Topoisomerase

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Template:STRUCTURE 2f4q

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 which is a type of TOPII, contains an ATP-binding domain ParE and a catalytic domain ParC. The images at the left and at the right correspond to one representative TOP, i.e. the crystal structure of Deinococcus radiodurans topoisomerase IB (2f4q).

3D Structures of Topoisomerase

Update December 2011

TOPI

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

TOPIIA

3l4j – yTOPII apo+DNA
3l4k - yTOPII+DNA+Zn
2rgr - yTOPIIA+DNA
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 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
3qx3 – hTOPIIB + DNA + etoposide

TOPIII

2o19, 2o54, 2o59, 2o5c, 2o5e, 1i7d – EcTOPIII+DNA
1d6m - EcTOPIII

TOPIV

3fv5 – EcTOPIV subunit B
1zvt, 1zvu - EcTOPIV subunit A
1s14 – EcTOPIV ParE
1s16 - EcTOPIV ParE+ADPNP
3ltn, 3k9f, 3ksb - SpTOPIV subunit A+B+DNA
3foe, 3fof - SpTOPIV subunit A+B+DNA+quinolone
2nov - SpTOPIV subunit A
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

TOPV

2csb, 2csd – TOPV – Methanopyrus kandleri
3m6k, 3m7g – MkTOPV N-terminal
3m6z - MkTOPV N-terminal+guanidine
3m7d - MkTOPV N-terminal+dioxane