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Conserved domains on  [gi|11225260|ref|NP_003277|]
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DNA topoisomerase 1 [Homo sapiens]

Protein Classification

Topoisomer_IB_N_htopoI_like and Topo_IB_C domain-containing protein( domain architecture ID 11556523)

Topoisomer_IB_N_htopoI_like and Topo_IB_C domain-containing protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
TOPEUc smart00435
DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina ...
360-737 0e+00

DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras


:

Pssm-ID: 214661 [Multi-domain]  Cd Length: 391  Bit Score: 640.94  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260    360 LFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEK 439
Cdd:smart00435   1 LFRGRGEHPKTGKLKRRIMPEDITINIGKDAPVPEPPPGHKWKEVRHDNTVTWLASWKENINGSIKYVFLAASSSLKGQS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260    440 DWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEgETADTVGCCSLRVEHINLHPELD 519
Cdd:smart00435  81 DRKKYEKARKLKKHIDKIRKDYTKDLKSKEMKVRQRATALYLIDKLALRAGNEKGE-DEADTVGCCSLRVEHVTLKPPNK 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260    520 gqeyvVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQ 599
Cdd:smart00435 160 -----VIFDFLGKDSIRYYNEVEVDKQVFKNLKIFMKPKKPGDDLFDRLNTSKLNKHLKELMPGLTAKVFRTYNASITLQ 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260    600 QQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLA-------------DARRDLK 666
Cdd:smart00435 235 EQLKELTAKDGNVAEKILAYNRANREVAILCNHQRTVSKTHEKSMEKLQEKIKALKYQLKrlkkmillfemisDLKRKLK 314
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11225260    667 SA------KADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNYLDPRITVAWCKKWG 737
Cdd:smart00435 315 SKferdneKLDAEVKEKKKEKKKEEKKKKQIERLEERIEKLEVQATDKEENKTVALGTSKINYIDPRITVAWCKKFD 391
Topoisomer_IB_N_htopoI_like cd03488
Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA ...
216-430 5.84e-133

Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain.


:

Pssm-ID: 239570  Cd Length: 215  Bit Score: 392.47  E-value: 5.84e-133
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 216 KWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIIT 295
Cdd:cd03488   1 KWTTLEHNGPVFAPPYEPLPKNVKFYYDGKPVKLSPEAEEVATFYAKMLEHDYATKEIFQKNFFKDFKKVMTKEEKVIIK 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 296 NLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKR 375
Cdd:cd03488  81 DFSKCDFTQMFAYFKAQKEEKKAMSKEEKKAIKAEKEKLEEEYGFCILDGHKEKVGNFRIEPPGLFRGRGAHPKTGKLKR 160
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*
gi 11225260 376 RIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLN 430
Cdd:cd03488 161 RIMPEDIIINIGKDAKVPEPPPGHKWKEVRHDNTVTWLASWTENINGSIKYVMLN 215
 
Name Accession Description Interval E-value
TOPEUc smart00435
DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina ...
360-737 0e+00

DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras


Pssm-ID: 214661 [Multi-domain]  Cd Length: 391  Bit Score: 640.94  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260    360 LFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEK 439
Cdd:smart00435   1 LFRGRGEHPKTGKLKRRIMPEDITINIGKDAPVPEPPPGHKWKEVRHDNTVTWLASWKENINGSIKYVFLAASSSLKGQS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260    440 DWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEgETADTVGCCSLRVEHINLHPELD 519
Cdd:smart00435  81 DRKKYEKARKLKKHIDKIRKDYTKDLKSKEMKVRQRATALYLIDKLALRAGNEKGE-DEADTVGCCSLRVEHVTLKPPNK 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260    520 gqeyvVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQ 599
Cdd:smart00435 160 -----VIFDFLGKDSIRYYNEVEVDKQVFKNLKIFMKPKKPGDDLFDRLNTSKLNKHLKELMPGLTAKVFRTYNASITLQ 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260    600 QQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLA-------------DARRDLK 666
Cdd:smart00435 235 EQLKELTAKDGNVAEKILAYNRANREVAILCNHQRTVSKTHEKSMEKLQEKIKALKYQLKrlkkmillfemisDLKRKLK 314
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11225260    667 SA------KADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNYLDPRITVAWCKKWG 737
Cdd:smart00435 315 SKferdneKLDAEVKEKKKEKKKEEKKKKQIERLEERIEKLEVQATDKEENKTVALGTSKINYIDPRITVAWCKKFD 391
Topoisomer_IB_N_htopoI_like cd03488
Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA ...
216-430 5.84e-133

Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain.


Pssm-ID: 239570  Cd Length: 215  Bit Score: 392.47  E-value: 5.84e-133
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 216 KWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIIT 295
Cdd:cd03488   1 KWTTLEHNGPVFAPPYEPLPKNVKFYYDGKPVKLSPEAEEVATFYAKMLEHDYATKEIFQKNFFKDFKKVMTKEEKVIIK 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 296 NLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKR 375
Cdd:cd03488  81 DFSKCDFTQMFAYFKAQKEEKKAMSKEEKKAIKAEKEKLEEEYGFCILDGHKEKVGNFRIEPPGLFRGRGAHPKTGKLKR 160
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*
gi 11225260 376 RIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLN 430
Cdd:cd03488 161 RIMPEDIIINIGKDAKVPEPPPGHKWKEVRHDNTVTWLASWTENINGSIKYVMLN 215
Topoisom_I_N pfam02919
Eukaryotic DNA topoisomerase I, DNA binding fragment; Topoisomerase I promotes the relaxation ...
215-429 3.60e-131

Eukaryotic DNA topoisomerase I, DNA binding fragment; Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. This family may be more than one structural domain.


Pssm-ID: 460746  Cd Length: 213  Bit Score: 387.99  E-value: 3.60e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260   215 IKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMtnEEKNII 294
Cdd:pfam02919   1 IKWTTLEHNGVLFPPPYEPLPHNVKLKYDGKPVDLPPEAEEVATFYAAMLETDYAQNPVFNKNFFNDFRKVL--KEKGGI 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260   295 TNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLK 374
Cdd:pfam02919  79 KDFEKCDFSPIYEYFEQEKEKKKAMSKEEKKALKEEKEKLEEPYGYCLVDGRKEKVGNFRVEPPGLFRGRGEHPKTGKLK 158
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 11225260   375 RRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIML 429
Cdd:pfam02919 159 KRVQPEDVTINIGKDAPVPEPPPGHKWKEVVHDNTVTWLASWKENINGQFKYVML 213
Topoisom_I pfam01028
Eukaryotic DNA topoisomerase I, catalytic core; Topoisomerase I promotes the relaxation of DNA ...
432-635 2.15e-128

Eukaryotic DNA topoisomerase I, catalytic core; Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination.


Pssm-ID: 460030 [Multi-domain]  Cd Length: 198  Bit Score: 380.32  E-value: 2.15e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260   432 SSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEgETADTVGCCSLRVEH 511
Cdd:pfam01028   1 SSKLKGESDWKKYEKARKLKKHIDKIREDYTKDLKSKDMKERQRATAVYLIDKLALRVGNEKDE-DEADTVGCCSLRVEH 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260   512 INLHPEldgqeYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRT 591
Cdd:pfam01028  80 VKLHPP-----NTVEFDFLGKDSIRYYNTVEVDLQVFKNLKIFKKNKKPGDDLFDRLNTSKLNKYLKELMPGLTAKVFRT 154
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 11225260   592 YNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQRA 635
Cdd:pfam01028 155 YNASITLQEQLKELVPKEGSVAEKLLAYNRANREVAILCNHQRS 198
Topo_IB_C cd00659
DNA topoisomerase IB, C-terminal catalytic domain; Topoisomerase I promotes the relaxation of ...
438-638 3.90e-91

DNA topoisomerase IB, C-terminal catalytic domain; Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses, and bacterial versions of Topo IB. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases.


Pssm-ID: 271176 [Multi-domain]  Cd Length: 210  Bit Score: 284.17  E-value: 3.90e-91
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 438 EKDWQKYETARRLKKCVDKIRNQYREDWKSKE-MKVRQRAVALYFIDKLALRAGNEKEEgETADTVGCCSLRVEHINLHP 516
Cdd:cd00659   1 ERDAKKFERARRLKKAIPKIRRRYRKDLKSKElMKERQLAVALYLIDKFALRVGNEKYE-EENDTVGCCTLRKEHVTLEP 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 517 EldgqeyVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMenKQPEDDLFD-----RLNTGILNKHLQDLMEGLTAKVFRT 591
Cdd:cd00659  80 N------VVEFDFLGKDSIRYYNEVPVDPRVFKNLKIFM--KLPGDDLFDyvdvrRLNTSKLNAYLRELMGGLTAKDFRT 151
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 11225260 592 YNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAPPK 638
Cdd:cd00659 152 YGASLTLQQQLKELTAPDSNIPAKKKVYNRANRAVAILCNHTPAVSK 198
Top1 COG3569
DNA topoisomerase IB [Replication, recombination and repair];
440-627 5.53e-06

DNA topoisomerase IB [Replication, recombination and repair];


Pssm-ID: 442790  Cd Length: 345  Bit Score: 49.02  E-value: 5.53e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 440 DWQ------KYETARRLKKCVDKIRNQYREDWKSKEMKvRQRAVALYF--IDKLALRAGNE---KEEGetadTVGCCSLR 508
Cdd:COG3569  89 DWRevrdetKFDRLLAFGRALPRIRRRVARDLRRRGLP-REKVLAAVVrlLDRTLIRVGNEeyaRENG----SYGLTTLR 163
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 509 VEHInlhpELDGQEyvVEFDFLGKDSIRyyNKVPVEK----RVFKNLQlfmenKQPEDDLFD---------RLNTGILNK 575
Cdd:COG3569 164 KRHV----KVDGDT--VRFRFRGKSGKE--HEVTLRDrrlaRLVRRLQ-----DLPGQELFQyrdedgerhPVDSGDVNA 230
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|...
gi 11225260 576 HLQDLM-EGLTAKVFRTYNASITLQQQLKELTAPDENIPAKiLSYNRANRAVA 627
Cdd:COG3569 231 YLREITgEDFTAKDFRTWAGTVLAAEALAEAGPAESERARK-KNVVAAVDAVA 282
 
Name Accession Description Interval E-value
TOPEUc smart00435
DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina ...
360-737 0e+00

DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras


Pssm-ID: 214661 [Multi-domain]  Cd Length: 391  Bit Score: 640.94  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260    360 LFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEK 439
Cdd:smart00435   1 LFRGRGEHPKTGKLKRRIMPEDITINIGKDAPVPEPPPGHKWKEVRHDNTVTWLASWKENINGSIKYVFLAASSSLKGQS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260    440 DWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEgETADTVGCCSLRVEHINLHPELD 519
Cdd:smart00435  81 DRKKYEKARKLKKHIDKIRKDYTKDLKSKEMKVRQRATALYLIDKLALRAGNEKGE-DEADTVGCCSLRVEHVTLKPPNK 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260    520 gqeyvVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQ 599
Cdd:smart00435 160 -----VIFDFLGKDSIRYYNEVEVDKQVFKNLKIFMKPKKPGDDLFDRLNTSKLNKHLKELMPGLTAKVFRTYNASITLQ 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260    600 QQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLA-------------DARRDLK 666
Cdd:smart00435 235 EQLKELTAKDGNVAEKILAYNRANREVAILCNHQRTVSKTHEKSMEKLQEKIKALKYQLKrlkkmillfemisDLKRKLK 314
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11225260    667 SA------KADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNYLDPRITVAWCKKWG 737
Cdd:smart00435 315 SKferdneKLDAEVKEKKKEKKKEEKKKKQIERLEERIEKLEVQATDKEENKTVALGTSKINYIDPRITVAWCKKFD 391
Topoisomer_IB_N_htopoI_like cd03488
Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA ...
216-430 5.84e-133

Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain.


Pssm-ID: 239570  Cd Length: 215  Bit Score: 392.47  E-value: 5.84e-133
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 216 KWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIIT 295
Cdd:cd03488   1 KWTTLEHNGPVFAPPYEPLPKNVKFYYDGKPVKLSPEAEEVATFYAKMLEHDYATKEIFQKNFFKDFKKVMTKEEKVIIK 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 296 NLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKR 375
Cdd:cd03488  81 DFSKCDFTQMFAYFKAQKEEKKAMSKEEKKAIKAEKEKLEEEYGFCILDGHKEKVGNFRIEPPGLFRGRGAHPKTGKLKR 160
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*
gi 11225260 376 RIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLN 430
Cdd:cd03488 161 RIMPEDIIINIGKDAKVPEPPPGHKWKEVRHDNTVTWLASWTENINGSIKYVMLN 215
Topoisom_I_N pfam02919
Eukaryotic DNA topoisomerase I, DNA binding fragment; Topoisomerase I promotes the relaxation ...
215-429 3.60e-131

Eukaryotic DNA topoisomerase I, DNA binding fragment; Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. This family may be more than one structural domain.


Pssm-ID: 460746  Cd Length: 213  Bit Score: 387.99  E-value: 3.60e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260   215 IKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMtnEEKNII 294
Cdd:pfam02919   1 IKWTTLEHNGVLFPPPYEPLPHNVKLKYDGKPVDLPPEAEEVATFYAAMLETDYAQNPVFNKNFFNDFRKVL--KEKGGI 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260   295 TNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLK 374
Cdd:pfam02919  79 KDFEKCDFSPIYEYFEQEKEKKKAMSKEEKKALKEEKEKLEEPYGYCLVDGRKEKVGNFRVEPPGLFRGRGEHPKTGKLK 158
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 11225260   375 RRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIML 429
Cdd:pfam02919 159 KRVQPEDVTINIGKDAPVPEPPPGHKWKEVVHDNTVTWLASWKENINGQFKYVML 213
Topoisom_I pfam01028
Eukaryotic DNA topoisomerase I, catalytic core; Topoisomerase I promotes the relaxation of DNA ...
432-635 2.15e-128

Eukaryotic DNA topoisomerase I, catalytic core; Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination.


Pssm-ID: 460030 [Multi-domain]  Cd Length: 198  Bit Score: 380.32  E-value: 2.15e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260   432 SSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEgETADTVGCCSLRVEH 511
Cdd:pfam01028   1 SSKLKGESDWKKYEKARKLKKHIDKIREDYTKDLKSKDMKERQRATAVYLIDKLALRVGNEKDE-DEADTVGCCSLRVEH 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260   512 INLHPEldgqeYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRT 591
Cdd:pfam01028  80 VKLHPP-----NTVEFDFLGKDSIRYYNTVEVDLQVFKNLKIFKKNKKPGDDLFDRLNTSKLNKYLKELMPGLTAKVFRT 154
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 11225260   592 YNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQRA 635
Cdd:pfam01028 155 YNASITLQEQLKELVPKEGSVAEKLLAYNRANREVAILCNHQRS 198
Topoisomer_IB_N cd00660
Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) ...
216-430 5.14e-127

Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I differ from human topo I in their sensitivity to CPTs and other classical topo I inhibitors. Trypanosomatid topos I play putative roles in organizing the kinetoplast DNA network unique to these parasites. This family may represent more than one structural domain.


Pssm-ID: 238356  Cd Length: 215  Bit Score: 377.38  E-value: 5.14e-127
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 216 KWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIIT 295
Cdd:cd00660   1 KWTTLEHNGVIFPPPYEPLPKNVKFYYDGKPVKLPPEAEEVATFFAVMLETDYATKEVFRKNFFKDFRKILTKEEKHIIK 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 296 NLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKR 375
Cdd:cd00660  81 KLSKCDFTPIYQYFEEEKEKKKAMSKEEKKAIKEEKEKLEEPYGYCLVDGHKEKVGNFRIEPPGLFRGRGEHPKMGKLKR 160
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*
gi 11225260 376 RIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLN 430
Cdd:cd00660 161 RIMPEDITINIGKDAPVPEPPAGHKWKEVRHDNTVTWLASWKENINGQFKYVMLA 215
Topo_IB_C cd00659
DNA topoisomerase IB, C-terminal catalytic domain; Topoisomerase I promotes the relaxation of ...
438-638 3.90e-91

DNA topoisomerase IB, C-terminal catalytic domain; Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses, and bacterial versions of Topo IB. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases.


Pssm-ID: 271176 [Multi-domain]  Cd Length: 210  Bit Score: 284.17  E-value: 3.90e-91
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 438 EKDWQKYETARRLKKCVDKIRNQYREDWKSKE-MKVRQRAVALYFIDKLALRAGNEKEEgETADTVGCCSLRVEHINLHP 516
Cdd:cd00659   1 ERDAKKFERARRLKKAIPKIRRRYRKDLKSKElMKERQLAVALYLIDKFALRVGNEKYE-EENDTVGCCTLRKEHVTLEP 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 517 EldgqeyVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMenKQPEDDLFD-----RLNTGILNKHLQDLMEGLTAKVFRT 591
Cdd:cd00659  80 N------VVEFDFLGKDSIRYYNEVPVDPRVFKNLKIFM--KLPGDDLFDyvdvrRLNTSKLNAYLRELMGGLTAKDFRT 151
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 11225260 592 YNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAPPK 638
Cdd:cd00659 152 YGASLTLQQQLKELTAPDSNIPAKKKVYNRANRAVAILCNHTPAVSK 198
Topoisomer_IB_N_LdtopoI_like cd03489
Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding fragment found in eukaryotic DNA ...
216-429 5.65e-67

Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I differ from human topo I in their sensitivity to CPTs and other classical topo I inhibitors. Trypanosomatid topo I play putative roles in organizing the kinetoplast DNA network unique to these parasites. This family may represent more than one structural domain.


Pssm-ID: 239571  Cd Length: 212  Bit Score: 220.52  E-value: 5.65e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 216 KWKFLEHKGPVFAPPYEPlpENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRkEMTNEEKNIIT 295
Cdd:cd03489   1 RWTTLVHNGVLFPPPYKP--HGIPILYNGQPFDMTPEEEEVATMFAVMKEHDYYRKEVFRRNFFESWR-EILDKRHHPIR 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 296 NLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKR 375
Cdd:cd03489  78 KLELCDFTPIYEWHLREKEKKKSRTKEEKKALKEEKDKEAEPYMWCVWDGVKEQVANFRVEPPGLFRGRGEHPKMGKLKK 157
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....
gi 11225260 376 RIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIML 429
Cdd:cd03489 158 RIQPEDITINIGKGAPIPECPAGHKWKEVKHDNTVTWLAMWRDPIAGNFKYVML 211
Topoisomer_IB_N_1 cd03490
Topoisomer_IB_N_1: A subgroup of the N-terminal DNA binding fragment found in eukaryotic DNA ...
216-430 1.46e-56

Topoisomer_IB_N_1: A subgroup of the N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB. Topo IB proteins include the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topos I differ from human topo I in their sensitivity to CPTs and other classical topo I inhibitors. Trypanosomatid topos I have putative roles in organizing the kinetoplast DNA network unique to these parasites. This family may represent more than one structural domain.


Pssm-ID: 239572  Cd Length: 217  Bit Score: 192.81  E-value: 1.46e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 216 KWKFLEHKGPVFAPPYepLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNI-I 294
Cdd:cd03490   1 QWKYLEHNGMIFTPPY--VPHNVPIMYKGETIHLPPNLEEIATYWAQSMGTNYETKEKFCKNFWKVFVNSFEKDHKFIrR 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 295 TNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLK 374
Cdd:cd03490  79 CKLSDADFSLIKNHLEEEKEKKKNLNKEEKEAKKKERAKREYPFNYALVDWIREKVSSNKLEPPGLFKGRGEHPKQGLLK 158
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 11225260 375 RRIMPEDIIINCSKDAKVPSPP---PGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLN 430
Cdd:cd03490 159 SRIFPEDVILNISKDAPVPKVTnfmEGHSWKDIYHDNSVTWLAYYKDSINDQFKYMFLS 217
Topo_C_assoc pfam14370
C-terminal topoisomerase domain; This domain is found at the C-terminal of topoisomerase and ...
695-763 4.43e-35

C-terminal topoisomerase domain; This domain is found at the C-terminal of topoisomerase and other similar enzymes.


Pssm-ID: 464154 [Multi-domain]  Cd Length: 68  Bit Score: 127.30  E-value: 4.43e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 11225260   695 EEQLMKLEVQATDREENKQIALGTSKLNYLDPRITVAWCKKWGVPIEKIYNKTQREKFAWAIDmADEDY 763
Cdd:pfam14370   1 KERIKKLELQLKDKEENKTVALGTSKINYIDPRITVAWCKKHDVPIEKIFSKTLREKFPWAMD-VDPDW 68
Top1 COG3569
DNA topoisomerase IB [Replication, recombination and repair];
440-627 5.53e-06

DNA topoisomerase IB [Replication, recombination and repair];


Pssm-ID: 442790  Cd Length: 345  Bit Score: 49.02  E-value: 5.53e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 440 DWQ------KYETARRLKKCVDKIRNQYREDWKSKEMKvRQRAVALYF--IDKLALRAGNE---KEEGetadTVGCCSLR 508
Cdd:COG3569  89 DWRevrdetKFDRLLAFGRALPRIRRRVARDLRRRGLP-REKVLAAVVrlLDRTLIRVGNEeyaRENG----SYGLTTLR 163
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11225260 509 VEHInlhpELDGQEyvVEFDFLGKDSIRyyNKVPVEK----RVFKNLQlfmenKQPEDDLFD---------RLNTGILNK 575
Cdd:COG3569 164 KRHV----KVDGDT--VRFRFRGKSGKE--HEVTLRDrrlaRLVRRLQ-----DLPGQELFQyrdedgerhPVDSGDVNA 230
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|...
gi 11225260 576 HLQDLM-EGLTAKVFRTYNASITLQQQLKELTAPDENIPAKiLSYNRANRAVA 627
Cdd:COG3569 231 YLREITgEDFTAKDFRTWAGTVLAAEALAEAGPAESERARK-KNVVAAVDAVA 282
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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