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PR00416

Identifier
EUTPISMRASEI  [View Relations]  [View Alignment]  
Accession
PR00416
No. of Motifs
6
Creation Date
23-NOV-1995  (UPDATE 24-JUN-1999)
Title
Eukaryotic DNA topoisomerase I signature
Database References

PROSITE; PS00176 TOPOISOMERASE_I_EUK
PFAM; PF01028 Topoisomerase_I
INTERPRO; IPR001631
Literature References
1. ZHOU, B.S., BASTOW, K.F. AND CHENG, Y.C.
Characterization of the 3' region of the human DNA topoisomerase I gene.
CANCER RES. 49 3922-3927 (1989).
 
2. TAMURA, H., KOHCHI, C., YAMADA, R., IKEDA, T., KOIWAI, O., PATTERSON,
E., KEENE, J.D., OKADA, K., KJELDSEN, E. AND NISHIKAWA, K.
Molecular cloning of a cDNA of a camptothecin-resistant human DNA
topoisomerase I and identification of mutation sites.
NUCLEIC ACIDS RES. 19 69-75 (1991).

Documentation
Eukaryotic topoisomerase I, otherwise known as relaxing enzyme, untwisting 
enzyme or swivelase, catalyses the ATP-independent breakage of single-
stranded DNA, followed by passage and rejoining of another single-stranded 
DNA region [1]. This reaction brings about the conversion of one topological
DNA isomer into another: e.g., relaxation of positive and negative super-
coils; interconversion of simple and knotted rings of single-stranded DNA;
and intertwisting of single-stranded rings of complementary sequences [1,2].
 
A tyrosine residue at the active site is involved in the transient breakage
of a DNA strand and formation of a covalent protein-DNA intermediate [1].
Human topoisomerase I has been shown to be inhibited by camptothecin (CPT),
a plant alkaloid with antitumour activity [2].
 
EUTPISMRASEI is a 6-element fingerprint that provides a signature for 
eukaryotic topoisomerase I. The fingerprint was derived from an initial 
alignment of 7 sequences: the motifs were drawn from conserved regions 
throughout the alignment length - motif 6 contains part of the region
encoded by PROSITE pattern TOPOISOMERASE_I_EUK (PS00176), the tyrosine
residue of which is involved in creating the covalent protein-DNA
intermediate. Two iterations on OWL26.3 were required to reach convergence,
at which point a true set comprising 16 sequences was identified.
 
An update on SPTR37_9f identified a true set of 28 sequences, and 6
partial matches.
Summary Information
  28 codes involving  6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
6282828282828
5000000
4000000
3000000
2010010
123456
True Positives
O13463        O17965        O17966        O24307        
O59891 O60013 P79994 P93119
Q26024 Q27529 Q84147 Q85387
Q89220 Q94705 Q98254 TOP1_ARATH
TOP1_CANAL TOP1_CRIGR TOP1_DROME TOP1_HUMAN
TOP1_MOUSE TOP1_SCHPO TOP1_SFVKA TOP1_USTMA
TOP1_VACCV TOP1_VARV TOP1_XENLA TOP1_YEAST
True Positive Partials
Codes involving 2 elements
P87507
Sequence Titles
O13463      TOPOISOMERASE I - EMERICELLA NIDULANS (ASPERGILLUS NIDULANS). 
O17965 M01E5.5B PROTEIN - CAENORHABDITIS ELEGANS.
O17966 M01E5.5A PROTEIN - CAENORHABDITIS ELEGANS.
O24307 TOPOISOMERASE I - PISUM SATIVUM (GARDEN PEA).
O59891 TOPOISOMERASE I - CRYPTOCOCCUS NEOFORMANS (FILOBASIDIELLA NEOFORMANS).
O60013 DNA TOPOISOMERASE I - PNEUMOCYSTIS CARINII.
P79994 DNA TOPOISOMERASE I - GALLUS GALLUS (CHICKEN).
P93119 TOPOISOMERASE I (EC 5.99.1.2) (DNA TOPOISOMERASE) (DNA TOPOISOMERASE I) (RELAXING ENZYME) (UNTWISTING ENZYME) (SWIVELASE) (TYPE I DNA TOPOISOMERASE) (NICKING-CLOSING ENZYME) (OMEGA-PROTEIN) - DAUCUS CAROTA (CARROT).
Q26024 TOPOISOMERASE I - PLASMODIUM FALCIPARUM.
Q27529 DNA TOPOISOMERASE I (EC 5.99.1.2) - CAENORHABDITIS ELEGANS.
Q84147 TOPOISOMERASE - ORF VIRUS.
Q85387 HOMOLOG OF VACCINIA VIRUS CDS H6R - VARIOLA VIRUS.
Q89220 ORF7R - VARIOLA VIRUS.
Q94705 DNA TOPOISOMERASE I - PHYSARUM POLYCEPHALUM (SLIME MOLD).
Q98254 MC087R - MOLLUSCUM CONTAGIOSUM VIRUS SUBTYPE 1 (MCVI).
TOP1_ARATH DNA TOPOISOMERASE I (EC 5.99.1.2) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
TOP1_CANAL DNA TOPOISOMERASE I (EC 5.99.1.2) - CANDIDA ALBICANS (YEAST).
TOP1_CRIGR DNA TOPOISOMERASE I (EC 5.99.1.2) - CRICETULUS GRISEUS (CHINESE HAMSTER).
TOP1_DROME DNA TOPOISOMERASE I (EC 5.99.1.2) - DROSOPHILA MELANOGASTER (FRUIT FLY).
TOP1_HUMAN DNA TOPOISOMERASE I (EC 5.99.1.2) - HOMO SAPIENS (HUMAN).
TOP1_MOUSE DNA TOPOISOMERASE I (EC 5.99.1.2) - MUS MUSCULUS (MOUSE).
TOP1_SCHPO DNA TOPOISOMERASE I (EC 5.99.1.2) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
TOP1_SFVKA DNA TOPOISOMERASE I (EC 5.99.1.2) - SHOPE FIBROMA VIRUS (STRAIN KASZA) (SFV).
TOP1_USTMA DNA TOPOISOMERASE I (EC 5.99.1.2) - USTILAGO MAYDIS (SMUT FUNGUS).
TOP1_VACCV DNA TOPOISOMERASE I (EC 5.99.1.2) (LATE PROTEIN H6) - VACCINIA VIRUS (STRAIN WR), AND VACCINIA VIRUS (STRAIN COPENHAGEN).
TOP1_VARV DNA TOPOISOMERASE I (EC 5.99.1.2) - VARIOLA VIRUS.
TOP1_XENLA DNA TOPOISOMERASE I (EC 5.99.1.2) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
TOP1_YEAST DNA TOPOISOMERASE I (EC 5.99.1.2) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).

P87507 DNA TOPOISOMERASE - AMSACTA MOOREI ENTOMOPOXVIRUS (AMEPV).
Scan History
OWL26_3    2  100  NSINGLE    
SPTR37_9f 3 400 NSINGLE
Initial Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
LFRGRGNHPK TOP1_MOUSE 362 362 -
LFRGRGEHPK TOP1_DROME 583 583 -
LFRGRGNHPK TOP1_HUMAN 360 360 -
LFRGRGSHPK TOP1_SCHPO 337 337 -
LFRGRGEHPK TOP1_ARATH 510 510 -
IFVGSDSKGR TOP1_VACCV 58 58 -
IFVGSDSKGR TOP1_VARV 58 58 -

Motif 2 width=20
Element Seqn Id St Int Rpt
QRAVALYFIDKLALRAGNEK TOP1_HUMAN 474 104 -
QRAVALYFIDKLALRAGNEK TOP1_MOUSE 476 104 -
QRAVALYFIDKLALRAGNEK TOP1_DROME 697 104 -
QRGTAMYLIDVFALRAGNEK TOP1_SCHPO 451 104 -
QIAVATYLIDKLALRAGNEK TOP1_ARATH 626 106 -
QLAVFMLMETMFFIRFGKMK TOP1_VACCV 116 48 -
QLAVFMLMETMFFIRFGKMK TOP1_VARV 116 48 -

Motif 3 width=15
Element Seqn Id St Int Rpt
QADTVGCCSLRVEHV TOP1_DROME 720 3 -
TADTVGCCSLRVEHI TOP1_HUMAN 498 4 -
TADTVGCCSLRVEHI TOP1_MOUSE 500 4 -
EADTVGCCSLRYEHV TOP1_SCHPO 474 3 -
EADTVGCCTLKVGNV TOP1_ARATH 649 3 -
ENETVGLLTLKNKHI TOP1_VACCV 139 3 -
ENETVGLLTLKNKHI TOP1_VARV 139 3 -

Motif 4 width=17
Element Seqn Id St Int Rpt
IVIKFVGKDKVSHEFVV TOP1_VARV 160 6 -
VEFDFLGKDSIRYYNKV TOP1_HUMAN 525 12 -
VEFDFPGKDSIRYYNKV TOP1_MOUSE 527 12 -
VVFDFPGKDSIRYYNEV TOP1_DROME 747 12 -
VVFDFLGKDSIRYYNEV TOP1_SCHPO 496 7 -
IKFDFLGKDSIQYVNTV TOP1_ARATH 671 7 -
IVIKFVGKDKVSHEFVV TOP1_VACCV 160 6 -

Motif 5 width=15
Element Seqn Id St Int Rpt
GIRIKDLRTYGVNYT TOP1_VACCV 216 39 -
GLTAKVFRTYNASIT TOP1_HUMAN 583 41 -
GLTAKVFRTYNASIT TOP1_MOUSE 585 41 -
GLTAKVFRTYNASKT TOP1_DROME 805 41 -
GLSAKVFRTYNASYT TOP1_SCHPO 555 42 -
GLTAKVFRTYNASIT TOP1_ARATH 729 41 -
GIRIKDLRTYGVNYT TOP1_VARV 216 39 -

Motif 6 width=12
Element Seqn Id St Int Rpt
SISKRAYMATTI TOP1_VACCV 268 37 -
GTSKLNYLDPRI TOP1_MOUSE 719 119 -
GTSKLNYLDPRI TOP1_DROME 924 104 -
GTSKINYIDPRL TOP1_SCHPO 765 195 -
GTSKINYLDPRI TOP1_ARATH 866 122 -
GTSKLNYLDPRI TOP1_HUMAN 717 119 -
SISKRAYMATTI TOP1_VARV 268 37 -
Final Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
LFRGRGNHPK P79994 361 361 -
LFRGRGNHPK TOP1_MOUSE 362 362 -
LFRGRGDHPK TOP1_XENLA 416 416 -
LFRGRGEHPK TOP1_DROME 583 583 -
LFRGRGNHPK TOP1_CRIGR 362 362 -
VFRGRGGHPK O17965 330 330 -
VFRGRGGHPK O17966 402 402 -
LFRGRGNHPK TOP1_HUMAN 360 360 -
VFRGRGGHPK Q27529 402 402 -
LFRGRGSHPK TOP1_SCHPO 337 337 -
LFRGRGDHPK O60013 287 287 -
LFRGRGAHPK TOP1_YEAST 292 292 -
LFRGRGEHPK TOP1_ARATH 510 510 -
LFKGRGEHPK O59891 368 368 -
LFRGRGEHPK O24307 484 484 -
LFRGRGEHPK O13463 393 393 -
LFRGRGAHPK TOP1_CANAL 302 302 -
LFRGRGEHPK Q26024 308 308 -
LFLGRGAHPK Q94705 553 553 -
LVKGRNGQPL P93119 211 211 -
LFLGRGAHPK TOP1_USTMA 313 313 -
IFVGSDSKGR Q85387 58 58 -
IFVGSDSKGR Q89220 58 58 -
IFVGSDSKGR TOP1_VACCV 58 58 -
IFVGSDSKGR TOP1_VARV 58 58 -
IFVGLDSKGR TOP1_SFVKA 58 58 -
IFVGRDAKGR Q84147 58 58 -
VFVGLDSKQR Q98254 59 59 -

Motif 2 width=20
Element Seqn Id St Int Rpt
QRAVALYFIDKLALRAGNEK TOP1_HUMAN 474 104 -
QRAVALYFIDKLALRAGNEK P79994 475 104 -
QRAVALYFIDKLALRAGNEK TOP1_MOUSE 476 104 -
QRAVALYFIDKLALRAGNEK TOP1_XENLA 530 104 -
QRAVALYFIDKLALRAGNEK TOP1_DROME 697 104 -
QRAVALYFIDKLALRAGNEK TOP1_CRIGR 476 104 -
QRATALYFIDKLALRAGNEK O17965 444 104 -
QRATALYFIDKLALRAGNEK O17966 516 104 -
QRATALYFIDKLALRAGNEK Q27529 516 104 -
QRGTAMYLIDVFALRAGNEK TOP1_SCHPO 451 104 -
QRATAMYLIDLFALRAGNEK O60013 401 104 -
QKAVAIYLIDVFALRAGGEK TOP1_YEAST 406 104 -
QIAVATYLIDKLALRAGNEK TOP1_ARATH 626 106 -
QRATALYFIDRLALRAGNEK O59891 482 104 -
QIAVATYLIDKLALRAGNEK O24307 600 106 -
QKATAVYLIDQFALRAGNEK O13463 507 104 -
QMATAMYLIDVFALRAGGEK TOP1_CANAL 416 104 -
QLGTAVYLIDFLALRVGGEK Q26024 425 107 -
QRATAIYLIDRLALRVGNEK Q94705 667 104 -
QIAVATYLIDKLALRAGNEK P93119 476 255 -
QIATIVCLIDNFSLRAGNEK TOP1_USTMA 428 105 -
QLAVFMLMETMFFIRFGKMK Q85387 116 48 -
QLAVFMLMETMFFIRFGKMK Q89220 116 48 -
QLAVFMLMETMFFIRFGKMK TOP1_VACCV 116 48 -
QLAVFMLMETMFFIRFGKMK TOP1_VARV 116 48 -
QLGVFMLMETSFFIRMGKVK TOP1_SFVKA 115 47 -
QMAAFLLMETSFFIRVGKTR Q84147 115 47 -
QLAIFLLMETSFYIRTGKMR Q98254 119 50 -

Motif 3 width=15
Element Seqn Id St Int Rpt
AADTVGCCSLRVEHI O17966 540 4 -
TADTVGCCSLRVEHI TOP1_HUMAN 498 4 -
TADTVGCCSLRVEHI P79994 499 4 -
TADTVGCCSLRVEHI TOP1_MOUSE 500 4 -
TADTVGCCSLRVEHI TOP1_XENLA 554 4 -
QADTVGCCSLRVEHV TOP1_DROME 720 3 -
TADTVSCCSLRVEHI TOP1_CRIGR 500 4 -
AADTVGCCSLRVEHI O17965 468 4 -
AADTVGCCSLRVEHI Q27529 540 4 -
EADTVGCCSLRYEHV TOP1_SCHPO 474 3 -
EADTVGCCSLRYEHI O60013 424 3 -
EADTVGCCSLRYEHV TOP1_YEAST 429 3 -
EADTVGCCTLKVGNV TOP1_ARATH 649 3 -
EADTVGCCSLRYEHV O59891 505 3 -
EADTVGCCTLKVENV O24307 623 3 -
EAETVGCCSLKYENV O13463 530 3 -
EADTVGCCSLRYEHV TOP1_CANAL 439 3 -
EADTVGCCSLRVEHI Q26024 449 4 -
TADTVGCCSLRVEHV Q94705 690 3 -
EADTVGCCTLKVENV P93119 499 3 -
ETETYGVCSLRCEHA TOP1_USTMA 451 3 -
ENETVGLLTLKNKHI Q85387 139 3 -
ENETVGLLTLKNKHI Q89220 139 3 -
ENETVGLLTLKNKHI TOP1_VACCV 139 3 -
ENETVGLLTLKNKHI TOP1_VARV 139 3 -
ENDTVGLLTLKNKNI TOP1_SFVKA 138 3 -
ESGTVGMLTLRNKHL Q84147 138 3 -
ENETVGMLTLKNRHL Q98254 142 3 -

Motif 4 width=17
Element Seqn Id St Int Rpt
LAIRFVGKDQVTHEFRV Q98254 163 6 -
VEFDFLGKDSIRYYNKV TOP1_HUMAN 525 12 -
VEFDFLGKDSIRYYNKV P79994 526 12 -
VEFDFPGKDSIRYYNKV TOP1_MOUSE 527 12 -
VEFDFPGKDSIRYYNKV TOP1_XENLA 581 12 -
VVFDFPGKDSIRYYNEV TOP1_DROME 747 12 -
VEFDFPGKDSIRYYNKV TOP1_CRIGR 527 12 -
VEFDFLGKDSIRYFNRV O17965 502 19 -
VEFDFLGKDSIRYFNRV O17966 574 19 -
VEFDFLGKDSIRYFNRV Q27529 574 19 -
VVFDFLGKDSIRYYNEV TOP1_SCHPO 496 7 -
VVFDFLGKDSIRYYNEV O60013 446 7 -
VIFDFLGKDSIRFYQEV TOP1_YEAST 451 7 -
IKFDFLGKDSIQYVNTV TOP1_ARATH 671 7 -
IIFDFLGKDSMRFHQEV O59891 527 7 -
LKFNFLGKDSIKYENTV O24307 645 7 -
VIFDFLGKDSIRFYDEV O13463 552 7 -
VIFDLLGKDSIRFYQEV TOP1_CANAL 461 7 -
ITLDFLGKDSIRYFNTV Q26024 505 41 -
VTLDFLGKDSMRYHNTV Q94705 712 7 -
LKFDFLGKDSIRYQNEV P93119 521 7 -
IHLEFLGKDSMKFEEDL TOP1_USTMA 473 7 -
IVIKFVGKDKVSHEFVV Q85387 160 6 -
IVIKFVGKDKVSHEFVV Q89220 160 6 -
IVIKFVGKDKVSHEFVV TOP1_VACCV 160 6 -
IVIKFVGKDKVSHEFVV TOP1_VARV 160 6 -
ILIHFVGKDKIIHNFTV TOP1_SFVKA 159 6 -
IRVAFVGKDRVAHEFAV Q84147 161 8 -

Motif 5 width=15
Element Seqn Id St Int Rpt
GIRIKDLRTYGVNYT TOP1_VACCV 216 39 -
GLTAKVFRTYNASIT TOP1_HUMAN 583 41 -
GLTAKVFRTYNASIT P79994 584 41 -
GLTAKVFRTYNASIT TOP1_MOUSE 585 41 -
GLTAKVFRTYNASIT TOP1_XENLA 639 41 -
GLTAKVFRTYNASKT TOP1_DROME 805 41 -
GLTAKVFRTYNASIT TOP1_CRIGR 585 41 -
GLTVKVFRTYNASIT O17965 560 41 -
GLTVKVFRTYNASIT O17966 632 41 -
GLTVKVFRTYNASIT Q27529 632 41 -
GLSAKVFRTYNASYT TOP1_SCHPO 555 42 -
GLSAKVFRTHNASYT O60013 505 42 -
GLTAKVFRTYNASKT TOP1_YEAST 510 42 -
GLTAKVFRTYNASIT TOP1_ARATH 729 41 -
GLTAKVFRTYNASWT O59891 586 42 -
GLTAKVFRTFNASIT O24307 703 41 -
GLTAKVFRTYNASHT O13463 611 42 -
GLTAKVFRTYNASKT TOP1_CANAL 520 42 -
TLSAKVFRTYNASIT Q26024 563 41 -
NLSAKVFRTYNASLT Q94705 777 48 -
GLTAKVFRTYNASIT P93119 579 41 -
GLSAKVFRTYNASVT TOP1_USTMA 554 64 -
GIRIKDLRTYGVNYT Q85387 216 39 -
GIRIKDLRTYGVNYT Q89220 216 39 -
GIRIKDLRTYGVNYT TOP1_VARV 216 39 -
GIRLKDLRTYGVNYT TOP1_SFVKA 215 39 -
GIRVKDLRTYGVNYT Q84147 217 39 -
GVRVKDLRTYGVNVT Q98254 219 39 -

Motif 6 width=12
Element Seqn Id St Int Rpt
SISRSAYMATAV Q84147 269 37 -
STSKLNYLDPRI P79994 718 119 -
GTSKLNYLDPRI TOP1_MOUSE 719 119 -
GTSKLNYLDPRI TOP1_XENLA 773 119 -
GTSKLNYLDPRI TOP1_DROME 924 104 -
GTSKLNYLDPRI TOP1_CRIGR 719 119 -
GTSKLNYIDPRI O17965 683 108 -
GTSKLNYIDPRI O17966 755 108 -
GTSKLNYIDPRI Q27529 755 108 -
GTSKINYIDPRL TOP1_SCHPO 765 195 -
GTSKINYIDPRL O60013 716 196 -
GTSKINYIDPRL TOP1_YEAST 721 196 -
GTSKINYLDPRI TOP1_ARATH 866 122 -
GTSKINYIDPRL O59891 796 195 -
GTSKINYLDPRI O24307 840 122 -
GTSKLNYLDPRI TOP1_HUMAN 717 119 -
GTSKINYIDPRL O13463 823 197 -
GTSKMNYIDPRL TOP1_CANAL 730 195 -
GTSKINYMDPRI Q26024 792 214 -
TTSKINYIDPRI Q94705 968 176 -
GTSKINYLDPRI P93119 743 149 -
STSKLNYIDPRI TOP1_USTMA 816 247 -
SISKRAYMATTI Q85387 268 37 -
SISKRAYMATTI Q89220 268 37 -
SARKLVALSIRQ Q98254 250 16 -
SISKRAYMATTI TOP1_VACCV 268 37 -
SISKRAYMATTI TOP1_VARV 268 37 -
SISKRAYIANTV TOP1_SFVKA 267 37 -