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Helicase
From Proteopedia
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===3D structures of helicase=== | ===3D structures of helicase=== | ||
| - | [[3oc3]] – Hel MOT1 heat domain + TFIID-1 – Encephalitozoon cuniculi<BR /> | + | [[3oc3]] – Hel MOT1 heat domain + TFIID-1 – ''Encephalitozoon cuniculi''<BR /> |
| - | [[2p6r]] – AfHel 308 + DNA – Archaeoglobus fulgidus<BR /> | + | [[2p6r]] – AfHel 308 + DNA – ''Archaeoglobus fulgidus''<BR /> |
[[2p6u]] - AfHel 308 | [[2p6u]] - AfHel 308 | ||
===DNA helicase=== | ===DNA helicase=== | ||
| - | [[3lfu]] – EcHel II – Escherichia coli<BR /> | + | [[3lfu]] – EcHel II – ''Escherichia coli''<BR /> |
[[2is1]], [[2is2]] - EcHel II (mutant) + DNA<BR /> | [[2is1]], [[2is2]] - EcHel II (mutant) + DNA<BR /> | ||
[[2is4]], [[2is6]] - EcHel II (mutant) + ADP + DNA<BR /> | [[2is4]], [[2is6]] - EcHel II (mutant) + ADP + DNA<BR /> | ||
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===ATP-dependent helicase Rho=== | ===ATP-dependent helicase Rho=== | ||
| - | [[3l0o]] – Rho – Thermotoga maritima<BR /> | + | [[3l0o]] – Rho – ''Thermotoga maritima''<BR /> |
[[3ice]] – EcRho + ADP + BeF3 + RNA<BR /> | [[3ice]] – EcRho + ADP + BeF3 + RNA<BR /> | ||
[[2ht1]] - EcRho + RNA<BR /> | [[2ht1]] - EcRho + RNA<BR /> | ||
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[[2eqs]] – hDHX8 S1 domain<BR /> | [[2eqs]] – hDHX8 S1 domain<BR /> | ||
[[1vec]] – hP54 N terminal<BR /> | [[1vec]] – hP54 N terminal<BR /> | ||
| - | [[2hjv]] – BsDBPA domain 2 – Bacillus subtilis<BR /> | + | [[2hjv]] – BsDBPA domain 2 – ''Bacillus subtilis''<BR /> |
[[2g0c]] - BsDBPA RNA-binding domain | [[2g0c]] - BsDBPA RNA-binding domain | ||
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[[2j0s]], [[2j0q]], [[2hyi]] – hDDX48 + protein mago nashi homolog + RNA-binding protein 8A + protein CASC3 + RNA<BR /> | [[2j0s]], [[2j0q]], [[2hyi]] – hDDX48 + protein mago nashi homolog + RNA-binding protein 8A + protein CASC3 + RNA<BR /> | ||
[[2j0u]] - hDDX48 + protein CASC3<BR /> | [[2j0u]] - hDDX48 + protein CASC3<BR /> | ||
| - | [[2db3]] – VASA residues 200-623 + RNA – Drosophila melanogaster | + | [[2db3]] – VASA residues 200-623 + RNA – ''Drosophila melanogaster'' |
===ATP-dependent RNA helicase=== | ===ATP-dependent RNA helicase=== | ||
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===ATP-dependent RNA helicase HEF=== | ===ATP-dependent RNA helicase HEF=== | ||
| - | [[1x2i]] – HEF DNA-binding domain – Pyrococcus furiosus | + | [[1x2i]] – HEF DNA-binding domain – ''Pyrococcus furiosus'' |
===Werner syndrome ATP-dependent DNA helicase=== | ===Werner syndrome ATP-dependent DNA helicase=== | ||
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===ATP-dependent DNA helicase RecQ=== | ===ATP-dependent DNA helicase RecQ=== | ||
| - | [[3iuo]] – RecQ residues 604-725 – Porphyromonas gingivalis<BR /> | + | [[3iuo]] – RecQ residues 604-725 – ''Porphyromonas gingivalis''<BR /> |
| - | [[2rhf]]– RecQ HRDC domain 3 – Deinococcus radiodurans<BR /> | + | [[2rhf]]– RecQ HRDC domain 3 – ''Deinococcus radiodurans''<BR /> |
[[1wud]] - EcRecQ HRDC domain<BR /> | [[1wud]] - EcRecQ HRDC domain<BR /> | ||
[[1oyw]] - EcRecQ catalytic domain<BR /> | [[1oyw]] - EcRecQ catalytic domain<BR /> | ||
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===ATP-dependent DNA helicase RuvA, RuvB=== | ===ATP-dependent DNA helicase RuvA, RuvB=== | ||
| - | [[2ztc]], [[2ztd]], [[2zte]], [[2h5x]] – MtRuvA – Mycobacterium tuberculosis<BR /> | + | [[2ztc]], [[2ztd]], [[2zte]], [[2h5x]] – MtRuvA – ''Mycobacterium tuberculosis''<BR /> |
| - | [[1bvs]] - RuvA – Mycobacterium leprae<BR /> | + | [[1bvs]] - RuvA – ''Mycobacterium leprae''<BR /> |
[[1d8l]] – EcRuvA N terminal<BR /> | [[1d8l]] – EcRuvA N terminal<BR /> | ||
[[1c7y]], [[1bdx]] – EcRuvA + DNA<BR /> | [[1c7y]], [[1bdx]] – EcRuvA + DNA<BR /> | ||
| - | [[1ixr]], [[1ixs]] – RuvA + RuvB (mutant) – Thermus thermophilus<BR /> | + | [[1ixr]], [[1ixs]] – RuvA + RuvB (mutant) – ''Thermus thermophilus''<BR /> |
[[1in4]] – TmRuvB<BR /> | [[1in4]] – TmRuvB<BR /> | ||
[[1in5]], [[1in6]], [[1in7]], [[1in8]], [[1j7k]] – TmRuvB (mutant) | [[1in5]], [[1in6]], [[1in7]], [[1in8]], [[1j7k]] – TmRuvB (mutant) | ||
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===ATP-dependent DNA helicase PcrA=== | ===ATP-dependent DNA helicase PcrA=== | ||
| - | [[1qhg]] – GsPcrA (mutant) + ADPNP – Geobacillus stearothermophilus<BR /> | + | [[1qhg]] – GsPcrA (mutant) + ADPNP – ''Geobacillus stearothermophilus''<BR /> |
[[2pjr]], [[3pjr]] - GsPcrA + DNA | [[2pjr]], [[3pjr]] - GsPcrA + DNA | ||
===DnaB helicase=== | ===DnaB helicase=== | ||
| - | [[3gxv]] – DnaB – Helicobacter pylori<BR /> | + | [[3gxv]] – DnaB – ''Helicobacter pylori''<BR /> |
| - | [[2vyf]] – GkDnaC – Geobacillus kaustophilus<BR /> | + | [[2vyf]] – GkDnaC – ''Geobacillus kaustophilus''<BR /> |
| - | [[2r6d]] – BsDnaB – Bacillus stearothermophilus<BR /> | + | [[2r6d]] – BsDnaB – ''Bacillus stearothermophilus''<BR /> |
[[2r6e]] - GsDnaB <BR /> | [[2r6e]] - GsDnaB <BR /> | ||
[[2r5u]] – MtDnaB N terminal<BR /> | [[2r5u]] – MtDnaB N terminal<BR /> | ||
[[3bgw]] – BpDnaB-like – Bacillus phage SPP1<BR /> | [[3bgw]] – BpDnaB-like – Bacillus phage SPP1<BR /> | ||
[[3bh0]] - BpDnaB-like G40P ATPase domain<BR /> | [[3bh0]] - BpDnaB-like G40P ATPase domain<BR /> | ||
| - | [[2q6t]] – DnaB – Thermus aquaticus<BR /> | + | [[2q6t]] – DnaB – ''Thermus aquaticus''<BR /> |
| - | [[1mi8]] – DnaB – Synechocystis<BR /> | + | [[1mi8]] – DnaB – ''Synechocystis''<BR /> |
[[1b79]] - EcDnaB N terminal<BR /> | [[1b79]] - EcDnaB N terminal<BR /> | ||
[[1jwe]] - EcDnaB N terminal - NMR<BR /> | [[1jwe]] - EcDnaB N terminal - NMR<BR /> | ||
Revision as of 08:28, 27 July 2011
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.
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
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