Helicase

Function

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.

• ATP-dependent helicase Rho is a protein involved in termination of transcription in prokaryotes. Rho binds to the transcription terminator site on single-stranded RNA. Rho forms a ring-shaped hexamer and advances along the mRNA until it reaches the RNA polymerase and causing it to dissociate from the DNA and end transcription.
  
• ATP-dependent helicase RuvB-like 1 (RuvBL1) or TIP49 is a human protein which forms hexamers. The hexamer forms dodecamer upon association with RuvBL2 or TIP48 and the complex possesses single-stranded DNA-stimulated ATPase and helicase activities.
• DnaB and DinG exhibit helicase and ATPase activities^[1].
• BLM helicase or Bloom syndrome protein can unwind DNA secondary structures^[2].
• Sen1 helicese has a role in transcription termination of nonpolyadenylated and polyadenylated RNA polymerase II transcripts^[3].
• Snf2 helicase and Swr1 helicase regulate the structure and dynamic properties of chromatin^[4].
• Ski2 helicase is involved in RNA processing and degradation^[5].
• XPD helicase or Rad3 in yeast is a component of transcription factor IIH^[6].
• Cas3 helicase exhibits helicase, nuclease and ATPase activities^[7].
• Aquarius helicase is an RNA helicase that binds pre-mRNA introns to defined position^[8].

For details of PcrA helicase see

• Molecular Playground/PcrA Helicase
  e
• 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 ATP-dependent helicase HepA see

• RapA, a Swi2/Snf2 protein.
  

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
  

For helicase XPD see

• XPD Helicase (3CRV)
  

For helicase II or UvrD see

• DNA Repair
  

For SARS-CoV-2 helicase nsp13 see

• SARS-CoV-2 enzyme Hel
  

See also

• Transcription and RNA Processing
• Brr2 - pre-mRNA-splicing helicase.

What is a Helicase?

Spacefill 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_Structure

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 alpha helical has the highly conserved 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, (Enzyme Substrate Structure) and another a truncated form embebed in sulfate (pdb id: 2pjr (Enzyme Product Structure), 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]

Inchworm or Mexicanwave model

PcrA Movie

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

Helicase 3D structures