Topoisomerase

From Proteopedia

Revision as of 06:44, 21 August 2014

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Topoisomerase (TOP) winds and unwinds DNA double helix in order to enable DNA replication.

• TOPI cuts one strand of the double helix. It has 3 subclasses: TOPIA which shares its mechanism with TOPII and TOPIB which uses rotary mechanism and includes topo I and topo III. TOPIC called TOPV shares its mechanism with TOPIB but is structurally unique.
  
• TOPII cuts both strands of the double helix. Its subclasses are TOPIIA including topo II and TOPIIB which includes topo VI.
  
• TOPIV is a type of TOPII, contains an ATP-binding domain ParE and a catalytic domain ParC.
  

See also Variola Topoisomerase 1B.

Function

The reaction catalyzed by topoisomerases leads to the conversion of one topological isomer of DNA to another. TOP3 is a potent decatenase.

GO Annotations

Copied from [1] Last updated Dec 2 2010

3D Structures of Topoisomerase

Updated on 21-August-2014

TOPI (ATP-independent)

3igc, 2h7f, 2h7g – TOPI+DNA – Smallpox virus
2gai, 2gaj – TOPI – Thermotoga maritime
2f4q – TOPIB – Deinococcus radiodurans
1tl8, 1sc7 – hTOPI+DNA+indenoisoquinoline – human
1seu - hTOPI+DNA+indolocarbazole
1t8i, 1rr8, 1rrj - hTOPI+DNA+camptothesin
1r49 – hTOPI (mutant)
1mw8 – hTOPI (mutant) N-terminal+DNA
1mw9 - hTOPI (mutant) N-terminal
1nh3 – hTOPI C-terminal+DNA+Ara-C
1k4s, 1lpq, 1ej9, 1a31, 1a35, 1a36 – hTOPI+DNA
1k4t - hTOPI+DNA+topotecan
1cy0 – EcTOPI+DNA - Escherichia coli
3px7 – EcTOPI (mutant) +DNA
1cy2, 1cy1 – EcTOPI+5’TPTPTP3’
1cy6, 1cy7, 1cy8 – EcIOPI+TMP
1cy9, 1cyy – EcTOPI domain II+III
1yua – EcTOPI C-terminal
1ecl, 1cy4 - EcTOPI N-terminal
3pwt - EcTOPIA N-terminal (mutant)
1a41 – VvTOPI C-terminal – Vaccinia virus
1vcc – VvTOPI N-terminal
1ois – yTOPI N-terminal - yeast

TOPI (ATP-dependent) – reverse gyrase

4ddt, 4ddu, 4ddv, 4ddw, 4ddx – TmTOPI

TOPIIA

3l4j – yTOPII apo+DNA
3l4k - yTOPII+DNA+Zn
2rgr - yTOPIIA+DNA
4gfh - yTOPIIA+DNA + ANPPNP
1qzr – yTOPII N-terminal+dexrazoxane
1pvg – yTOPII N-terminal
1bjt, 1bgw – yTOPII core
3ksa, 2ksb – SpTOPIIA+DNA – Streptococcus pneumoniae
1zxm – hTOPIIA+AMP-PNP
1zxn - hTOPIIA+ADP
4fm9 - hTOPIIA+DNA
3kua – TOPII residues 362-493 + CCDB – Vibrio fischeri

TOPIIB topo VI

2zbk – SsTOPIIB subunit A+B – Sulfolobus shibatae
2hkj, 1mu5, 1mx0 - SsTOPIIB subunit B
1z59, 1z5a - SsTOPIIB subunit B+ADP
1z5b - SsTOPIIB subunit B+ADP+AlF4
1z5c - SsTOPIIB subunit B+ADP+Pi
2q2e - TOPIIB subunit A+B – Methanosarcina mazei
1d3y - TOPIIB subunit A - Methanocaldococcus janaschii
4j3n - hTOPIIB subunit A+B + DNA
4g0w, 3qx3, 4g0v, 4g0u - hTOPIIB + DNA + anti-cancer drug

TOPIII

2o19, 2o54, 2o59, 2o5c, 2o5e, 1i7d – EcTOPIII+DNA
1d6m - EcTOPIII
4cgy, 4cht – hTOPIIIα + RecQ-mediated genome instability protein

TOPIV

3fv5 – EcTOPIV subunit B
4hz0 - EcTOPIV subunit B + inhibitor
1zvt, 1zvu - EcTOPIV subunit A
4mn4 - EcTOPIV subunit A + MukB
1s14 – EcTOPIV ParE
1s16 - EcTOPIV ParE+ADPNP
3ltn, 3k9f, 3ksb, 3rad, 3rae, 3raf, 4i3h, 4juo - SpTOPIV subunit A+B+DNA
3foe, 3fof - SpTOPIV subunit A+B+DNA+quinolone
2nov - SpTOPIV subunit A
4em7, 4emv, 4lp0, 4lpb, 4mb9, 4mbc, 4mot - SpTOPIV subunit B + inhibitor
2inr - TOPIV subunit A – Staphylococcus aureus
1wp5 – TOPIV C-terminal – Geobacillus stearothermophilus
2xkj – AbTOPIV pare+parc subunits – Acinetobacter baumannii
2xkk - AbTOPIV pare+parc subunits+DNA
3lnu, 3lps - TOPIV subunit B N-terminal – Xanthomonas oryzae
4hxz, 4hy1 - hTOPIV subunit B + inhibitor
4hym, 4kqv - TOPIV subunit B + inhibitor – Francisella tularensis
4hz5 - TOPIV subunit B + inhibitor – Enterococcus faecalis

TOPV

2csb, 2csd, 4gfj – TOPV – Methanopyrus kandleri
3m6k, 3m7g – MkTOPV N-terminal
3m6z - MkTOPV N-terminal+guanidine
3m7d - MkTOPV N-terminal+dioxane
Created with the participation of Sonny Zhao.