1zqv, 1zqw, 1zqx, 1zqy, 1zqz, 7ice, 7icf, 7ici, 7icj, 7icl, 7icm, 7icp, 7icr, 7ict, 7icu, 7icv, 8icb, 8icc, 9icj, 9ick, 9icl, 9icm, 9icp, 9icw, 9icx, 9icy, 7icg, 7ich, 7ick, 7icn, 7ico, 7icq, 7ics, 1zqe - hDpo β + DNA
3jpn, 3jpo, 3jpp, 3jpq, 3jpr, 3jpt, 3jps, 3isd, 3c2k, 3c2l, 3c2m, 2pxi, 2iso, 2isp, 2i9g, 2fmp, 2fmq, 2fms, 1zjn, 1mq2, 1mq3, 1bpy, 8ica, 8ice, 8icf, 8icg, 8ich, 8ici, 8icj, 8ick, 8icl, 8icm, 8icn, 8ico, 8icp, 8icq, 8icr, 8ics, 8ict, 8icu, 8icv, 8icw, 8icx, 8icz, 9ice, 9icg, 9ich, 9ici, 9icq, 9ics, 9ict, 9icu, 9icv, 9icr, 9icn, 9ico, 8icy, 9ica, 9icb, 9icc, 9icf - hDpo β + DNA + nucleotide
2p66 - hDpo β + DNA + nucleotide analog
3ogu - hDpo β (mutant) + DNA
2v6z - hDpo β N-terminal (mutant) - NMR
3k75, 3lqc - hDpo β + DNA repair protein XRCC1
2jw5 - hDpo λ BRCT domain
1xsl - hDpo λ catalytic domain
1nzp - hDpo λ lyase domain - NMR
3pmn, 3pnc, 3mda, 2gws, 2bcq, 2bcr, 2bcs, 2bcu, 2bcv, 1xsp, 1rzt - hDpo λ + DNA
3mgh, 3c5f, 3c5g, 2pfn - hDpo λ (mutant) + DNA
3pml, 3mdc, 1xsn - hDpo λ + DNA + nucleotide
3mgi, 3hw8, 3hwt, 3hx0, 2pfo, 2pfp, 2pfq - hDpo λ (mutant) + DNA + nucleotide
2htf, 2dun - hDpo μ BRCT domain – NMR
2ihm - mDpo μ catalytic domain + DNA – mouse
1rpl, 2bpc, 1bpe, 1bpb, 1bpd - rDpo β – rat
2van, 1jn3 - rDpo β (mutant)
1dk2, 1dk3, 1bno, 1bnp - rDpo β N-terminal – NMR
1nom - rDpo β C-terminal
1huo, 1huz - rDpo β + DNA
1bpe - rDpo β + nucleotide
2bpf, 2bpg - rDpo β + DNA + nucleotide
1jms – mTdT
1kej – mTdT+ nucleotide
1kdh - mTdT+ nucleotide + DNA
2w9m – Dpo X – Deinococcus radiodurans
Family Y – translesion DpoFamily Y – translesion Dpo
2i5o - hDpo η ubiquitin-binding zinc finger - NMR
3abd, 3abe - hDpo ξ catalytic subunit Rev3 + mitotic spindle assembly checkpoint protein Rev7
3gqc – hRev1 + DNA + nucleotide
2ebw – hRev1 BRCT domain – NMR
3bjy, 2aq4 – yRev1 catalytic domain + DNA + nucleotide
3q8r, 3q8s, 3h4b, 3h4d, 3gv5, 3gv7, 3gv8, 3epg, 3epi, 2fll, 2fln, 2flp, 2dpi, 2dpj, 2alz, 1zet, 1t3n - hDpo τ + DNA + nucleotide
3ngd, 3osn - hDpo τ catalytic fragment + DNA
3h40 - hDpo τ DNA binding domain + DNA
2ktf - hDpo τ + ubiquitin
2l0f, 2l0g - hDpo τ + ubiquitin – NMR
1t94 - hDpo κ
3in5 - hDpo κ + DNA
2w7o, 2w7p, 2oh2 - hDpo κ + DNA + nucleotide
2kwu, 2kwv - mDpo τ C-terminal + ubiquitin - NMR
3ai4 - mDpo τ/yEGFP
1jih – yDpo η catalytic domain
2rdi - SsDpo IV - Sulfolobus solfataricus
3pr4, 3pr5, 2r8g, 2r8h, 2r8i, 2uvr, 2uvu, 2uvv, 2uvw - SsDpo IV (mutant) + DNA + nucleotide
2xc9, 3m9m, 3m9n, 3m9o, 2v4q, 2v4r, 2ago, 1ryr, 1rys, 2w9a, 2w9b, 2w9c, 3gii, 3gij, 3gik, 3gil, 3gim, 3qz7, 3qz8, 3pvx, 3pw0, 3pw2, 3pw4, 3pw5, 3pw7, 3raq, 3rax, 3rb0, 3rb3, 3rb4, 3rb6, 3rbd, 3rbe- SsDpo IV + DNA
2xca, 2xcp, 3khg, 3khh, 3khl, 3khr, 2w8k, 2w8l, 2rdj, 2v9w, 2va2, 2va3, 2ia6, 2ibk, 2jef, 2jeg, 2jei, 2jej, 2imw, 2j6s, 2j6t, 2j6u, 2asd, 2asj, 2asl, 2atl, 2au0, 2c22, 2c28, 2c2d, 2c2e, 2c2r, 2agp, 2agq, 2bqr, 2bqu, 2br0, 2bq3, 1s9f, 1s97, 1s0m, 1s0n, 1s0o, 1s10, 1n48, 1n56, 1jx4, 1jxl - SsDpo IV + DNA + nucleotide
3fds – SsDpo IV + PCNA B + PCNA C
3bq2 – SaDpo IV + DNA – Sulfolobus acidocaldarius
3bq1 - SaDpo IV + DNA + nucleotide
3bq0 - SaDpo IV + DNA
Prokaryotic Pol I – DNA repairProkaryotic Pol I – DNA repair
1s5j – SsDpo I
3eyz - BsDpo I (mutant) + DNA - Bacillus stearothermophilus
3ez5 - BsDpo I (mutant) + DNA + nucleotide
3pv8, 3px0, 3px4, 3px6 - GkDpo I (mutant) + DNA – Geobacillus kaustophilus
Prokaryotic Pol II – DNA repairProkaryotic Pol II – DNA repair
3o59 - PhDpo II large subunit - Pyrococcus horikoshii
2kxe - PhDpo II small subunit
1qqc – DeDpo II
Prokaryotic Pol III – DNA elongation and proofreadingProkaryotic Pol III – DNA elongation and proofreading
2hpi, 2hpm - TaDpo III α subunit
3e0d - TaDpo III α subunit + DNA
3f2b, 3f2c, 3f2d – GkDpo III α subunit + DNA + nucleotide
1zd7, 1zde, 3nzm - Dpo III α subunit – Synechocystis
2avt - Dpo III β subunit – Streptococcus pyogenes
2awa - Dpo III β subunit – Streptococcus pneumoniae
2p1j – TmDpo III exonuclease domain – Thermotoga maritima
1vpk - TmDpo III β subunit
2gno - TmDpo III γ subunit
2keq - Dpo III α subunit – Nostoc punctiforme
3d1f - EcDpo III β subunit + polypeptide
3p16 - Dpo III β subunit – Mycobacterrium tuberculosis