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DNA_topoisomerase_II

Euk-Vir

Noumeavirus

DNA_topoisomerase_II__YP_009345560__Noumeavirus__1955558

Identity

Accession:
YP_009345560 ↗
Protein ID:
DNA_topoisomerase_II
Kingdom:
euk

Quality

87.0 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Pimascovirales› Marseilleviridae› Marseillevirus› Noumeavirus

TaxID: 1955558

Cluster

View cluster (39 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 79-217
PDB
Domain cluster: rep: IMGVR_UViG_3300039190_000305-3300039190-Ga0399989_003201_3_1937__D82-97_167-336
D2 high residues 253-399
PDB
Domain cluster: rep: topoisomerase_IIA__YP_009001040__Pithovirus_sibericum__1450746__D250-321_335-390
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00204.32 best DNA_gyraseB 34.5 2.10e-08 95.9% 52.3%
D3 high residues 417-546_585-667
PDB
Domain cluster: rep: DNA_topoisomerase_2__YP_009162467__Salmon_gill_poxvirus__1680908__D385-517_553-621_640-664
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF01751.29 best Toprim 36.2 7.60e-09 53.0% 89.6%
PF16898.11 TOPRIM_C 42.1 1.40e-10 47.9% 67.2%
D4 high residues 678-818_830-845
PDB
Domain cluster: rep: DNA_topoisomerase_2__YP_009162467__Salmon_gill_poxvirus__1680908__D669-796
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00521.27 best DNA_topoisoIV 144.6 5.90e-42 93.6% 32.0%
D5 high residues 970-1089
PDB
Domain cluster: rep: putative_DNA_topoisomerase__YP_294202__Emiliania_huxleyi_virus_86__181082__D963-1088
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00521.27 best DNA_topoisoIV 32.1 8.10e-08 92.5% 26.5%
D6 medium residues 16-78
PDB
Domain cluster: rep: hypothetical_protein_MIV086L__YP_654658__Invertebrate_iridescent_virus_3__345201__D21-79
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1pvgA01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.93 82.0 5.32e-01 100.0% 24.2%
3so6A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.63 43.0 3.41e-01 73.0% 93.4%
4mtnA01 3.30.1480.10 Alpha Beta › 2-Layer Sandwich › N Utilization Substance Protein A; Chain:P; domain 4 › NusA, N-terminal domain 0.61 34.0 2.98e-01 71.4% 35.8%
1fneA01 3.10.320.10 Alpha Beta › Roll › Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 › Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 0.59 40.0 3.82e-01 73.0% 74.7%
5axmB00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.57 43.0 2.91e-01 82.5% 62.3%
3venA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 39.0 2.68e-01 73.0% 51.8%
3dsbA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.56 31.0 2.62e-01 95.2% 32.7%
3mk7C01 6.10.280.130 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 40.0 3.56e-01 88.9% 52.1%
1lwdA00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.54 41.0 2.51e-01 82.5% 94.9%
2w40A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.54 46.0 3.11e-01 98.4% 46.6%
4c0dB00 2.30.30.1020 Mainly Beta › Roll › SH3 type barrels. › CCR4-NOT complex subunit 2/3/5, C-terminal domain 0.53 36.0 2.72e-01 90.5% 24.1%
3t5tB01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.52 36.0 2.37e-01 74.6% 18.1%
4ivkA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.51 39.0 2.40e-01 84.1% 67.6%
3aonA00 1.10.287.3240 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.50 42.0 3.01e-01 93.7% 41.0%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3998214 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.93 84.0 5.37e-01 100.0% 23.5%
3594649 225.1.1.0 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.90 82.0 5.32e-01 100.0% 25.3%
4617838 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.90 82.0 5.30e-01 100.0% 25.3%
3789605 225.1.1.0 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.89 79.0 5.14e-01 100.0% 24.5%
3317524 225.1.1.0 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.88 74.0 4.97e-01 100.0% 26.1%
3941757 101.1.9.32 ↗ alpha arrays › HTH › HTH › Putative DNA-binding domain › ANT 0.68 35.0 2.77e-01 77.8% 23.8%
3503534 5057.1.1.1 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.67 41.0 3.12e-01 90.5% 26.2%
5028435 4040.1.1.1 ↗ alpha bundles › Fic-like › Fic-like › Fic-like › Fic 0.67 39.0 2.57e-01 96.8% 13.8%
3711985 3883.1.1.1 ↗ alpha bundles › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-OH_P_transf 0.61 46.0 3.11e-01 82.5% 22.0%
3215999 5001.1.1.111 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1, 7TM_GPCR_Srw 0.60 46.0 2.85e-01 82.5% 72.4%
4983372 304.48.1.20 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Thg1 0.60 44.0 3.02e-01 82.5% 56.8%
3880867 2484.1.1.145 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1_7 0.60 53.0 3.22e-01 100.0% 73.3%
3608646 4096.1.1.1 ↗ a+b two layers › NAP-like › NAP-like › NAP-like › NAP 0.58 39.0 2.55e-01 92.1% 16.3%
5077859 2002.1.1.12 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_1 0.57 41.0 2.73e-01 85.7% 17.2%
3946915 2484.1.1.53 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › MreB_Mbl 0.57 38.0 2.74e-01 88.9% 21.5%
3170708 632.1.1.6 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › Pho88 0.56 44.0 3.50e-01 90.5% 41.4%
3494833 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.56 43.0 2.62e-01 85.7% 36.7%
3447255 7.1.1.5 ↗ beta barrels › PDZ domain › PDZ domain › PDZ domain › PDZ_2 0.56 39.0 3.24e-01 74.6% 64.2%
3714105 304.48.1.11 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RNA_pol 0.56 48.0 3.46e-01 100.0% 51.5%
3938245 375.1.1.179 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › TFIIE_alpha 0.55 43.0 3.02e-01 85.7% 51.4%
5018200 2004.1.1.220 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SWI2_SNF2 0.55 37.0 2.15e-01 100.0% 8.5%
5082704 375.1.1.179 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › TFIIE_alpha 0.55 43.0 2.99e-01 84.1% 85.1%
3937794 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.55 41.0 2.66e-01 84.1% 45.5%
4974744 375.1.1.179 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › TFIIE_alpha 0.54 43.0 3.14e-01 87.3% 59.4%
3714786 2004.1.1.19 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.54 45.0 3.21e-01 95.2% 81.5%
3691054 246.2.1.0 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases 0.53 43.0 2.61e-01 90.5% 79.3%
3175336 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.53 39.0 3.68e-01 77.8% 76.0%
3484809 4096.1.1.1 ↗ a+b two layers › NAP-like › NAP-like › NAP-like › NAP 0.53 34.0 2.72e-01 96.8% 30.0%
3791945 5054.1.1.2 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans 0.53 40.0 2.82e-01 85.7% 27.1%
3740226 5051.1.1.7 ↗ alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Nramp 0.52 42.0 2.53e-01 92.1% 62.0%
2095505 1170.1.2.1 ↗ beta barrels › IL8-related › IL8-related › chemokine-related domain in glycoprotein L (gL) › Cytomega_gL 0.52 39.0 3.38e-01 82.5% 50.5%
3743779 101.1.2.31 ↗ alpha arrays › HTH › HTH › winged helix domain › TFIIE_alpha 0.52 41.0 3.22e-01 93.7% 71.0%
4029392 375.1.1.179 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › TFIIE_alpha 0.51 44.0 3.17e-01 96.8% 65.4%
3941746 301.13.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › Dak1 0.51 35.0 2.57e-01 71.4% 46.3%
3899483 3226.1.1.3 ↗ alpha complex topology › Uracil Transporter UraA › Uracil Transporter UraA › Uracil Transporter UraA › HCO3_cotransp 0.51 43.0 2.47e-01 90.5% 13.9%
4985406 878.1.1.1 ↗ a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 › DUF3194 0.50 37.0 3.44e-01 87.3% 63.3%
D7 medium residues 549-583
PDB
Domain cluster: rep: DNA_topoisomerase_II__YP_009238657__Brazilian_marseillevirus__1813599__D550-583
D8 medium residues 819-829_846-961
PDB
Domain cluster: rep: DNA_topoisomerase_2__YP_003986988__Acanthamoeba_polyphaga_mimivirus__212035__D908-982_1022-1083
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00521.27 best DNA_topoisoIV 38.1 1.30e-09 99.2% 28.5%