TOP1_MYCS2
ID TOP1_MYCS2 Reviewed; 936 AA.
AC A0R5D9;
DT 17-FEB-2016, integrated into UniProtKB/Swiss-Prot.
DT 09-JAN-2007, sequence version 1.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=DNA topoisomerase 1 {ECO:0000255|HAMAP-Rule:MF_00952};
DE EC=5.6.2.1 {ECO:0000255|HAMAP-Rule:MF_00952};
DE AltName: Full=DNA topoisomerase I {ECO:0000255|HAMAP-Rule:MF_00952};
GN Name=topA {ECO:0000255|HAMAP-Rule:MF_00952};
GN OrderedLocusNames=MSMEG_6157, MSMEI_5999;
OS Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium
OS smegmatis).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycolicibacterium.
OX NCBI_TaxID=246196;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155;
RA Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C.,
RA Fraser C.M.;
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=17295914; DOI=10.1186/gb-2007-8-2-r20;
RA Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C.,
RA Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.;
RT "Interrupted coding sequences in Mycobacterium smegmatis: authentic
RT mutations or sequencing errors?";
RL Genome Biol. 8:R20.1-R20.9(2007).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=18955433; DOI=10.1101/gr.081901.108;
RA Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M.,
RA Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.;
RT "Ortho-proteogenomics: multiple proteomes investigation through orthology
RT and a new MS-based protocol.";
RL Genome Res. 19:128-135(2009).
RN [4]
RP PROTEIN SEQUENCE OF 2-11, FUNCTION, COFACTOR, BIOPHYSICOCHEMICAL
RP PROPERTIES, ACTIVE SITE, AND DNA-BINDING.
RC STRAIN=ATCC 27204 / DSM 43464 / SN2;
RX PubMed=9593741; DOI=10.1074/jbc.273.22.13925;
RA Bhaduri T., Bagui T.K., Sikder D., Nagaraja V.;
RT "DNA topoisomerase I from Mycobacterium smegmatis. An enzyme with distinct
RT features.";
RL J. Biol. Chem. 273:13925-13932(1998).
RN [5]
RP FUNCTION, SUBSTRATE SPECIFICITY, AND DNA-BINDING.
RC STRAIN=ATCC 27204 / DSM 43464 / SN2;
RX PubMed=10734203; DOI=10.1093/nar/28.8.1830;
RA Sikder D., Nagaraja V.;
RT "Determination of the recognition sequence of Mycobacterium smegmatis
RT topoisomerase I on mycobacterial genomic sequences.";
RL Nucleic Acids Res. 28:1830-1837(2000).
CC -!- FUNCTION: Releases the supercoiling and torsional tension of DNA, which
CC is introduced during the DNA replication and transcription, by
CC transiently cleaving and rejoining one strand of the DNA duplex.
CC Introduces a single-strand break via transesterification at a target
CC site in duplex DNA. The scissile phosphodiester is attacked by the
CC catalytic tyrosine of the enzyme, resulting in the formation of a DNA-
CC (5'-phosphotyrosyl)-enzyme intermediate (PubMed:9593741) and the
CC expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes
CC passage around the unbroken strand, thus removing DNA supercoils.
CC Finally, in the religation step, the DNA 3'-OH attacks the covalent
CC intermediate to expel the active-site tyrosine and restore the DNA
CC phosphodiester backbone (By similarity). {ECO:0000255|HAMAP-
CC Rule:MF_00952, ECO:0000269|PubMed:9593741}.
CC -!- FUNCTION: Relaxes negatively (but not positively) supercoiled DNA,
CC concatanates and knots circular ssDNA at 52 but not 37 degrees Celsius
CC (PubMed:9593741). Preferentially nicks supercoiled DNA at C(G/T)CTT,
CC cutting between the TT residues, binds ss and dsDNA with the
CC recognition site (PubMed:10734203). {ECO:0000269|PubMed:10734203,
CC ECO:0000269|PubMed:9593741}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-independent breakage of single-stranded DNA, followed by
CC passage and rejoining.; EC=5.6.2.1; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00952};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00952,
CC ECO:0000269|PubMed:9593741};
CC Note=Binds two Mg(2+) per subunit. {ECO:0000255|HAMAP-Rule:MF_00952};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Temperature dependence:
CC Optimum temperature is 30-42 degrees Celsius. Partially active up to
CC 65 degrees Celsius (PubMed:9593741). {ECO:0000269|PubMed:9593741};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_00952}.
CC -!- SIMILARITY: Belongs to the type IA topoisomerase family.
CC {ECO:0000255|HAMAP-Rule:MF_00952}.
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DR EMBL; CP000480; ABK69586.1; -; Genomic_DNA.
DR EMBL; CP001663; AFP42431.1; -; Genomic_DNA.
DR RefSeq; WP_011731080.1; NZ_SIJM01000072.1.
DR RefSeq; YP_890377.1; NC_008596.1.
DR PDB; 6PCM; X-ray; 3.11 A; A/B=1-839.
DR PDBsum; 6PCM; -.
DR AlphaFoldDB; A0R5D9; -.
DR SMR; A0R5D9; -.
DR STRING; 246196.MSMEI_5999; -.
DR PRIDE; A0R5D9; -.
DR EnsemblBacteria; ABK69586; ABK69586; MSMEG_6157.
DR EnsemblBacteria; AFP42431; AFP42431; MSMEI_5999.
DR GeneID; 66737443; -.
DR KEGG; msg:MSMEI_5999; -.
DR KEGG; msm:MSMEG_6157; -.
DR PATRIC; fig|246196.19.peg.5996; -.
DR eggNOG; COG0550; Bacteria.
DR eggNOG; COG1754; Bacteria.
DR OMA; YAQPKQR; -.
DR OrthoDB; 223233at2; -.
DR Proteomes; UP000000757; Chromosome.
DR Proteomes; UP000006158; Chromosome.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003917; F:DNA topoisomerase type I (single strand cut, ATP-independent) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
DR CDD; cd00186; TOP1Ac; 1.
DR CDD; cd03363; TOPRIM_TopoIA_TopoI; 1.
DR Gene3D; 1.10.290.10; -; 1.
DR Gene3D; 1.10.460.10; -; 1.
DR Gene3D; 2.70.20.10; -; 1.
DR HAMAP; MF_00952; Topoisom_1_prok; 1.
DR InterPro; IPR000380; Topo_IA.
DR InterPro; IPR003601; Topo_IA_2.
DR InterPro; IPR023406; Topo_IA_AS.
DR InterPro; IPR013497; Topo_IA_cen.
DR InterPro; IPR013824; Topo_IA_cen_sub1.
DR InterPro; IPR013825; Topo_IA_cen_sub2.
DR InterPro; IPR013826; Topo_IA_cen_sub3.
DR InterPro; IPR023405; Topo_IA_core_domain.
DR InterPro; IPR003602; Topo_IA_DNA-bd_dom.
DR InterPro; IPR005733; TopoI_bac-type.
DR InterPro; IPR028612; Topoisom_1_IA.
DR InterPro; IPR025589; Toprim_C_rpt.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR034149; TOPRIM_TopoI.
DR PANTHER; PTHR42785; PTHR42785; 2.
DR Pfam; PF01131; Topoisom_bac; 1.
DR Pfam; PF01751; Toprim; 1.
DR Pfam; PF13368; Toprim_C_rpt; 4.
DR PRINTS; PR00417; PRTPISMRASEI.
DR SMART; SM00437; TOP1Ac; 1.
DR SMART; SM00436; TOP1Bc; 1.
DR SMART; SM00493; TOPRIM; 1.
DR SUPFAM; SSF56712; SSF56712; 1.
DR TIGRFAMs; TIGR01051; topA_bact; 1.
DR PROSITE; PS00396; TOPOISOMERASE_I_PROK; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; DNA-binding; Isomerase; Magnesium;
KW Metal-binding; Reference proteome; Topoisomerase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:9593741"
FT CHAIN 2..936
FT /note="DNA topoisomerase 1"
FT /id="PRO_0000435621"
FT DOMAIN 15..139
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT REGION 188..193
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT REGION 661..688
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 732..767
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 841..884
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 903..936
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 913..936
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 339
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952,
FT ECO:0000305|PubMed:9593741"
FT BINDING 21
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT BINDING 108
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT BINDING 108
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT BINDING 110
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 45
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 164
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 165
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 168
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 173
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 180
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 341
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 542
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT CONFLICT 5
FT /note="D -> S (in Ref. 4; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 11
FT /note="T -> A (in Ref. 4; AA sequence)"
FT /evidence="ECO:0000305"
FT STRAND 16..21
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 23..32
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 37..41
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 46..48
FT /evidence="ECO:0007829|PDB:6PCM"
FT TURN 53..55
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 58..62
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 67..71
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 72..74
FT /evidence="ECO:0007829|PDB:6PCM"
FT TURN 84..86
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 87..97
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 101..105
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 111..124
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 130..132
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 140..148
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 155..182
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 193..208
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 214..222
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 224..226
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 236..243
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 246..248
FT /evidence="ECO:0007829|PDB:6PCM"
FT TURN 255..257
FT /evidence="ECO:0007829|PDB:6PCM"
FT TURN 263..265
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 271..280
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 285..294
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 306..316
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 321..333
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 349..362
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 391..395
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 399..402
FT /evidence="ECO:0007829|PDB:6PCM"
FT TURN 403..405
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 408..423
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 429..439
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 443..445
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 448..459
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 461..465
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 493..495
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 499..505
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 514..522
FT /evidence="ECO:0007829|PDB:6PCM"
FT TURN 523..525
FT /evidence="ECO:0007829|PDB:6PCM"
FT TURN 529..531
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 532..540
FT /evidence="ECO:0007829|PDB:6PCM"
FT TURN 541..543
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 544..547
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 549..554
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 556..568
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 570..573
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 576..589
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 595..604
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 610..612
FT /evidence="ECO:0007829|PDB:6PCM"
FT TURN 615..618
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 620..625
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 633..637
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 649..653
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 655..658
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 660..665
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 668..673
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 675..680
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 687..689
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 692..700
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 703..710
FT /evidence="ECO:0007829|PDB:6PCM"
FT TURN 712..714
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 717..722
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 724..731
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 762..764
FT /evidence="ECO:0007829|PDB:6PCM"
FT TURN 771..773
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 776..782
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 786..791
FT /evidence="ECO:0007829|PDB:6PCM"
FT TURN 793..795
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 798..804
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 807..812
FT /evidence="ECO:0007829|PDB:6PCM"
FT STRAND 815..818
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 824..827
FT /evidence="ECO:0007829|PDB:6PCM"
FT HELIX 830..836
FT /evidence="ECO:0007829|PDB:6PCM"
SQ SEQUENCE 936 AA; 102499 MW; CCFB66C8A9AD3F22 CRC64;
MAGGDRGSGG TGNVRRLVIV ESPTKARKIA GYLGSNYVVE SSRGHIRDLP RNAADVPAKF
KSEPWARLGV NVDQNFEPLY IVSPEKKSTV TELKGLLKDV DELYLATDGD REGEAIAWHL
LETLKPRVPV KRMVFHEITE PAIRNAAENP RDLDIALVDA QETRRILDRL YGYEVSPVLW
KKVAPKLSAG RVQSVATRII VQRERERMAF HSASYWDVTA ELDASVSDPS ASPPKFTAKL
NTVDGRRVAT GRDFDSLGQL KRPDEVLVLD EASAGALASG LRGAQLAVTS VEQKPYTRRP
YAPFMTSTLQ QEAARKLRFS SERTMSIAQR LYENGYITYM RTDSTTLSES AINAARTQAR
QLYGEEYVHP SPRQYTRKVK NAQEAHEAIR PAGDVFQTPG QLHSALDTDE FRLYELIWQR
TVASQMADAR GTTLSLRIGG SASSGEQVVF NASGRTITFP GFLKAYVESI DELAGGESDD
AESRLPNLTQ GQRVDAADLS ADGHQTSPPA RYTEASLIKA LEELGIGRPS TYSSIIKTIQ
DRGYVQKKGS ALVPSWVAFA VVGLLEQHFG RLVDYDFTAA MEDELDEIAN GQEQRTNWLN
NFYFGGEHGV EGSIARAGGL KQLVGGNLEG IDAREVNSIK VFDDSEGRPV YVRVGRNGPY
LERMVDDPDN PGEQKPQRAN LKEDLTPDEL TPELAEKLFA TPQEGRSLGI DPETGHEIVA
KDGRFGPYVT EVLPEPEDGG DDGTAGTPAK KGKKPTGPKP RTGSLFRSMD LETVTLEDAL
KLLSLPRVVG VDPTTNEEIT AQNGRYGPYL KRGTDSRSLA TEDQIFTITL DEALKIYAEP
KRRGRQAASA PPLRELGNDP VSGKPMVIKD GRFGPYVTDG ETNASLRKGD DVLTITDERA
SELLADRRAR GPVKKKAPAK KAAKKAPAKK AAAKKA
