DNA Helicase
This Jmol Exploration was created using the Jmol Exploration Webpage Creator from the MSOE Center for BioMolecular Modeling.
'Our genetic information is safely locked up inside the double helix of DNA. In order to use this information, the helix must be unwound to expose the bases, allowing polymerases access to build complementary DNA or RNA strands. Unwinding of DNA is trickier than you might expect. The interaction between bases is quite strong and there are many, many of them, so it takes appreciable energy to separate the strands. This is the job of DNA helicases: they are enzymes that pull apart the two strands in a DNA double helix.(5)
DNA helicase pries apart the two strands in a DNA double helix, powered by ATP.
Classification: HYDROLASE / DNA.
* Image below was taken from (5).
The DNA Helicase is composed of 3 polymers that contain 14 chains (454 amino acid residues long).
Primary Structure (Amino Acids)DNA Helicase is 46% helical and 10% beta sheet.
Secondary StructureThe tertiary structure of DNA Helicase is formed by interactions among the amino acid side chains in between the 3 polymers.
These interactions allow molecule to fold in such a way that is helpful for its function.
Most unique ligand: GUANOSINE-5'-DIPHOSPHATE - GDP
GDP binding pocket:
Asn 421(blue)
Ser 213(orange)
Gly 215(red)
Arg 250(yellow)
Thr 217(lime/green)
Lys 216(pink)
'Helicases separate nucleic acid duplexes into their component strands using energy from ATP hydrolysis.
The crystal structure of this DNA helicase from bacteriophage T7, reveals an hexagonal arrangement of six identical subunits. Surprisingly, the ring is not sixfold symmetric, but is slightly squished. A model for the mechanism of how the enzyme might work explains this structural asymmetry.
Of the six potential ATP binding sites, two opposing ones bind ATP tightly, two are more likely to bind ADP and phosphate, and two are empty. These three states may interconvert in a coordinate fashion as ATP is hydrolyzed, creating a ripple effect that continuously runs around the ring. Because of these conformational changes, the loops that extend into the center hole of the ring - that are proposed to bind DNA - oscillate up and down, as seen in this cross section. The oscillating loops might pull a DNA strand through the central hole, thus unwinding the double helix in the process. A frontal view shows the full dynamics of this fascinating protein machine.'(3)
''
'DNA polymerases can only synthesize nascent DNA from single-stranded DNA (ssDNA) templates. In bacteria, the unwinding of parental duplex DNA is carried out by the replicative DNA helicase (DnaB) that couples NTP hydrolysis to 50 to 30 translocation.
The crystal structure of the DnaB hexamer in complex with GDP-AlF4 and ssDNA reported here reveals that DnaB adopts a closed spiral staircase quaternary structure around an A-form ssDNA with each C-terminal domain coordinating two nucleotides of ssDNA.
The structure not only provides structural insights into the translocation mechanism of superfamily IV helicases but also suggests that members of this superfamily employ a translocation mechanismthat is distinct from other helicase superfamilies. We propose a hand-over-hand mechanism in which sequential hydrolysis of NTP causes a sequential 50 to 30 movement of the subunits along the helical axis of the staircase, resulting in the unwinding of two nucleotides per subunit.(2)
1)DNA replication - 3D [Video file]. (2015, June 26). Retrieved from https://www.youtube.com/
watch?v=TNKWgcFPHqw
2)Itsathitphaisarn, O., Wing, R. A., Eliason, W. K., Wang, J., & Steitz, T. A. (2012, October 12). The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation. http://dx.doi.org/10.1016/j.cell.2012.09.014
3)King, C. R. (2009, April 19). DNA helicase [Video file]. Retrieved from https://www.youtube.com/ watch?v=bePPQpoVUpM
4)The Protein Data Bank H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) Nucleic Acids Research, 28: 235-242. doi: 10.1093/nar/28.1.235
5)DNA Helicase, Molecule of the Month Retrieved from https://pdb101.rcsb.org/motm/168