TOP6B_SACSH
ID TOP6B_SACSH Reviewed; 530 AA.
AC O05207;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1997, sequence version 1.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=Type 2 DNA topoisomerase 6 subunit B {ECO:0000255|HAMAP-Rule:MF_00322};
DE EC=5.6.2.2 {ECO:0000255|HAMAP-Rule:MF_00322, ECO:0000269|PubMed:16920739};
DE AltName: Full=Type II DNA topoisomerase VI subunit B {ECO:0000255|HAMAP-Rule:MF_00322};
DE Short=TopoVI-B {ECO:0000255|HAMAP-Rule:MF_00322};
GN Name=top6B {ECO:0000255|HAMAP-Rule:MF_00322};
OS Saccharolobus shibatae (Sulfolobus shibatae).
OC Archaea; Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae;
OC Saccharolobus.
OX NCBI_TaxID=2286;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 492-506.
RC STRAIN=ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12;
RX PubMed=9121560; DOI=10.1038/386414a0;
RA Bergerat A., de Massy B., Gadelle D., Varoutas P.-C., Nicolas A.,
RA Forterre P.;
RT "An atypical topoisomerase II from Archaea with implications for meiotic
RT recombination.";
RL Nature 386:414-417(1997).
RN [2]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION, AND SUBUNIT.
RC STRAIN=ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12;
RX PubMed=7961685; DOI=10.1016/s0021-9258(18)47037-8;
RA Bergerat A., Gadelle D., Forterre P.;
RT "Purification of a DNA topoisomerase II from the hyperthermophilic archaeon
RT Sulfolobus shibatae. A thermostable enzyme with both bacterial and eucaryal
RT features.";
RL J. Biol. Chem. 269:27663-27669(1994).
RN [3]
RP FUNCTION, AND SUBUNIT.
RX PubMed=11485995; DOI=10.1074/jbc.m101823200;
RA Buhler C., Lebbink J.H., Bocs C., Ladenstein R., Forterre P.;
RT "DNA topoisomerase VI generates ATP-dependent double-strand breaks with
RT two-nucleotide overhangs.";
RL J. Biol. Chem. 276:37215-37222(2001).
RN [4] {ECO:0007744|PDB:1MU5, ECO:0007744|PDB:1MX0}
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 2-470 IN COMPLEX WITH ATP ANALOG.
RX PubMed=12505993; DOI=10.1093/emboj/cdg008;
RA Corbett K.D., Berger J.M.;
RT "Structure of the topoisomerase VI-B subunit: implications for type II
RT topoisomerase mechanism and evolution.";
RL EMBO J. 22:151-163(2003).
RN [5] {ECO:0007744|PDB:1Z59, ECO:0007744|PDB:1Z5A, ECO:0007744|PDB:1Z5B, ECO:0007744|PDB:1Z5C}
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 2-470 IN COMPLEXES WITH ATP
RP ANALOGS, AND SUBUNIT.
RX PubMed=15939019; DOI=10.1016/j.str.2005.03.013;
RA Corbett K.D., Berger J.M.;
RT "Structural dissection of ATP turnover in the prototypical GHL ATPase
RT TopoVI.";
RL Structure 13:873-882(2005).
RN [6] {ECO:0007744|PDB:2HKJ}
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 2-470 IN COMPLEX WITH RADICICOL,
RP CATALYTIC ACTIVITY, SUBUNIT, AND ACTIVITY REGULATION.
RX PubMed=16920739; DOI=10.1093/nar/gkl567;
RA Corbett K.D., Berger J.M.;
RT "Structural basis for topoisomerase VI inhibition by the anti-Hsp90 drug
RT radicicol.";
RL Nucleic Acids Res. 34:4269-4277(2006).
RN [7] {ECO:0007744|PDB:2ZBK}
RP X-RAY CRYSTALLOGRAPHY (3.56 ANGSTROMS) IN COMPLEX WITH TOP6A AND RADICICOL,
RP AND SUBUNIT.
RX PubMed=18334211; DOI=10.1016/j.str.2007.12.020;
RA Graille M., Cladiere L., Durand D., Lecointe F., Gadelle D.,
RA Quevillon-Cheruel S., Vachette P., Forterre P., van Tilbeurgh H.;
RT "Crystal structure of an intact type II DNA topoisomerase: insights into
RT DNA transfer mechanisms.";
RL Structure 16:360-370(2008).
CC -!- FUNCTION: Relaxes both positive and negative supercoils and exhibits a
CC strong decatenase and unknotting activity; it cannot introduce DNA
CC supercoils (PubMed:7961685). ATP is absolutely required for DNA
CC cleavage; the nonhydrolyzable analog AMP-PNP generates nicked or linear
CC products from a supercoiled dsDNA substrate. Generates staggered two-
CC nucleotide long 5' overhangs. The enzyme is covalently attached
CC transiently to the 5'-ends of the cleaved strands (PubMed:11485995).
CC {ECO:0000269|PubMed:11485995, ECO:0000269|PubMed:7961685}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-dependent breakage, passage and rejoining of double-
CC stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000255|HAMAP-Rule:MF_00322,
CC ECO:0000269|PubMed:16920739};
CC -!- ACTIVITY REGULATION: Not inhibited by the DNA gyrase inhibitor
CC novobiocin, instead inhibited by eukaryotic topoisomerase inhibitors
CC such as m- and o-amsacrine, ellipticine, and the quinolone CP-115,953
CC (PubMed:7961685). Radicicol inhibits the ATPase activity
CC (PubMed:16920739). {ECO:0000269|PubMed:16920739,
CC ECO:0000269|PubMed:7961685}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Temperature dependence:
CC Optimum temperature is 70-80 degrees Celsius.
CC {ECO:0000269|PubMed:7961685};
CC -!- SUBUNIT: Homodimer. Heterotetramer of two Top6A and two Top6B chains.
CC {ECO:0000255|HAMAP-Rule:MF_00322, ECO:0000269|PubMed:11485995,
CC ECO:0000269|PubMed:12505993, ECO:0000269|PubMed:15939019,
CC ECO:0000269|PubMed:16920739, ECO:0000269|PubMed:18334211,
CC ECO:0000269|PubMed:7961685}.
CC -!- INTERACTION:
CC O05207; O05208: top6A; NbExp=5; IntAct=EBI-9026762, EBI-6430603;
CC O05207; O05207: top6B; NbExp=3; IntAct=EBI-9026762, EBI-9026762;
CC -!- SIMILARITY: Belongs to the TOP6B family. {ECO:0000255|HAMAP-
CC Rule:MF_00322}.
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DR EMBL; Y10582; CAA71604.1; -; Genomic_DNA.
DR PDB; 1MU5; X-ray; 2.00 A; A=2-470.
DR PDB; 1MX0; X-ray; 2.30 A; A/B/C/D/E/F=1-470.
DR PDB; 1Z59; X-ray; 2.10 A; A=2-470.
DR PDB; 1Z5A; X-ray; 2.20 A; A/B=2-470.
DR PDB; 1Z5B; X-ray; 2.00 A; A/B=2-470.
DR PDB; 1Z5C; X-ray; 2.20 A; A/B=2-470.
DR PDB; 2HKJ; X-ray; 2.00 A; A=2-470.
DR PDB; 2ZBK; X-ray; 3.56 A; B/D/F/H=1-530.
DR PDBsum; 1MU5; -.
DR PDBsum; 1MX0; -.
DR PDBsum; 1Z59; -.
DR PDBsum; 1Z5A; -.
DR PDBsum; 1Z5B; -.
DR PDBsum; 1Z5C; -.
DR PDBsum; 2HKJ; -.
DR PDBsum; 2ZBK; -.
DR AlphaFoldDB; O05207; -.
DR SMR; O05207; -.
DR DIP; DIP-29416N; -.
DR IntAct; O05207; 1.
DR BRENDA; 5.6.2.2; 6162.
DR EvolutionaryTrace; O05207; -.
DR GO; GO:0009330; C:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003918; F:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
DR GO; GO:0006268; P:DNA unwinding involved in DNA replication; IEA:UniProtKB-UniRule.
DR CDD; cd00823; TopoIIB_Trans; 1.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.30.565.10; -; 1.
DR HAMAP; MF_00322; Top6B; 1.
DR InterPro; IPR003594; HATPase_C.
DR InterPro; IPR036890; HATPase_C_sf.
DR InterPro; IPR010979; Ribosomal_S13-like_H2TH.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR014721; Ribosomal_S5_D2-typ_fold_subgr.
DR InterPro; IPR005734; TopoVI_B.
DR InterPro; IPR015320; TopoVI_B_transducer.
DR PANTHER; PTHR10871:SF4; PTHR10871:SF4; 1.
DR Pfam; PF09239; Topo-VIb_trans; 1.
DR PIRSF; PIRSF006553; TopoVI_B; 1.
DR SMART; SM00387; HATPase_c; 1.
DR SUPFAM; SSF46946; SSF46946; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55874; SSF55874; 1.
DR TIGRFAMs; TIGR01052; top6b; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Direct protein sequencing; DNA-binding;
KW Isomerase; Nucleotide-binding; Topoisomerase.
FT CHAIN 1..530
FT /note="Type 2 DNA topoisomerase 6 subunit B"
FT /id="PRO_0000145470"
FT BINDING 42
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:12505993,
FT ECO:0000269|PubMed:15939019, ECO:0007744|PDB:1MX0,
FT ECO:0007744|PDB:1Z59, ECO:0007744|PDB:1Z5A,
FT ECO:0007744|PDB:1Z5B, ECO:0007744|PDB:1Z5C"
FT BINDING 76
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:12505993,
FT ECO:0000269|PubMed:15939019, ECO:0007744|PDB:1MX0,
FT ECO:0007744|PDB:1Z59, ECO:0007744|PDB:1Z5A,
FT ECO:0007744|PDB:1Z5B, ECO:0007744|PDB:1Z5C"
FT BINDING 96..98
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:12505993,
FT ECO:0000269|PubMed:15939019, ECO:0007744|PDB:1MX0,
FT ECO:0007744|PDB:1Z5A, ECO:0007744|PDB:1Z5B,
FT ECO:0007744|PDB:1Z5C"
FT BINDING 107..113
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:12505993,
FT ECO:0000269|PubMed:15939019, ECO:0007744|PDB:1MX0,
FT ECO:0007744|PDB:1Z59, ECO:0007744|PDB:1Z5A,
FT ECO:0007744|PDB:1Z5B, ECO:0007744|PDB:1Z5C"
FT BINDING 427
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:12505993,
FT ECO:0007744|PDB:1MX0"
FT HELIX 12..18
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 20..22
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 28..45
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 48..50
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 55..64
FT /evidence="ECO:0007829|PDB:1MU5"
FT TURN 65..68
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 69..75
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 83..85
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 86..91
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 92..97
FT /evidence="ECO:0007829|PDB:1Z5B"
FT STRAND 100..102
FT /evidence="ECO:0007829|PDB:1Z5B"
FT TURN 109..111
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 112..122
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 127..132
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 137..146
FT /evidence="ECO:0007829|PDB:1MU5"
FT TURN 148..150
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 153..162
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 169..177
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 180..197
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 202..206
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 212..215
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 233..235
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 238..244
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 254..258
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 261..264
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 267..276
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 285..287
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 292..302
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 311..313
FT /evidence="ECO:0007829|PDB:1Z5B"
FT HELIX 319..330
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 333..339
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 343..345
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 348..359
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 365..367
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 369..374
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 377..379
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 383..385
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 387..394
FT /evidence="ECO:0007829|PDB:1MU5"
FT HELIX 397..400
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 404..407
FT /evidence="ECO:0007829|PDB:1Z59"
FT STRAND 409..419
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 422..424
FT /evidence="ECO:0007829|PDB:1MU5"
FT STRAND 428..430
FT /evidence="ECO:0007829|PDB:1Z5B"
FT HELIX 434..468
FT /evidence="ECO:0007829|PDB:1MU5"
SQ SEQUENCE 530 AA; 60528 MW; 772F221FCD28441A CRC64;
MSAKEKFTSL SPAEFFKRNP ELAGFPNPAR ALYQTVRELI ENSLDATDVH GILPNIKITI
DLIDDARQIY KVNVVDNGIG IPPQEVPNAF GRVLYSSKYV NRQTRGMYGL GVKAAVLYSQ
MHQDKPIEIE TSPVNSKRIY TFKLKIDINK NEPIIVERGS VENTRGFHGT SVAISIPGDW
PKAKSRIYEY IKRTYIITPY AEFIFKDPEG NVTYYPRLTN KIPKPPQEVK PHPYGVDREE
IKILINNLKR DYTIKEFLVN EFQSIGDTTA DKILELAGLK PNKKVKNLTE EEITRLVETF
KKDEDFRSPS ADSLSVIGED LIELGLKKIF NPDFAASITR KPKAYQGHPF IVEAGVAFGG
SIPVGEEPIV LRYANKIPLI YDEKSDVIWK VVEELDWKRY GIESDQYQMV VMVHLCSTKI
PYKSAGKESI AEVENIEKEI KNALMEVARK LKQYLSEKRK EQEAKKKLLA YLKYIPEVSR
SLATFLASGN KELVSKYQNE ISEGLFKLIS KKLDLINIEE YRKVYRVDSE
