Helicase

From Proteopedia

Revision as of 12:07, 20 February 2012

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 and PcrA helicase. For ATP-dependent helicase Rho see Transcription Termination Factor Rho. For ATP-dependent helicase Q see Human RecQ-Like protein 1. See also Transcription and RNA Processing.

3D structures of helicase

Updated November 2011

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 – TmRho – Thermotoga maritima
3ice – EcRho + ADP + BeF3 + RNA
2ht1 - EcRho + RNA
1a8v – EcRho RNA-binding domain
2a8v – EcRho RNA-binding domain + RNA
1pv4 – EcRho + DNA
1pvo – EcRho + ssRNA + ANPPNP
1xpr, 1xpu - EcRho + ssRNA + antibiotic

ATP-dependent helicase MFD

3hjh – EcMFD motor domain

ATP-dependent helicase E1

2v9p – PvE1 helicase domain – Bovine papillomavirus
2gxa – PvE1 + DNA + Mg-ADP
1tue – PvE1 + E2 – human papillomavirus

ATP-dependent helicase CHD1

2h1e, 2xb0, 3mwy – yCHD1 chromodomain
2dy7 - yCHD1 chromodomain 1 – NMR
2dy8 - yCHD1 chromodomain 2 – NMR
3ted - yCHD1 chromodomain 1 + DNA

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
3i4u– hDHX8 residues 950-1183
1vec – hP54 N terminal
2hjv – BsDBPA domain 2 – Bacillus subtilis
2g0c - BsDBPA RNA-binding domain
3eaq, 3ear, 3eas – TtHera residues 215-426 - Thermus thermophiles
3i31 - TtHera residues 431-517
3i32 - TtHera residues 218-517
3nej - TtHera N terminal (mutant)

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
3fmp – hDDX19B + Nup214
3g0h – hDDX19B residues 54-275 + ATP analog + RNA
3ews - hDDX19B residues 54-275 + ADP
3dkp – hDDX52 domain I + ADP
3tmi - hDHX58 residues 232-925 + RNA
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
3nbf - TtHera N terminal (mutant) + 8-oxo-ADP
3moj - BsDBPA RNA-binding domain + RNA

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
3sqw, 3sqx - yMSS116 residues 88-664 + 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, 2wv9 - 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, 1a1v - 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
2vbc - DvHel NS3 residues 1475-2092 + NS2A peptide

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 Repa

1uaa – EcRepa + DNA
1nlf - EcRepa + sulfate
1g8y, 1olo - EcRepa

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
2e6l, 2e6m- WRN exonuclease domain - mouse

ATP-dependent DNA helicase Q

2v1x - hQ1 residues 49-616
2wwy – hQ1 residues 49-616 + DNA
2kmu – hQ4 N terminal - NMR

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 – TtRuvA + RuvB (mutant)
1in4 – TmRuvB
1in5, 1in6, 1in7, 1in8, 1j7k – TmRuvB (mutant)
3pfi – RuvB + ADP – Campylobacter jejuni

ATP-dependent DNA helicase UVSW

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

ATP-dependent DNA helicase UVRD

2is1 - EcUVRD + DNA

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
1qhh - GsPcrA + ADPNP
2pjr, 3pjr - GsPcrA + DNA
1pjr - GsPcrA

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

Helicase SNF2

1z5z – SsSNF2 C terminal – Sulfolobus solfataricus
1z63 - SsSNF2 ATPase core + DNA
1z6a - SsSNF2 ATPase core

2va8 – SsSKI2

3crv, 3crw – XPD – Sulfolobus acidocaldarius
3hib, 3im1, 3im2 – yBrr2 2nd SEC63 domain