DNA polymerase
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).
3D Structures of DNA polymerase3D Structures of DNA polymerase
Family A – replicative and repair DpoFamily A – replicative and repair Dpo
2ajq – T7Dpo (mutant) + thioredoxin (mutant) + DNA - Enterobacteria phage T7
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
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 - 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
Family B – 3’-5’ exonuclease activityFamily B – 3’-5’ exonuclease activity
1ih7 – EpDpo - Enterobacteria phage RB69 1waf, 1waj - EpDpo + nucleotide 3nci, 3lds, 3l8b, 3cq8 - EpDpo (mutant) + DNA 3ndk, 3ne6, 3ngi, 3nhg, 3nae, 3lzj, 3lzi, 2ozs, 2p5g, 2dy4, 1q9x, 1q9y, 1ig9 - EpDpo (mutant) + DNA + nucleotide 1clq - EpDpo + DNA + nucleotide 2oyq, 2ozm, 2p5o, 2dtu - EpDpo (mutant) + DNA + nucleotide analog 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 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 - 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 catalytic domain + DNA + nucleotide 2xgp, 2xgq, 2wtf - yDpo + 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 Dpo
2hnh, 2hqa - EcDpo III subunit catalytic fragment 2gui – EcDpo III subunit N-terminal 1j53, 1j54 - EcDpo III subunit N-terminal exonuclease domain 2ido - EcDpo III subunit + HOT protein 1ok7 - EcDpo III + EcDpo IV C-terminal 1mmi, 2pol - EcDpo III subunit 2xur, 3f1v - EcDpo III subunit (mutant) 3d1e - EcDpo III subunit + EcDpo II C-terminal 1unn - EcDpo III subunit + EcDpo IV little finger 3d1g - EcDpo III subunit + inhibitor 3bep - EcDpo III subunit + DNA 1njf 1njg - EcDpo III subunit N-terminal domains 1-2 1jqj, 1jql - EcDpo III subunit (mutant) 1a5t - EcDpo III subunit ’ 1xxh, 1jr3 - EcDpo III subunit ’ 1xxi - EcDpo III subunit ’ + nucleotide 3glh - EcDpo III subunit ’ 3glf - EcDpo III subunit ’ DNA 3gli - EcDpo III subunit ’ DNA 3glg - EcDpo III subunit ’mutant DNA 2axd, 2ae9, 1du2 - EcDpo III subunit - NMR 2aya - EcDpo III subunit 1em8 - EcDpo III subunit , 1bgx – TaDpo + TP7 MAB
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, 1zqp1zqq, 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 + 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 + DNA + nucleotide 2p66 - hDpo + DNA + nucleotide analog 3ogu - hDpo (mutant) + DNA 2v6z - hDpo N-terminal (mutant) - NMR 3k75, 3lqc - hDpo + DNA repair protein XRCC1 2jw5 - hDpo BRCT domain 1xsl - hDpo catalytic domain 1nzp - hDpo lyase domain - NMR 3pmn, 3pnc, 3mda, 2gws, 2bcq, 2bcr, 2bcs, 2bcu, 2bcv, 1xsp, 1rzt - hDpo + DNA 3mgh, 3c5f, 3c5g, 2pfn - hDpo (mutant) + DNA 3pml, 3mdc, 1xsn - hDpo + DNA + nucleotide 3mgi, 3hw8, 3hwt, 3hx0, 2pfo, 2pfp, 2pfq - hDpo (mutant) + DNA + nucleotide 2htf, 2dun - hDpo BRCT domain – NMR 2ihm - mDpo catalytic domain + DNA – mouse 1rpl, 2bpc, 1bpe, 1bpb, 1bpd - rDpo – rat 2van, 1jn3 - rDpo (mutant) 1dk2, 1dk3, 1bno, 1bnp - rDpo N-terminal – NMR 1nom - rDpo C-terminal 1huo, 1huz - rDpo + DNA 1bpe - rDpo + nucleotide 2bpf, 2bpg - rDpo + DNA + nucleotide 1jms – mTdT 1kej – mTdT+ nucleotide 1kdh - mTdT+ nucleotide + DNA 2w9m – Dpo X – Deinococcus radiodurans
Family Y – translesion Dpo
2i5o - hDpo ubiquitin-binding zinc finger - NMR 3abd, 3abe - hDpo 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 + DNA + nucleotide 3ngd, 3osn - hDpo catalytic fragment + DNA 3h40 - hDpo DNA binding domain + DNA 2ktf - hDpo + ubiquitin 2l0f, 2l0g - hDpo + ubiquitin – NMR 1t94 - hDpo 3in5 - hDpo + DNA 2w7o, 2w7p, 2oh2 - hDpo + DNA + nucleotide 2kwu, 2kwv - mDpo C-terminal + ubiquitin - NMR 3ai4 - mDpo /yEGFP 1jih – yDpo 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 - 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 repair
1s5j – SsDpo I 3eyz - BsDpo I (mutant) + DNA - Bacillus stearothermophilus 3ez5 - BsDpo I (mutant) + DNA + nucleotide
Prokaryotic 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 proofreading
2hpi, 2hpm - TaDpo III subunit 3e0d - TaDpo III subunit + DNA 3f2b, 3f2c, 3f2d – Dpo III subunit + DNA + nucleotide – Geobacillus kaustophilus 1zd7, 1zde - Dpo III subunit – Synechocystis 2avt - Dpo III subunit – Streptococcus pyogenes 2awa - Dpo III subunit – Streptococcus pneumoniae 2p1j – TmDpo III exonuclease domain – Thermotoga maritime 1vpk - TmDpo III subunit