Helicase

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===3D structures of helicase===
===3D structures of helicase===
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[[3oc3]] – Hel MOT1 heat domain + TFIID-1 – Encephalitozoon cuniculi<BR />
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[[2p6r]] – AfHel 308 + DNA – Archaeoglobus fulgidus<BR />
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[[2p6u]] - AfHel 308
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===DNA helicase===
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[[3lfu]] – EcHel II – Escherichia coli<BR />
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[[2is1]], [[2is2]] - EcHel II (mutant) + DNA<BR />
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[[2is4]], [[2is6]] - EcHel II (mutant) + ADP + DNA<BR />
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[[3fld]] – EcHel I C terminal<BR />
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[[2q7t]], [[2q7u]] – EcHel I relaxase domain (mutant) <BR />
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[[1p4d]] - EcHel I relaxase domain<BR />
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[[2a0i]] - EcHel I (mutant) + DNA<BR />
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[[1q2z]], [[1rw2]] – hHel II KU86 C terminal – NMR<BR />
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[[1e0j]], [[1e0k]] – Hel 4D domain – Phage T7
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===ATP-dependent helicase ATRX===
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[[3qln]] - hATRX ADD domain – human<BR />
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[[2ld1]], [[2jm1]] - hATRX ADD domain - NMR<BR />
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[[3ql9]] – hATRX ADD domain + histone H3 peptide <BR />
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[[2lbm]] - hATRX ADD domain + histone H3 peptide – NMR<BR />
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[[3qla]], [[3qlc]] - hATRX ADD domain (mutant) + histone H3 peptide<BR />
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[[2xzp]] - hRENT1 helicase domain<BR />
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[[2wjv]] - hRENT1 helicase CH and C terminal domains<BR />
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[[2wjy]] - hRENT1 helicase CH domains<BR />
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[[2xzo]] – hRENT1 helicase domain + RNA<BR />
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===ATP-dependent helicase Rho===
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[[3l0o]] – Rho – Thermotoga maritima<BR />
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[[3ice]] – EcRho + ADP + BeF3 + RNA<BR />
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[[2ht1]] - EcRho + RNA<BR />
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===ATP-dependent helicase MFD===
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[[3hjh]] – EcMFD motor domain
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===ATP-dependent helicase E1===
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[[2v9p]] – E1 helicase domain – Bovine papillomavirus
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===ATP-dependent helicase CHD1===
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[[2h1e]] – yCHD1 chromodomain<BR />
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[[2dy7]] - yCHD1 chromodomain 1 – NMR<BR />
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[[2yd8]] - yCHD1 chromodomain 2 – NMR<BR />
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===Dead box ATP-dependent RNA helicase===
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[[3fho]] – DBP5 – fission yeast<BR />
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[[2kbe]] – yDBP5 N terminal – NMR<BR />
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[[2kbf]] - yDBP5 C terminal – NMR<BR />
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[[3gfp]] - yDBP5 C-terminal<BR />
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[[2i4i]] – hDDX3X<BR />
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[[2jgn]] – hDDX3X helicase domain<BR />
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[[3ly5]] – hDDX18 dead domain<BR />
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[[2rb4]] – hDDX25 helicase domain<BR />
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[[2p6n]] – hDDX41 helicase domain (mutant) <BR />
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[[2e29]] - hDDX50 GUCT domain]] - NMR<BR />
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[[2rqa]] – hDHX58 C terminal – NMR<BR />
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[[3eqt]] - hDHX58 C terminal + RNA<BR />
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[[2eqs]] – hDHX8 S1 domain<BR />
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[[1vec]] – hP54 N terminal<BR />
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[[2hjv]] – BsDBPA domain 2 – Bacillus subtilis<BR />
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[[2g0c]] - BsDBPA RNA-binding domain
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===Dead box ATP-dependent RNA helicase complexes===
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[[3rrm]] – yDBP5 residues 91-482 (mutant) + GLE1 + NUP159 + ADP + IP6 – yeast<BR />
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[[3rrn]] - yDBP5 residues 91-482 (mutant) + GLE1 + IP6<BR />
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[[3pew]], [[3pey]] - yDBP5 residues 91-482 (mutant) + ADP + BeF3 + RNA<BR />
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[[3peu]], [[3pev]] - yDBP5 C-terminal (mutant) + GLE1 + IP6<BR />
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[[3jrv]] – DDX3X + protein K7 – Vaccinia virus<BR />
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[[3fmo]], [[3fhc]] – hDBP5 + Nup214<BR />
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[[3fht]] – hDBP5 + AMPPNP + RNA<BR />
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[[3g0h]] – hDDX19B residues 54-275 + ATP analog + RNA<BR />
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[[3ews]] - hDDX19B residues 54-275 + ADP<BR />
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[[3dkp]] – hDDX52 domain I + ADP<BR />
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[[2wax]], [[2way]] – hDDX6 C terminal + EDC3-FDF peptide<BR />
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[[2j0s]], [[2j0q]], [[2hyi]] – hDDX48 + protein mago nashi homolog + RNA-binding protein 8A + protein CASC3 + RNA<BR />
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[[2j0u]] - hDDX48 + protein CASC3<BR />
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[[2db3]] – VASA residues 200-623 + RNA – Drosophila melanogaster
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===ATP-dependent RNA helicase===
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[[2xzl]] – yNAM7 CH and helicase domains + RNA<BR />
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[[2xgj]] – yDOB1 residues 81-1073 + RNA<BR />
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[[3l9o]] - yDOB1 residues 1-1073 + peptide<BR />
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[[2xau]], [[3kx2]] – yPRP43 + ADP<BR />
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[[3i5x]], [[3i5y]] – yMSS116 residues 37-597 + AMPPNP + RNA<BR />
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[[3i61]] - yMSS116 residues 37-597 + ADP + BeF3 + RNA<BR />
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[[3i62]] - yMSS116 residues 37-597 + ADP + AlF4 + RNA<BR />
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[[2vso]], [[2vsx]] – yEIF4A + initiation factor 4F middle domain<BR />
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[[2g9n]] - hEIF4A dead domain
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===Viral ATP-dependent RNA helicase NS3===
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[[3o8b]], [[3o8d]], [[1cu1]], [[8ohm]], [[1hei]] – HvHel NS3 – Hepatitis C virus<BR />
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[[1onb]], [[1jr6]] - HvHel NS3 arginine-rich domain – NMR<BR />
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[[2jlq]], [[2bhr]], [[2bmf]] – DvHel NS3 residues 1646-2092 – Dengue virus<BR />
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[[2z83]] – Hel NS3 residues 167-624 – Japanese encephalitis virus<BR />
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[[2v8o]] - Hel NS3 helicase domain – Murray valley encephalitis virus<BR />
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[[2qeq]] - Hel NS3 residues 1691-2124 – Kunjin virus<BR />
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[[2v6i]] – KvHel helicase domain – Kokobera virus<BR />
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[[2v6j]] - KvHel helicase domain (mutant)
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===Viral ATP-dependent RNA helicase NS3 complexes===
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[[3o8c]], [[3o8r]], [[3kqh]], [[3kqk]], [[3kql]], [[3kqn]], [[3kqu]] - HvHel NS3 + RNA<BR />
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[[2f9v]] - HvHel NS3 protease domain + polyprotein<BR />
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[[2a4g]], [[1rtl]], [[1w3c]], [[1dxp]] - HvHel NS3 protease domain + NS4A peptide<BR />
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[[2a4q]], [[2a4r]], [[2f9u]], [[2fm2]], [[1dy8]], [[1dy9]] - HvHel NS3 protease domain + NS4A peptide + inhibitor<BR />
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[[2jlr]] - DvHel NS3 residues 1646-2092 + AMPPNP<BR />
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[[2jls]] - DvHel NS3 residues 1646-2092 + ADP<BR />
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[[2jlu]], [[2jlw]] - DvHel NS3 residues 1646-2092 + RNA<BR />
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[[2jlv]] - DvHel NS3 residues 1646-2092 + AMPPNP + RNA<BR />
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[[2jlx]], [[2jly]], [[2jlz]] - DvHel NS3 residues 1646-2092 + ADP + RNA<BR />
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===ATP-dependent RNA helicase SUV3===
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[[3rc3]] – hSUV3 residues 47-722<BR />
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[[3og8]] – hDDX58 C terminal + RNA<BR />
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[[3rc8]] - hSUV3 residues 47-722 + RNA<BR />
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===ATP-dependent RNA helicase A===
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[[3llm]] – hHel A<BR />
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[[1whq]] – Hel A RNA-binding domain – mouse - NMR<BR />
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===ATP-dependent RNA helicase REP===
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[[1uaa]] – EcREP + DNA
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===ATP-dependent RNA helicase HEF===
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[[1x2i]] – HEF DNA-binding domain – Pyrococcus furiosus
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===Werner syndrome ATP-dependent DNA helicase===
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[[2e1e]], [[2e1f]], [[2dgz]] – hWRN HRDC domain<BR />
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[[2fbt]] - hWRN exonuclease domain<BR />
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[[2fbv]], [[2fbx]], [[2fby]], [[2fc0]] - hWRN exonuclease domain + metal ion
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[[3aaf]] – hWRN C terminal + DNA
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===ATP-dependent DNA helicase Q1===
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[[2v1x]] - hQ1 residues 49-616<BR />
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[[2wwy]] – hQ1 residues 49-616 + DNA
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===ATP-dependent DNA helicase RecQ===
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[[3iuo]] – RecQ residues 604-725 – Porphyromonas gingivalis<BR />
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[[2rhf]]– RecQ HRDC domain 3 – Deinococcus radiodurans<BR />
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[[1wud]] - EcRecQ HRDC domain<BR />
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[[1oyw]] - EcRecQ catalytic domain<BR />
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[[1oyy]] - EcRecQ catalytic domain + ATP<BR />
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[[1d8b]] - yRecQ HRDC domain - NMR<BR />
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===ATP-dependent DNA helicase RuvA, RuvB===
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[[2ztc]], [[2ztd]], [[2zte]], [[2h5x]] – MtRuvA – Mycobacterium tuberculosis<BR />
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[[1bvs]] - RuvA – Mycobacterium leprae<BR />
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[[1d8l]] – EcRuvA N terminal<BR />
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[[1c7y]], [[1bdx]] – EcRuvA + DNA<BR />
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[[1ixr]], [[1ixs]] – RuvA + RuvB (mutant) – Thermus thermophilus<BR />
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[[1in4]] – TmRuvB<BR />
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[[1in5]], [[1in6]], [[1in7]], [[1in8]], [[1j7k]] – TmRuvB (mutant)
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===ATP-dependent DNA helicase UVSW===
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[[2oca]], [[1rif]]- T4UVSW (mutant) – Enterobacteria phage T4<BR />
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[[2jpn]] - T4UVSW
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===ATP-dependent DNA helicase PriA===
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[[2d7e]] – EcPriA DNA-binding domain<BR />
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[[2d7g]], [[2d7h]], [[2dwl]], [[2dwm]], [[2dwn]] – EcPriA N terminal + polynucleotide
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===ATP-dependent DNA helicase PcrA===
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[[1qhg]] – GsPcrA (mutant) + ADPNP – Geobacillus stearothermophilus<BR />
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[[2pjr]], [[3pjr]] - GsPcrA + DNA
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===DnaB helicase===
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[[3gxv]] – DnaB – Helicobacter pylori<BR />
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[[2vyf]] – GkDnaC – Geobacillus kaustophilus<BR />
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[[2r6d]] – BsDnaB – Bacillus stearothermophilus<BR />
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[[2r6e]] - GsDnaB <BR />
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[[2r5u]] – MtDnaB N terminal<BR />
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[[3bgw]] – BpDnaB-like – Bacillus phage SPP1<BR />
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[[3bh0]] - BpDnaB-like G40P ATPase domain<BR />
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[[2q6t]] – DnaB – Thermus aquaticus<BR />
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[[1mi8]] – DnaB – Synechocystis<BR />
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[[1b79]] - EcDnaB N terminal<BR />
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[[1jwe]] - EcDnaB N terminal - NMR<BR />
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[[2vye]] – GkDnaC + DNA<BR />
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[[2r6c]], [[2r6a]] – BsDnaB + DnaG helicase-binding domain
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===Helicase NSP2===
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[[2hwk]] – NSP2 – Venzuelan equine encephalitis virus
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[[Category:Topic Page]]
[[Category:Topic Page]]

Revision as of 08:25, 27 July 2011

Template:STRUCTURE 3fht

Helicase (Hel) is a motor protein which separates nucleic acid strands like DNA double helix or self-annealed RNA. They use ATP hydrolysis for energy. Hel falls into 5 superfamilies (SF1-SF5). Some Hel contain a Helicase and RNase D C terminal Domain (HRDC). The α-thalassemia and mental retardation X-linked syndrome helicase (ATRX ), contains an ATRX-Dnmt3-Dnmt3L (ADD) domain in which many disease-related mutations are found. For details of PcrA helicase see Molecular Playground/PcrA Helicase.

Contents

3D structures of helicase

3oc3 – Hel MOT1 heat domain + TFIID-1 – Encephalitozoon cuniculi
2p6r – AfHel 308 + DNA – Archaeoglobus fulgidus
2p6u - AfHel 308

DNA helicase

3lfu – EcHel II – Escherichia coli
2is1, 2is2 - EcHel II (mutant) + DNA
2is4, 2is6 - EcHel II (mutant) + ADP + DNA
3fld – EcHel I C terminal
2q7t, 2q7u – EcHel I relaxase domain (mutant)
1p4d - EcHel I relaxase domain
2a0i - EcHel I (mutant) + DNA
1q2z, 1rw2 – hHel II KU86 C terminal – NMR
1e0j, 1e0k – Hel 4D domain – Phage T7

ATP-dependent helicase ATRX

3qln - hATRX ADD domain – human
2ld1, 2jm1 - hATRX ADD domain - NMR
3ql9 – hATRX ADD domain + histone H3 peptide
2lbm - hATRX ADD domain + histone H3 peptide – NMR
3qla, 3qlc - hATRX ADD domain (mutant) + histone H3 peptide
2xzp - hRENT1 helicase domain
2wjv - hRENT1 helicase CH and C terminal domains
2wjy - hRENT1 helicase CH domains
2xzo – hRENT1 helicase domain + RNA

ATP-dependent helicase Rho

3l0o – Rho – Thermotoga maritima
3ice – EcRho + ADP + BeF3 + RNA
2ht1 - EcRho + RNA

ATP-dependent helicase MFD

3hjh – EcMFD motor domain

ATP-dependent helicase E1

2v9p – E1 helicase domain – Bovine papillomavirus

ATP-dependent helicase CHD1

2h1e – yCHD1 chromodomain
2dy7 - yCHD1 chromodomain 1 – NMR
2yd8 - yCHD1 chromodomain 2 – NMR

Dead box ATP-dependent RNA helicase

3fho – DBP5 – fission yeast
2kbe – yDBP5 N terminal – NMR
2kbf - yDBP5 C terminal – NMR
3gfp - yDBP5 C-terminal
2i4i – hDDX3X
2jgn – hDDX3X helicase domain
3ly5 – hDDX18 dead domain
2rb4 – hDDX25 helicase domain
2p6n – hDDX41 helicase domain (mutant)
2e29 - hDDX50 GUCT domain]] - NMR
2rqa – hDHX58 C terminal – NMR
3eqt - hDHX58 C terminal + RNA
2eqs – hDHX8 S1 domain
1vec – hP54 N terminal
2hjv – BsDBPA domain 2 – Bacillus subtilis
2g0c - BsDBPA RNA-binding domain

Dead box ATP-dependent RNA helicase complexes

3rrm – yDBP5 residues 91-482 (mutant) + GLE1 + NUP159 + ADP + IP6 – yeast
3rrn - yDBP5 residues 91-482 (mutant) + GLE1 + IP6
3pew, 3pey - yDBP5 residues 91-482 (mutant) + ADP + BeF3 + RNA
3peu, 3pev - yDBP5 C-terminal (mutant) + GLE1 + IP6
3jrv – DDX3X + protein K7 – Vaccinia virus
3fmo, 3fhc – hDBP5 + Nup214
3fht – hDBP5 + AMPPNP + RNA
3g0h – hDDX19B residues 54-275 + ATP analog + RNA
3ews - hDDX19B residues 54-275 + ADP
3dkp – hDDX52 domain I + ADP
2wax, 2way – hDDX6 C terminal + EDC3-FDF peptide
2j0s, 2j0q, 2hyi – hDDX48 + protein mago nashi homolog + RNA-binding protein 8A + protein CASC3 + RNA
2j0u - hDDX48 + protein CASC3
2db3 – VASA residues 200-623 + RNA – Drosophila melanogaster

ATP-dependent RNA helicase

2xzl – yNAM7 CH and helicase domains + RNA
2xgj – yDOB1 residues 81-1073 + RNA
3l9o - yDOB1 residues 1-1073 + peptide
2xau, 3kx2 – yPRP43 + ADP
3i5x, 3i5y – yMSS116 residues 37-597 + AMPPNP + RNA
3i61 - yMSS116 residues 37-597 + ADP + BeF3 + RNA
3i62 - yMSS116 residues 37-597 + ADP + AlF4 + RNA
2vso, 2vsx – yEIF4A + initiation factor 4F middle domain
2g9n - hEIF4A dead domain

Viral ATP-dependent RNA helicase NS3

3o8b, 3o8d, 1cu1, 8ohm, 1hei – HvHel NS3 – Hepatitis C virus
1onb, 1jr6 - HvHel NS3 arginine-rich domain – NMR
2jlq, 2bhr, 2bmf – DvHel NS3 residues 1646-2092 – Dengue virus
2z83 – Hel NS3 residues 167-624 – Japanese encephalitis virus
2v8o - Hel NS3 helicase domain – Murray valley encephalitis virus
2qeq - Hel NS3 residues 1691-2124 – Kunjin virus
2v6i – KvHel helicase domain – Kokobera virus
2v6j - KvHel helicase domain (mutant)

Viral ATP-dependent RNA helicase NS3 complexes

3o8c, 3o8r, 3kqh, 3kqk, 3kql, 3kqn, 3kqu - HvHel NS3 + RNA
2f9v - HvHel NS3 protease domain + polyprotein
2a4g, 1rtl, 1w3c, 1dxp - HvHel NS3 protease domain + NS4A peptide
2a4q, 2a4r, 2f9u, 2fm2, 1dy8, 1dy9 - HvHel NS3 protease domain + NS4A peptide + inhibitor
2jlr - DvHel NS3 residues 1646-2092 + AMPPNP
2jls - DvHel NS3 residues 1646-2092 + ADP
2jlu, 2jlw - DvHel NS3 residues 1646-2092 + RNA
2jlv - DvHel NS3 residues 1646-2092 + AMPPNP + RNA
2jlx, 2jly, 2jlz - DvHel NS3 residues 1646-2092 + ADP + RNA

ATP-dependent RNA helicase SUV3

3rc3 – hSUV3 residues 47-722
3og8 – hDDX58 C terminal + RNA
3rc8 - hSUV3 residues 47-722 + RNA

ATP-dependent RNA helicase A

3llm – hHel A
1whq – Hel A RNA-binding domain – mouse - NMR

ATP-dependent RNA helicase REP

1uaa – EcREP + DNA

ATP-dependent RNA helicase HEF

1x2i – HEF DNA-binding domain – Pyrococcus furiosus

Werner syndrome ATP-dependent DNA helicase

2e1e, 2e1f, 2dgz – hWRN HRDC domain
2fbt - hWRN exonuclease domain
2fbv, 2fbx, 2fby, 2fc0 - hWRN exonuclease domain + metal ion 3aaf – hWRN C terminal + DNA

ATP-dependent DNA helicase Q1

2v1x - hQ1 residues 49-616
2wwy – hQ1 residues 49-616 + DNA

ATP-dependent DNA helicase RecQ

3iuo – RecQ residues 604-725 – Porphyromonas gingivalis
2rhf– RecQ HRDC domain 3 – Deinococcus radiodurans
1wud - EcRecQ HRDC domain
1oyw - EcRecQ catalytic domain
1oyy - EcRecQ catalytic domain + ATP
1d8b - yRecQ HRDC domain - NMR

ATP-dependent DNA helicase RuvA, RuvB

2ztc, 2ztd, 2zte, 2h5x – MtRuvA – Mycobacterium tuberculosis
1bvs - RuvA – Mycobacterium leprae
1d8l – EcRuvA N terminal
1c7y, 1bdx – EcRuvA + DNA
1ixr, 1ixs – RuvA + RuvB (mutant) – Thermus thermophilus
1in4 – TmRuvB
1in5, 1in6, 1in7, 1in8, 1j7k – TmRuvB (mutant)

ATP-dependent DNA helicase UVSW

2oca, 1rif- T4UVSW (mutant) – Enterobacteria phage T4
2jpn - T4UVSW

ATP-dependent DNA helicase PriA

2d7e – EcPriA DNA-binding domain
2d7g, 2d7h, 2dwl, 2dwm, 2dwn – EcPriA N terminal + polynucleotide

ATP-dependent DNA helicase PcrA

1qhg – GsPcrA (mutant) + ADPNP – Geobacillus stearothermophilus
2pjr, 3pjr - GsPcrA + DNA

DnaB helicase

3gxv – DnaB – Helicobacter pylori
2vyf – GkDnaC – Geobacillus kaustophilus
2r6d – BsDnaB – Bacillus stearothermophilus
2r6e - GsDnaB
2r5u – MtDnaB N terminal
3bgw – BpDnaB-like – Bacillus phage SPP1
3bh0 - BpDnaB-like G40P ATPase domain
2q6t – DnaB – Thermus aquaticus
1mi8 – DnaB – Synechocystis
1b79 - EcDnaB N terminal
1jwe - EcDnaB N terminal - NMR
2vye – GkDnaC + DNA
2r6c, 2r6a – BsDnaB + DnaG helicase-binding domain

Helicase NSP2

2hwk – NSP2 – Venzuelan equine encephalitis virus

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Wayne Decatur, Joel L. Sussman

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