TOP2M_DICDI
ID TOP2M_DICDI Reviewed; 1284 AA.
AC P90520; Q54WC7;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 04-DEC-2007, sequence version 2.
DT 03-AUG-2022, entry version 154.
DE RecName: Full=DNA topoisomerase 2, mitochondrial;
DE Short=DNA topoisomerase II;
DE EC=5.6.2.2 {ECO:0000255|PROSITE-ProRule:PRU00995};
DE Flags: Precursor;
GN Name=top2mt; Synonyms=topA; ORFNames=DDB_G0279737;
OS Dictyostelium discoideum (Slime mold).
OC Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC Dictyosteliaceae; Dictyostelium.
OX NCBI_TaxID=44689;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], SUBCELLULAR LOCATION, AND DEVELOPMENTAL
RP STAGE.
RC STRAIN=AX3;
RX PubMed=9177484; DOI=10.1016/s0167-4781(96)00229-1;
RA Komori K., Kuroe K., Yanagisawa K., Tanaka Y.;
RT "Cloning and characterization of the gene encoding a mitochondrially
RT localized DNA topoisomerase II in Dictyostelium discoideum. Western blot
RT analysis.";
RL Biochim. Biophys. Acta 1352:63-72(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=15875012; DOI=10.1038/nature03481;
RA Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT "The genome of the social amoeba Dictyostelium discoideum.";
RL Nature 435:43-57(2005).
CC -!- FUNCTION: Control of topological states of DNA by transient breakage
CC and subsequent rejoining of DNA strands. Topoisomerase II makes double-
CC strand breaks (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-dependent breakage, passage and rejoining of double-
CC stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU00995};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00995};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00995};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00995};
CC Note=Binds two Mg(2+) per subunit. The magnesium ions form salt bridges
CC with both the protein and the DNA. Can also accept other divalent metal
CC cations, such as Mn(2+) or Ca(2+). {ECO:0000255|PROSITE-
CC ProRule:PRU00995};
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:9177484}.
CC -!- DEVELOPMENTAL STAGE: Present in growth phase and during development,
CC although levels declined as development proceeded.
CC {ECO:0000269|PubMed:9177484}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA11510.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; D82024; BAA11510.1; ALT_FRAME; Genomic_DNA.
DR EMBL; AAFI02000032; EAL67548.1; -; Genomic_DNA.
DR PIR; T30577; T30577.
DR RefSeq; XP_641531.1; XM_636439.1.
DR AlphaFoldDB; P90520; -.
DR SMR; P90520; -.
DR STRING; 44689.DDB0214907; -.
DR PaxDb; P90520; -.
DR EnsemblProtists; EAL67548; EAL67548; DDB_G0279737.
DR GeneID; 8622204; -.
DR KEGG; ddi:DDB_G0279737; -.
DR dictyBase; DDB_G0279737; top2mt.
DR eggNOG; KOG0355; Eukaryota.
DR HOGENOM; CLU_001935_1_0_1; -.
DR InParanoid; P90520; -.
DR OMA; VWANDEK; -.
DR PhylomeDB; P90520; -.
DR Reactome; R-DDI-4615885; SUMOylation of DNA replication proteins.
DR PRO; PR:P90520; -.
DR Proteomes; UP000002195; Chromosome 3.
DR GO; GO:0005739; C:mitochondrion; IDA:dictyBase.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003918; F:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IEA:InterPro.
DR GO; GO:0000712; P:resolution of meiotic recombination intermediates; IBA:GO_Central.
DR GO; GO:0000819; P:sister chromatid segregation; IBA:GO_Central.
DR CDD; cd00187; TOP4c; 1.
DR CDD; cd03365; TOPRIM_TopoIIA; 1.
DR Gene3D; 1.10.268.10; -; 1.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.30.565.10; -; 1.
DR Gene3D; 3.40.50.670; -; 1.
DR Gene3D; 3.90.199.10; -; 1.
DR InterPro; IPR003594; HATPase_C.
DR InterPro; IPR036890; HATPase_C_sf.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR014721; Ribosomal_S5_D2-typ_fold_subgr.
DR InterPro; IPR001241; Topo_IIA.
DR InterPro; IPR013760; Topo_IIA-like_dom_sf.
DR InterPro; IPR013758; Topo_IIA_A/C_ab.
DR InterPro; IPR013757; Topo_IIA_A_a_sf.
DR InterPro; IPR013759; Topo_IIA_B_C.
DR InterPro; IPR013506; Topo_IIA_bsu_dom2.
DR InterPro; IPR002205; Topo_IIA_dom_A.
DR InterPro; IPR018522; TopoIIA_CS.
DR InterPro; IPR031660; TOPRIM_C.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR034157; TOPRIM_TopoII.
DR Pfam; PF00204; DNA_gyraseB; 1.
DR Pfam; PF00521; DNA_topoisoIV; 1.
DR Pfam; PF02518; HATPase_c; 1.
DR Pfam; PF01751; Toprim; 1.
DR Pfam; PF16898; TOPRIM_C; 1.
DR SMART; SM00433; TOP2c; 1.
DR SMART; SM00434; TOP4c; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55874; SSF55874; 1.
DR SUPFAM; SSF56719; SSF56719; 1.
DR PROSITE; PS00177; TOPOISOMERASE_II; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 2: Evidence at transcript level;
KW ATP-binding; DNA-binding; Isomerase; Magnesium; Metal-binding;
KW Mitochondrion; Nucleotide-binding; Reference proteome; Topoisomerase;
KW Transit peptide.
FT TRANSIT 1..35
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 36..1284
FT /note="DNA topoisomerase 2, mitochondrial"
FT /id="PRO_0000034820"
FT DOMAIN 560..677
FT /note="Toprim"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT REGION 445..447
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT REGION 1245..1284
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1251..1271
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 900
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000250"
FT BINDING 183
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 212
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 240..242
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 253..260
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 478..480
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 566
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 646
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 646
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 648
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 594
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 597
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 768
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 818
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 852
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 858
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 899
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250"
FT SITE 951
FT /note="Important for DNA bending; intercalates between base
FT pairs of target DNA"
FT /evidence="ECO:0000250"
FT CONFLICT 902..904
FT /note="FTK -> LQ (in Ref. 1; BAA11510)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1284 AA; 146400 MW; C145F3F139297C1E CRC64;
MSKLLNNNNH KNLTNYLKFG KGIINNLNNK SKQVGIISFI SQSSIQSQSS IQSQSFLSIN
NNSNNKYFST KLNKNEKISE KTTTRKIEDI YQKKTPTEHV LLRPDSYIGT IEKIEDDMWV
LSNSMFNKEK KTIELNNDNN EKNVESTTTT TTKTNKKPLT YIHPIKATYI PGLLKIYDEI
LVNAADNKKR DSKMSFIKVE INPNENSISI MNDGKGIPVV MHQTENCYVV EMVMGNLMSG
SNFNDSELKV VGGRNGFGAK LTNIFSKEFT VETVDKSSGK KYFQRWSNNM GDRSEPIITP
IGEGESDYTK ITFKPDLEKF KIKSLWDDNI LQLMERRLYD IAGCNTELMV TLNGKRLNYN
FQSYVKLYEH HLNNSTKRED NEEQYREESF EFGEISPRWK IGIGLSETGQ FTQVSFVNSI
NTVKGGTHVN FLADQIVRYV GEKLKKKHSD LEIRPMNIKH HLALFVNCLV DNPSFDSQSK
ETLTTKPMLF GSTPEIPESL LAQFVKNSKI IERVAGWALM KQKADLIHST SGRQSKTTLI
KSISKLDDAN WAGGLKSKEC TLIITEGDSA KSLALAGLSV VGRNSYGVFP LRGKLLNVRD
VASKQLLSNE EINNLTTILG LSHKNSYDTD ESMEDLRYGR VMIMADQDHD GSHIKGLVMN
FIHYFWPNLL KRGFLVEFVT PIIKATKSST QKKSFFTIKD YEKWRETISS DQLKQYTIKY
YKGLGTSTSA EAKEYFSNLD KHVIKFIWGD EADDLIKMAF AKDLSSLRQR WIKETDMSQG
IDHSIKEITY PDFINKELIH YSWAANLRSI PSLIDGLKPG QRKILFASFK RRLTNEIKVS
QLSGYVAEQT SYHHGEQSLN STIVKMAHNF VGSNNLPLLT PSGQFGTRLQ GGSDSASARY
IFTKLEPVAR YLFNELDDPL LNYLEEEGES IQPDYYIPII PMLLVNGSEG IGVGMSTSIP
LFSPIDIIDQ LMLRLNNQVA LKKLIPWYRG FKGTISPDRH TYRTNGVIKL VGRNLEITEL
PIGRWTSDYK EVLNDLIDKD VIKSFQESNT ENSVHFTILL NNNQLEQMED LTENELIKLF
KLSASLNFHL TCFDENSKIQ KLESVEEIID QFYKVRLQFY GKRREYLLKS LDNQIKRLTT
TIQFLEVIAS GKLKIQGRSK QDLIKELESG EIVGFENFGT HPPEVYQHLF SLSILDITKE
RIDNLTNQLT KRKSEHQSIS SSDPKSLWTA DLQQLKEYLE KSDKEFQKKP LKTSSSSSFD
VSSSSESAKL SSTRKSKTDK IKSK
