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Conserved domains on  [gi|1831509381|ref|NP_001368107|]
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DNA topoisomerase [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
TOP1Ac super family cl30544
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
1-88 1.49e-24

DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.


The actual alignment was detected with superfamily member cd00186:

Pssm-ID: 357420 [Multi-domain]  Cd Length: 381  Bit Score: 103.07  E-value: 1.49e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381   1 MEKHGIGTDASIPVHINTITQRNYVTVEsGRRLVPTRLGQCLVRGYWKVDPELVLPTMRAELEEQLNLVASGKADYLDVK 80
Cdd:cd00186   292 MEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEKLDEIAEGKKDYQEVL 370

                  ....*...
gi 1831509381  81 NHALKMFE 88
Cdd:cd00186   371 EEFYEEFK 378
PRK07219 super family cl35562
DNA topoisomerase I; Validated
1-234 5.89e-18

DNA topoisomerase I; Validated


The actual alignment was detected with superfamily member PRK07219:

Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 85.44  E-value: 5.89e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381   1 MEKHGIGTDASIPVHINTITQRNYVTveSGRRLVPTRLGQCLVRGYWKVDPELVLPTMRAELEEQLNLVASGKADYLDVK 80
Cdd:PRK07219  486 MEKRGLGTKATRHDIIEKLYKRGYVI--EGDPPRPTDLGIAVIEALEKYAPEIVSEEMTAQLEADMQAIEDGKKKKEDVT 563
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381  81 NHALKMFEMKFQYFVTNIPAVDTLFEASFTTLSDTGKPFSRCGKCRRYMKLVQTKPQRLY--C---PTCQETYAVPnfKD 155
Cdd:PRK07219  564 EESREMLKEILSELKEKRKEIGDHLAGSLKAENRSLKTIGKCPECGGDLIIIRTDKGSRFvgCsgyPDCRNTFPLP--ST 641
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381 156 G---------------VLKVIG-----DHKCPLDDFDVILYQGPggklaRTFTLCPFCFNNPPFEKMPQGA--GCDTcvH 213
Cdd:PRK07219  642 GrikvldevcekcglpVIKILRgkqtfVVGCPDCEAEKEEEDPD-----EVIGPCPKCGGELAIKQLKYGSflGCTN--Y 714
                         250       260       270
                  ....*....|....*....|....*....|
gi 1831509381 214 PSCQYSISSN---------GVCgclQDCGG 234
Cdd:PRK07219  715 PKCKYTLPLPrrgkitvtdEKC---PECGL 741
 
Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
1-88 1.49e-24

DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.


Pssm-ID: 238110 [Multi-domain]  Cd Length: 381  Bit Score: 103.07  E-value: 1.49e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381   1 MEKHGIGTDASIPVHINTITQRNYVTVEsGRRLVPTRLGQCLVRGYWKVDPELVLPTMRAELEEQLNLVASGKADYLDVK 80
Cdd:cd00186   292 MEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEKLDEIAEGKKDYQEVL 370

                  ....*...
gi 1831509381  81 NHALKMFE 88
Cdd:cd00186   371 EEFYEEFK 378
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
1-79 2.49e-22

DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.


Pssm-ID: 426069 [Multi-domain]  Cd Length: 410  Bit Score: 97.31  E-value: 2.49e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1831509381   1 MEKHGIGTDASIPVHINTITQRNYVTVEsGRRLVPTRLGQCLVRGYwKVDPELVLPTMRAELEEQLNLVASGKADYLDV 79
Cdd:pfam01131 332 MEKAGIGTPATRATIIETLLERGYVERK-KKSLVPTELGKALVEAL-EKFPDLVDPELTAELEEKLDEIAEGKLDWKDV 408
PRK07219 PRK07219
DNA topoisomerase I; Validated
1-234 5.89e-18

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 85.44  E-value: 5.89e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381   1 MEKHGIGTDASIPVHINTITQRNYVTveSGRRLVPTRLGQCLVRGYWKVDPELVLPTMRAELEEQLNLVASGKADYLDVK 80
Cdd:PRK07219  486 MEKRGLGTKATRHDIIEKLYKRGYVI--EGDPPRPTDLGIAVIEALEKYAPEIVSEEMTAQLEADMQAIEDGKKKKEDVT 563
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381  81 NHALKMFEMKFQYFVTNIPAVDTLFEASFTTLSDTGKPFSRCGKCRRYMKLVQTKPQRLY--C---PTCQETYAVPnfKD 155
Cdd:PRK07219  564 EESREMLKEILSELKEKRKEIGDHLAGSLKAENRSLKTIGKCPECGGDLIIIRTDKGSRFvgCsgyPDCRNTFPLP--ST 641
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381 156 G---------------VLKVIG-----DHKCPLDDFDVILYQGPggklaRTFTLCPFCFNNPPFEKMPQGA--GCDTcvH 213
Cdd:PRK07219  642 GrikvldevcekcglpVIKILRgkqtfVVGCPDCEAEKEEEDPD-----EVIGPCPKCGGELAIKQLKYGSflGCTN--Y 714
                         250       260       270
                  ....*....|....*....|....*....|
gi 1831509381 214 PSCQYSISSN---------GVCgclQDCGG 234
Cdd:PRK07219  715 PKCKYTLPLPrrgkitvtdEKC---PECGL 741
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
1-88 2.86e-13

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 70.89  E-value: 2.86e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381   1 MEKHGIG---TDASIpvhINTITQRNYVTVEsGRRLVPTRLGQ---CLVRGYWkvdPELVLPTMRAELEEQLNLVASGKA 74
Cdd:COG0550   451 MEELGIGrpsTYASI---IETLQDRGYVERE-GKRLVPTELGFiviDLLEEHF---PDLVDYEFTAKMEEKLDEIAEGKL 523
                          90
                  ....*....|....
gi 1831509381  75 DYLDVKNHALKMFE 88
Cdd:COG0550   524 DWKDVLEEFYKPFK 537
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
1-39 6.55e-11

Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit


Pssm-ID: 214663 [Multi-domain]  Cd Length: 259  Bit Score: 61.88  E-value: 6.55e-11
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1831509381    1 MEKHGIGTDASIPVHINTITQRNYVTVEsGRRLVPTRLG 39
Cdd:smart00437 219 MEKRGIGRPSTYASIIETLLDRGYVTKK-KKKLIPTELG 256
PRK05776 PRK05776
DNA topoisomerase I; Provisional
1-127 9.26e-07

DNA topoisomerase I; Provisional


Pssm-ID: 235602 [Multi-domain]  Cd Length: 670  Bit Score: 50.76  E-value: 9.26e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381   1 MEKHGIGTDASIPVHINTITQRNYVTvESGRRLVPTRLGQCLVRGYWKVDPELVLPTMRAELEEQLNLVASGKADYLDVK 80
Cdd:PRK05776  483 MESVGIGTEATRARIIETLFKRGYLT-SNGKYIEVTPLGFGVAEVLEKYFPDIVSVELTRDFEEKLEMIRTGKATREEVI 561
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1831509381  81 NHALKMFEMKFQYFVTNIPAVDTLFeASFTTLSdtgKPFSRCGKCRR 127
Cdd:PRK05776  562 EEAKETLNKLLEEFKKNKDEIGEEL-AKALGLI---KPVGKCKICGR 604
 
Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
1-88 1.49e-24

DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.


Pssm-ID: 238110 [Multi-domain]  Cd Length: 381  Bit Score: 103.07  E-value: 1.49e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381   1 MEKHGIGTDASIPVHINTITQRNYVTVEsGRRLVPTRLGQCLVRGYWKVDPELVLPTMRAELEEQLNLVASGKADYLDVK 80
Cdd:cd00186   292 MEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEKLDEIAEGKKDYQEVL 370

                  ....*...
gi 1831509381  81 NHALKMFE 88
Cdd:cd00186   371 EEFYEEFK 378
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
1-79 2.49e-22

DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.


Pssm-ID: 426069 [Multi-domain]  Cd Length: 410  Bit Score: 97.31  E-value: 2.49e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1831509381   1 MEKHGIGTDASIPVHINTITQRNYVTVEsGRRLVPTRLGQCLVRGYwKVDPELVLPTMRAELEEQLNLVASGKADYLDV 79
Cdd:pfam01131 332 MEKAGIGTPATRATIIETLLERGYVERK-KKSLVPTELGKALVEAL-EKFPDLVDPELTAELEEKLDEIAEGKLDWKDV 408
PRK07219 PRK07219
DNA topoisomerase I; Validated
1-234 5.89e-18

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 85.44  E-value: 5.89e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381   1 MEKHGIGTDASIPVHINTITQRNYVTveSGRRLVPTRLGQCLVRGYWKVDPELVLPTMRAELEEQLNLVASGKADYLDVK 80
Cdd:PRK07219  486 MEKRGLGTKATRHDIIEKLYKRGYVI--EGDPPRPTDLGIAVIEALEKYAPEIVSEEMTAQLEADMQAIEDGKKKKEDVT 563
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381  81 NHALKMFEMKFQYFVTNIPAVDTLFEASFTTLSDTGKPFSRCGKCRRYMKLVQTKPQRLY--C---PTCQETYAVPnfKD 155
Cdd:PRK07219  564 EESREMLKEILSELKEKRKEIGDHLAGSLKAENRSLKTIGKCPECGGDLIIIRTDKGSRFvgCsgyPDCRNTFPLP--ST 641
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381 156 G---------------VLKVIG-----DHKCPLDDFDVILYQGPggklaRTFTLCPFCFNNPPFEKMPQGA--GCDTcvH 213
Cdd:PRK07219  642 GrikvldevcekcglpVIKILRgkqtfVVGCPDCEAEKEEEDPD-----EVIGPCPKCGGELAIKQLKYGSflGCTN--Y 714
                         250       260       270
                  ....*....|....*....|....*....|
gi 1831509381 214 PSCQYSISSN---------GVCgclQDCGG 234
Cdd:PRK07219  715 PKCKYTLPLPrrgkitvtdEKC---PECGL 741
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
1-88 2.86e-13

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 70.89  E-value: 2.86e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381   1 MEKHGIG---TDASIpvhINTITQRNYVTVEsGRRLVPTRLGQ---CLVRGYWkvdPELVLPTMRAELEEQLNLVASGKA 74
Cdd:COG0550   451 MEELGIGrpsTYASI---IETLQDRGYVERE-GKRLVPTELGFiviDLLEEHF---PDLVDYEFTAKMEEKLDEIAEGKL 523
                          90
                  ....*....|....
gi 1831509381  75 DYLDVKNHALKMFE 88
Cdd:COG0550   524 DWKDVLEEFYKPFK 537
PRK06599 PRK06599
DNA topoisomerase I; Validated
1-182 1.88e-11

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 65.26  E-value: 1.88e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381   1 MEKHGIG---TDASIpvhINTITQRNYVTVEsGRRLVPTRLG----QCLVRGYwkvdPELVLPTMRAELEEQLNLVASGK 73
Cdd:PRK06599  478 LEEYGIGrpsTYASI---ISTLQDREYVELE-KKRFIPTDLGrivnDFLVEHF----PKYVDYDFTAGLEDELDEIAEGK 549
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381  74 ADYLDVknhaLKMFemkFQYFVTNIPAVDTLFEASFTTLSDTGKPFSRCGKcrRYMKLVQTKPQR-LYC---PTCQETYA 149
Cdd:PRK06599  550 KDWKPV----LREF---WEPFISNLEKVEEDVRTEKVTQEETDETCPKCGG--GPLVLKLGKNGKfLGCsgyPECKYTKN 620
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1831509381 150 VPNFKDGV---LKVIGDHKCPLDDFDVILYQGPGGK 182
Cdd:PRK06599  621 ITRDEDEPieeEEIVEEEKCPKCGGPLVLKKGRYGK 656
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
1-39 6.55e-11

Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit


Pssm-ID: 214663 [Multi-domain]  Cd Length: 259  Bit Score: 61.88  E-value: 6.55e-11
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1831509381    1 MEKHGIGTDASIPVHINTITQRNYVTVEsGRRLVPTRLG 39
Cdd:smart00437 219 MEKRGIGRPSTYASIIETLLDRGYVTKK-KKKLIPTELG 256
PRK05776 PRK05776
DNA topoisomerase I; Provisional
1-127 9.26e-07

DNA topoisomerase I; Provisional


Pssm-ID: 235602 [Multi-domain]  Cd Length: 670  Bit Score: 50.76  E-value: 9.26e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381   1 MEKHGIGTDASIPVHINTITQRNYVTvESGRRLVPTRLGQCLVRGYWKVDPELVLPTMRAELEEQLNLVASGKADYLDVK 80
Cdd:PRK05776  483 MESVGIGTEATRARIIETLFKRGYLT-SNGKYIEVTPLGFGVAEVLEKYFPDIVSVELTRDFEEKLEMIRTGKATREEVI 561
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1831509381  81 NHALKMFEMKFQYFVTNIPAVDTLFeASFTTLSdtgKPFSRCGKCRR 127
Cdd:PRK05776  562 EEAKETLNKLLEEFKKNKDEIGEEL-AKALGLI---KPVGKCKICGR 604
PRK07220 PRK07220
DNA topoisomerase I; Validated
1-73 1.33e-04

DNA topoisomerase I; Validated


Pssm-ID: 180892 [Multi-domain]  Cd Length: 740  Bit Score: 43.98  E-value: 1.33e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1831509381   1 MEKHGIGTDASIPVHINTITQRNYVtveSGRRLVPTRLGQCLVRGYWKVDPELVLPTMRAELEEQLNLVASGK 73
Cdd:PRK07220  478 MEDLGLGTKATRHEIISKLYSRAYI---HGNPIQPTNTAFAVVDALEKYAPTITKPDMTSRLEEDMDKIAEGK 547
PRK08780 PRK08780
DNA topoisomerase I; Provisional
1-79 8.35e-04

DNA topoisomerase I; Provisional


Pssm-ID: 181555 [Multi-domain]  Cd Length: 780  Bit Score: 41.29  E-value: 8.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1831509381   1 MEKHGIG---TDASIpvhINTITQRNYVTVEsGRRLVPTRLGQCLVR---GYWK--VDPELVlptmrAELEEQLNLVASG 72
Cdd:PRK08780  484 LEEYGIGrpsTYASI---ISTLQFRKYVEME-GRRFRPTDVGRAVNKfltGHFTryVDYDFT-----ARLEDDLDAVSRG 554

                  ....*..
gi 1831509381  73 KADYLDV 79
Cdd:PRK08780  555 EKEWIPL 561
 
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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