Helicase

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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
  
• PcrA helicase.
  

For ATP-dependent helicase Rho see

• Transcription Termination Factor Rho.
  

For ATP-dependent helicase Q see

• Human RecQ-Like protein 1.
  

For ATP-dependent helicase RecG see

• RecG Bound to Three-Way DNA Junction.
  

For DEAD box ATP-dependent RNA helicase see

• C-terminal domain of the DEAD-box protein Dbp5
  
• DEAD-box RNA-helicase DDX19 in complex with ADP
  
• Dead-box RNA helicase DDX19, in complex with an ATP-analogue and RNA.
  
• Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa
  

See also

• Transcription and RNA Processing
• Brr2

Contents 1 What is a Helicase? 2 PcrA a Simple Model for Helicases 3 PcrA Biochemistry 4 PcrA Helicase Mechanism : The Mexican Wave 5 The Superfamily 1 (SF1) 6 3D structures of helicase 6.1 DNA helicase 6.2 ATP-dependent helicase ATRX 6.3 ATP-dependent helicase Rho 6.4 ATP-dependent helicase MFD 6.5 ATP-dependent helicase E1 6.6 ATP-dependent helicase CHD1 6.7 Dead box ATP-dependent RNA helicase 6.8 Dead box ATP-dependent RNA helicase complexes 6.9 ATP-dependent RNA helicase 6.10 Viral ATP-dependent RNA helicase NS3 6.11 Viral ATP-dependent RNA helicase NS3 complexes 6.12 ATP-dependent RNA helicase SUV3 6.13 ATP-dependent RNA helicase A 6.14 ATP-dependent RNA helicase Repa 6.15 ATP-dependent RNA helicase HEF 6.16 Werner syndrome ATP-dependent DNA helicase 6.17 ATP-dependent DNA helicase Q 6.18 ATP-dependent DNA helicase RecG 6.19 ATP-dependent DNA helicase RecQ 6.20 ATP-dependent DNA helicase RuvA, RuvB 6.21 ATP-dependent DNA helicase UVSW 6.22 ATP-dependent DNA helicase UVRD 6.23 ATP-dependent DNA helicase PriA 6.24 ATP-dependent DNA helicase PcrA 6.25 DnaB helicase 6.26 Helicase NSP2 6.27 Helicase SNF2 6.28 Helicase SKI2 7 References

What is a Helicase?

Helicases are nucleic acid–dependent ATP-ases that are capable of unwinding DNA [1] or RNA [2] duplex substrates. As a consequence, they play roles in almost every process in cells that involves nucleic acids, including DNA replication and repair, transcription, translation, ribosome synthesis (1).

PcrA a Simple Model for Helicases

PcrA is part of the replication machinery of the Geobacillus stearothermophilusa gram (+) bacteria, This helicase is part of the superfamily I of Helicases. Monomeric protein that is mainly has the Rec domians. This helicase was reported as a mutation in the gen PcrA from "Stapphylococcus aerous", this mutation was related to a deficiency in the replication of a reporter plasmid.[3]

PcrA Biochemistry

PcrA is has an ATPas activityt which directionality is from 3' to 5' helicase strand separation reaction. The enzyme shows a specificity for the DNA substrate in gel mobility assays with the preferred substrate being one containing both single and double stranded regions of DNA. In contrast to Rep and UvrD from E. coli, there is not evidence for dimerisation of the enzyme using gel filtration, or by crosslinking in the presence of combinations of Mg2+, nucleotides and DNA. Moreover, kcat for ATP hydrolysis is constant over a large range of protein concentrations. Therefore, the protein appears to be monomeric under all conditions tested, including in the structure of two crystal forms of PcrA.[4]

PcrA Helicase Mechanism : The Mexican Wave

Professor Dale B. Wigley' group in 1996-1999 was able to crystalize the intermediate states from PcrA, giving solution to the controversy of what kind of mechanism this helicase has. [5] Two crystal form of the enzyma, one couple with a 10 mer DNA and a non hydrolizable form of ATP (ATPnP) (pdb id: 3pjr, and another a truncated form embebed in sulfate (pdb id: 2pjr, give a light in a model for how ATP hydrolysis results in motor movement along ssDNA. In the figure below step 1 (top) is the ATP free (product) ssDNA conformation. The DNA bases are labelled arbitrarily. On binding ATP, F626 creates a new binding pocket for base 6. Likewise, F64 destroys an acceptor pocket for base 2, forcing it to move to the position occupied by base 1. After ATP hydrolysis, the grip on base 6 is released. When the Y257 pocket is re-opened due to movement of F64, bases 3-6 can now flip through the acceptor pockets to their new positions. This model predicts that each ATP hydrolysis event will advance PcrA one base along ssDNA.[6]

The link below show a movie with the principal characteristics of this protain as long with the inchworm mode. Pcr4 Helicase and Mexican Wave

The Superfamily 1 (SF1)

PcrA share structural domains with the Rec helicases, like UvrD (2is1) and RepD (1uaa) from E. coli, Superfamily 1 (SF1) helicases are probably the best characterized class, certainly from a structural perspective. All members characterized to date are bona fide helicases and α enzymes. Indeed, from their mode of translocation via the bases it is difficult to envisage how they could translocate along a duplex. However, they can have either A or B directional polarity.

3D structures of helicase

Updated on 10-April-2013

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 RecG

1gm5 – TmRecG + 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 – 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 – HpDnaB – Helicobacter pylori
4a1f – HpDnaB C terminal
2vyf – GkDnaC – Geobacillus kaustophilus
2r6d – BsDnaB – Bacillus stearothermophilus
2r6e, 2r6d - 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

Helicase SKI2

2va8 – SsSKI2
4a4k – ySKI2 insertion domain
4a4z – ySKI2 + AMPPNP

3crv, 3crw – XPD – Sulfolobus acidocaldarius

3hib, 3im1, 3im2 – yBrr2 2nd SEC63 domain

References

Crystal structure of a DExx box DNA helicase., Subramanya HS, Bird LE, Brannigan JA, Wigley DB, Nature. 1996 Nov 28;384(6607):379-83. PMID:8934527
^ Johnson DS, Bai L, Smith BY, Patel SS, Wang MD (2007). "Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped t7 helicase". Cell 129 (7): 1299–309. doi:10.1016/j.cell.2007.04.038. PMID 17604719.
^ a b "Researchers solve mystery of how DNA strands separate" (2007-07-03). Retrieved on 2007-07-05.
^ Dumont S, Cheng W, Serebrov V, Beran RK, Tinoco Jr I, Pylr AM, Bustamante C, "RNA Translocation and Unwinding Mechanism of HCV NS3 Helicase and its Coordination by ATP", Nature. 2006 Jan 5; 439: 105-108. Anand SP, Zheng H, Bianco PR, Leuba SH, Khan SA. DNA helicase activity of PcrA is not required for displacement of RecA protein from DNA or inhibition of RecA-mediated DNA strand exchange. Journal of Bacteriology (2007) 189 (12):4502-4509.
Bird L, Subramanya HS, Wigley DB, "Helicases: a unifying structural theme?", Current Opinion in Structural Biology. 1998 Feb; 8 (1): 14-18.
Betterton MD, Julicher F, "Opening of nucleic-acid double strands by helicases: active versus passive opening.", Physical Review E. 2005 Jan; 71 (1): 011904.

• Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell. 2006 Apr 21;125(2):287-300. PMID:16630817 doi:10.1016/j.cell.2006.01.054
• Sengoku T, Nureki O, Dohmae N, Nakamura A, Yokoyama S. Crystallization and preliminary X-ray analysis of the helicase domains of Vasa complexed with RNA and an ATP analogue. Acta Crystallogr D Biol Crystallogr. 2004 Feb;60(Pt 2):320-2. Epub 2004, Jan 23. PMID:14747711 doi:10.1107/S0907444903025897

• Created with the participation of Luis E Ramirez-Tapia, Wayne Decatur.