DNA polymerase 3D structures

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3D Structures of DNA polymerase

Updated on 06-February-2023 {{#tree:id=OrganizedByTopic|openlevels=0|

  • DNA polymerase I
  • DNA polymerase I klenow fragment or Taq polymerase
  • DNA polymerase II
    • 3maq, 3k57, 3k58, 3k59, 3k5l, 3k5m - EcDpo II (mutant) + DNA + nucleotide
    • 3k5n - EcDpo II (mutant) + DNA
    • 3k5o, 1q8i - EcDpo II (mutant)
    • 3o59, 5bkh - PhDpo II large subunit - Pyrococcus horikoshii
    • 2kxe - PhDpo II small subunit
    • 1qqc – DeDpo II – Desulfurococcus
    • 5ijl - PaDpo II large subunit
    • 5ihe - PaDpo II small subunit
    • 6hmf - PaDpo II small subunit (mutant)
    • 6hms - PaDpo II small+large subunits + DNA – Cryo EM
    • 6knb, 6knc - TkPol II small+large subunits + PCNA + DNA - Thermococcus kodakarensis – Cryo EM
    • 7rsr, 7rss, 7rsu, 7tqw - TkPol + purine derivative + DNA
    • 7om3, 7omb, 7omg - TkPol + DNA + nucleotide
    • 7e15 - TkPol II small subunit + GINS51 + ssDNA-specific exonuclease
  • DNA polymerase III subunit alpha
    • 2hnh, 2hqa - EcDpo III subunit  catalytic fragment
    • 4jom - EcDpo III  subunit catalytic fragment (mutant)
    • 5m1s, 5fkw, 5fkv, 5fku - EcDpo III (mutant) subunits + DNA – Cryo EM
    • 1ok7 - EcDpo III residues 1-366 + EcDpo IV C-terminal
    • 2hpi, 2hpm - TaDpo III  subunit
    • 3e0d - TaDpo III  subunit + DNA
    • 3f2b, 3f2c, 3f2d, 4iqj – GkDpo III  subunit + DNA + nucleotide
    • 1zd7, 1zde, 3nzm, 5ol5, 5ol1 - SyDpo III  subunit – Synechocystis
    • 4gig - SyDpo III  subunit (mutant)
    • 2keq, 4kl5, 4kl6 - NpDpo III  subunit – Nostoc punctiforme
    • 4lx3, 4qfq - NpDpo III  subunit + nucleic acid binding tRNA/helicase
    • 5lew - MtPol III  subunit – Mycobacterrium tuberculosis
    • 7pu7 - MtDpo III  subunit + DNA
  • DNA polymerase III subunit beta or sliding clamp
    • 1mmi, 2pol, 4k3s, 4pnv, 4pnw - EcDpo III subunit 
    • 2xur, 3f1v, 3pwe - EcDpo III subunit  (mutant)
    • 3d1e - EcDpo III subunit  + EcDpo II C-terminal
    • 1unn - EcDpo III subunit  + EcDpo IV little finger
    • 2avt - Dpo III  subunit – Streptococcus pyogenes
    • 2awa - Dpo III  subunit – Streptococcus pneumoniae
    • 4trt – DrDpo III  subunit – Deinococcus radiodurans
    • 2p1j – TmDpo III exonuclease domain – Thermotoga maritima
    • 1vpk - TmDpo III  subunit
    • 3t0p - Dpo III  subunit – Eubacterium rectale
    • 6ap4 - Dpo III  subunit – Acinetobacter baumannii
    • 6amq - Dpo III  subunit – Enterobacter cloacae
    • 5wyp, 5wce, 6izo, 6jir - Dpo III  subunit – Caulobacter crescentus
    • 5w7z - RcDpo III  subunit – Rickettsia conorii
    • 6man - Dpo III  subunit – Rickettsia bellii
    • 6d46 - RtDpo III  subunit – Rickettsia typhi
    • 6dlk - RrDpo III  subunit – Rickettsia rickettsii
    • 6d47 - MmDpo III  subunit – Mycobacterium marinum
    • 1jqj, 1jql - EcDpo III subunit (mutant)
    • 4tr6 - Pol III  subunit – Bacillus subtilis
    • 3p16, 3rb9, 4tr7 - MtPol III  subunit
    • 4tr8, 6ams - PsaPol III  subunit – Pseudomonas aeruginosa
    • 6pth - PsaPol III  subunit + griselimycin
    • 4s3i, 4rki - HpPol III  subunit – Helicobacter pylori
    • 6aig - Dpo III  subunit – Aeropyrum pernix
    • 6deg - BbDpo III  subunit – Bartonella birtlesii
    • 7rzm - Dpo III  subunit – Stenotrophomonas maltophilia
    • 8dt6 - Dpo III  subunit – Elizabethkingia anophelis
  • DNA polymerase III subunit beta or sliding clamp complex
  • DNA polymerase III subunit gamma
    • 5c51, 5c52, 5c53 - hDpo III  subunit + DNA + nucleotide
    • 1njf, 1njg - EcDpo III subunit  N-terminal domains 1-2
    • 2gno - TmDpo III  subunit
    • 1xxh, 1jr3 - EcDpo III subunit ’
    • 1xxi - EcDpo III subunit ’ + nucleotide
  • DNA polymerase III subunit delta
    • 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
  • DNA polymerase III subunit epsilon
    • 2gui – EcDpo III subunit  N-terminal
    • 1j53, 1j54 - EcDpo III subunit  N-terminal exonuclease domain
    • 2ido - EcDpo III subunit + HOT protein
    • 4gx8 - EcDpo III ε subunit/ EcDpo III α subunit
    • 4gx9 - EcDpo III ε subunit/ EcDpo III α subunit (mutant)
    • 2xy8 - EcDpo III subunit ,
  • DNA polymerase III subunit tau
    • 2aya - EcDpo III subunit 
    • 3glh - EcDpo III subunit ’
    • 3glf - EcDpo III subunit ’ DNA
    • 3glg - EcDpo III subunit ’mutant DNA
  • DNA polymerase III subunit xi
    • 3gli - EcDpo III subunit ’ DNA
  • DNA polymerase III subunit theta
  • DNA polymerase III subunit chi+phi
    • 1em8 - EcDpo III subunit ,
    • 3sxu - EcDpo III subunit , + peptide
  • DNA polymerase IV
  • DNA polymerase V
    • 8gmt - EcPol V subumit umud + RecA + DNA + nucleotide – Cryo EM
  • DNA polymerase from enterobacteria phage T7
  • DNA polymerase
  • DNA polymerase alpha
    • 4e2i – hDpo α subunit β + large T antigen – human
    • 4y97 - hDpo α catalytic+B subunits
    • 5iud - hDpo α catalytic subunit + DNA
    • 6as7 - hDpo α catalytic subunit (mutant) + DNA
    • 4bpx - hDpo α catalytic subunit + DNA primase small subunit
    • 5exr - hDpo α catalytic+B subunits + DNA primase small+large subunits
    • 7opl - hDpo α catalytic+B subunits + DNA primase small+large subunits + Nsp1 – Cryo EM
    • 7u5c, 8d08 - hDpo α catalytic+B subunits + DNA primase small+large subunits + CST + DNA – Cryo EM
    • 4q5v - hDpo α catalytic subunit + DNA + RNA + aphidicolin
    • 4qcl, 7n2m - hDpo α catalytic subunit + DNA + RNA + nucleotide
    • 2keb - hDpo B - NMR
    • 1n5g, 1k0p, 1k18 - hDpo  zinc finger domain – NMR
    • 7uy7, 7uy8l - Dpo α B subunit + DNA primase small+large subunits – Tetrahymena thermophile - Cryo EM
  • DNA polymerase beta

6ctq, 6ctp, 6cto, 6ctn, 6ctm, 6ctl, 6ctk, 6ctj, 6cti, 6crh, 6crc, 6crb, 6cr9, 6cr8, 6cr7, 6cr6, 6cr5, 6cr4, 6cr3, 6cpq, 6cly, 6bem, 6bel, 6ph6, 6u2o, 6u6b, 6uok, 6uol, 6uom, 6w2m, 7k96 - hDpo  + DNA + nucleotide analog

  • DNA polymerase beta-like protein
  • DNA polymerase gamma
  • DNA polymerase delta
    • 3e0j - hDpo 2+3
    • 3upq, 3uq0, 3uq2 - hDpo δ (mutant) + DNA
    • 4fo6 - hDpo δ (mutant) + DNA + nucleotide analog
    • 6s1m, 6s1n, 6s1o, 6tny - hDpo δ subunits catalytic+2+3+4 + PCNA + DNA + nucleotide analog – Cryo EM
    • 6tnz - hDpo δ subunits catalytic+2+3+4 + PCNA + FLAP endonuclease +DNA + nucleotide analog – Cryo EM
    • 7kc0 - hDpo δ + PCNA + POL31 + POL32 +DNA + nucleotide analog – Cryo EM
  • DNA polymerase epsilon
    • 5vbn - hDpo subunits A+2
  • DNA polymerase zeta
    • 3abd, 3abe - hDpo  catalytic subunit Rev3 + mitotic spindle assembly checkpoint protein Rev7
    • 6ekm, 6bi7, 6bcd, 6bc8 - hDpo  catalytic subunit + MAD2B
    • 3vu7, 4gk0, 6ws0 - hDpo  catalytic subunit + DNA repair protein Rev1 + MAD2B
    • 6ws5 - hDpo  catalytic subunit + DNA repair protein Rev1 + MAD2B + inhibitor
    • 4fjo, 4gk5 - hDpo  + hDpo  catalytic subunit + DNA repair protein Rev1 + MAD2B
    • 6v8p - hDpo  catalytic subunit + hDpo d subunits 3+small – Cryo EM
    • 6v93 - hDpo  catalytic+processivity subunits + hDpo d subunits 3+small + DNA + dCTP – Cryo EM
  • DNA polymerase eta
  • DNA polymerase iota
  • DNA polymerase kappa
  • DNA polymerase lambda
  • DNA polymerase mu or DNA-directed DNA/RNA polymerase
  • DNA polymerase nu
  • DNA polymerase chi or repair DNA polymerase chi
    • 2m2t – AsfvDpo X – African swine fever virus – NMR
    • 2m2u, 2m2v – AsfvDpo X + nucleotide – NMR
    • 2m2w – AsfvDpo X + nucleotide + DNA – NMR
    • 5xma, 5xm9, 5xm8 – AsfvDpo X + DNA
    • 2w9m – DrDpo X
  • DNA polymerase theta
    • 5a9j – hDpo helicase domain 1-894
    • 5a9f, 5aga – hDpo helicase domain + nucleotide
    • 4x0p, 4x0q – hDpo helicase domain + nucleotide + DNA
    • 6xbu, 7zus – hDpo polymerase domain 1819-2590 + nucleotide + DNA
    • 7zx0, 7zx1, 8e23, 8e24 – hDpo polymerase domain + inhibitor + DNA
    • 8ef9, 8efc, 8efk – Dpo polymerase domain + nucleotide + DNA – Lates calcarifer
  • DNA polymerase from yeast
    • 3oiq - yDpo  + cell division control protein 13
    • 3flo, 3lgb - yDpo  subunits A,B
    • 4b08, 4fvm - yDpo  subunit A
    • 4fxd, 4fyd - yDpo  subunit A + RNA + DNA
    • 5oki - yDpo  subunit A + DCC1 + chromosome fidelity protein
    • 3iay - yDpo  catalytic subunit + DNA
    • 6p1h - yDpo  catalytic+small+3 subunits + DNA + nucleotide – Cryo EM
    • 6wjv - yDpo II  – Cryo EM
    • 6hv8 - yDpo II  subunit A+B – Cryo EM
    • 3oha, 3ohb, 3mfh - yDpo  (mutant) + DNA
    • 6i8a, 6qib, 7r3x, 7r3y - yDpo II  subunit A + DNA + nucleotide 
    • 6g0a, 6fwk, 3mfi, 4m8o - yDpo II  subunit A (mutant) + DNA + nucleotide derivative
    • 6s1c, 6s2e, 6s2f - yDpo II  subunit A (mutant) + DCC1 + chromosome transmission fidelity proteins
    • 6hv9 - yDpo II  subunit A+B + CMG + DNA + nucleotide – Cryo EM
    • 2r8j, 2r8k, 4ptf - yDpo  catalytic domain + DNA + nucleotide 
    • 6h1v - yDpo  catalytic domain (mutant) + DNA + nucleotide 
    • 2xgp, 2xgq, 2wtf - yDpo  + DNA
    • 7lxd - yDpo  catalytic+processivity subunits + hDpo d subunits 3+small – Cryo EM
    • 7s0t - yDpo  catalytic+processivity subunits + hDpo d subunits 3+small + DNA – Cryo EM
    • 5y27, 5y26 - Dpo subunit D + transcription factor – fission yeast
    • 1jih, 5vtp – yDpo catalytic domain
  • DNA polymerase Rev1; Domains – BRCT 44-133; catalytic 330-833; UBM2 998-1040; C-terminal 1158-1251
    • 3gqc – hRev1 catalytic domain + DNA + nucleotide
    • 2ebw – hRev1 BRCT domain – NMR
    • 6axd – hRev1 UBM2 domain – NMR
    • 6asr – hRev1 UBM2 domain + ubiquitin
    • 5vzm – hRev1 UBM2 domain + ubiquitin - NMR
    • 2lsg, 2lsy – hRev1 C-terminal domain – NMR
    • 2n1g – hRev1 C-terminal domain + Dpo d subunit 3 – NMR
    • 2lsi – hRev1 C-terminal domain + hDpo  peptide
    • 2lsk – hRev1 C-terminal domain + hDpo  peptide
    • 4ext – hRev1 C-terminal domain + hDpo  catalytic subunit peptide + MAD2B
    • 4gk5 – hRev1 C-terminal domain + hDpo  peptide + hDpo  catalytic subunit peptide + MAD2B
    • 2lsj – mRev1 C-terminal domain + mDpo  peptide
    • 4fjo – mRev1 C-terminal domain + mDpo  peptide + MAD2B
    • 4id3, 5umv – yRev1 BRCT domain
    • 2m2i, 5vx7 – yRev1 BRCT domain – NMR
    • 6x70, 6x72, 6x73, 6x74, 6x76 – yRev1 catalytic domain + DNA
    • 3bjy, 2aq4, 3osp, 5wm1, 5wm8, 5wmb, 6x6z, 6x71, 6x75, 6x77 – yRev1 catalytic domain + DNA + nucleotide

 Terminal deoxynucleotidyl transferase

    • 2coe – TdT BRCT domain – NMR
    • 1jms – mTdT catalytic domain + Mg

Terminal deoxynucleotidyl transferase binary complex

    • 4iqt, 4iqu, 4iqv, 4iqw – mTdT catalytic domain + inhibitor
    • 4i2i – mTdT catalytic domain + Mg + Zn + adenosine-pentaphosphate
    • 4i2j – mTdT catalytic domain + CTP + Zn
    • 1kej – mTdT catalytic domain + ATP derivative + Co
    • 4i2d – mTdT catalytic domain + ATP derivative + Mg
    • 4i29 – mTdT catalytic domain + AMP derivative + Mn
    • 4i2b – mTdT catalytic domain + AMPCPP + Mg
    • 4i2c – mTdT catalytic domain + AMPCPP + Mn
    • 4i2a – mTdT catalytic domain + UMP derivative + Mg

Terminal deoxynucleotidyl transferase ternary complex with DNA

    • 4i2e – mTdT catalytic domain + AMPCPP + Co + DNA
    • 4i2h – mTdT catalytic domain + AMPCPP + Zn + Mg + DNA
    • 4i27 – mTdT catalytic domain + TTP derivative + TMP + Mg + DNA
    • 1kdh – mTdT catalytic domain + UMP derivative + Mg + DNA
    • 4i28, 4i2f – mTdT catalytic domain + Mg + Zn + DNA
    • 4i2g – mTdT catalytic domain + Mg + Co + DNA

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Michal Harel, Joel L. Sussman

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