Helicase: Difference between revisions

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PcrA share structural domains with the Rec helicases, like UvrD and RepD 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.<applet load='2is1' size='300' frame='true' align='left' caption='DNA helicae II complex with DNA, [[2is1]]' scene=''|UvrD Structure /><applet load='1uaa' size='300' frame='true' align='center' caption='Rep helicase complex with DNA, [[1uaa]]' scene='' |RecD Structure />

~~==Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa (DEAD-box RNA helicase)==~~

{{STRUCTURE_2db3| PDB=2db3 | SCENE=2db3/2db3unit/1 |CAPTION= [[2db3]] asymmetric unit, resolution 2.20Å <br> Click <scene name='2db3/Vasalabeled/5'>here</scene> to display the biological molecule.}}

2DB3 is a 8 chains structure of sequences from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB3 OCA].

~~<scene name='2db3/2db3unit/1'>The crystallographic asymmetric unit of the solved structure contains 4 monomers of Vasa.</scene>~~

~~<scene name='2db3/Vasalabeled/5'>Each monomer of Vasa in the structure is bound to RNA and an ATP analog; this is presumed to represent the biological molecule.</scene>~~

~~<scene name='2db3/Vasadomains/3'>Each monomer of Vasa has an N-terminal domain that binds the 3' side of the RNA and a C-terminal domain that binds the 5' side of the RNA</scene>.~~

<scene name='2db3/Vasaconservedmotifs/5'>The 11 conserved motifs colored</scene> according to [http://www.sciencedirect.com/science?_ob=MiamiCaptionURL&_method=retrieve&_udi=B6WSN-4JS75DF-H&_image=fig1&_ba=1&_user=10&_rdoc=1&_fmt=full&_orig=search&_cdi=7051&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=ddca6b04cb5c204e01dd48186897bfc6 figure 1] of [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4JS75DF-H&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=4fc4ed285ab82e6628b1ffcc86eed0d7 the paper] describing the structure. {{Link Toggle FancyCartoonHighQualityView}}.

<scene name='2db3/Vasawedgehelix/1'>The wedge helix (overlapping with Motif Ib) clashes with the RNA continuing on in normal helix and forces a bend between nucleotide 5 and 6 in the structure.</scene> <nowiki>[</nowiki>Note: this view generates a surface area which may take half a minute to calculate.<nowiki>]</nowiki><br>

Motifs I and II bind the triphosphate of the ATP analog directly and through <scene name='2db3/Vasamg/3'>a magnesium ion</scene> and water. A <scene name='2db3/Vasamgwater/3'>red broken line connects the gamma-phosphorous atom and a well-ordered water</scene> located ~3.25Å away, situated ideally for a nucleophilic in-line attack. <scene name='2db3/Vasashielding/3'>Two arginines and a histidine shield the active site</scene> from the negative charge of the phosphates. <scene name='2db3/Vasaadenospec/4'>Gln272 recognizes the adenosine base moiety</scene>, specifying ATP vs. GTP.

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@@ Line 54: / Line 54: @@
 PcrA share structural domains with the Rec helicases, like UvrD and RepD 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.<applet load='2is1' size='300' frame='true' align='left' caption='DNA helicae II complex with DNA, [[2is1]]' scene=''|UvrD Structure /><applet load='1uaa' size='300' frame='true' align='center' caption='Rep helicase complex with DNA, [[1uaa]]' scene='' |RecD Structure />
 {{clear}}
-==Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa (DEAD-box RNA helicase)==
-{{STRUCTURE_2db3|  PDB=2db3  |  SCENE=2db3/2db3unit/1 |CAPTION= [[2db3]] asymmetric unit, resolution 2.20&Aring; <br> Click <scene name='2db3/Vasalabeled/5'>here</scene> to display the biological molecule.}}
-DB3 is a 8 chains structure of sequences from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB3 OCA].
-<scene name='2db3/2db3unit/1'>The crystallographic asymmetric unit of the solved structure contains 4 monomers of Vasa.</scene>
-<scene name='2db3/Vasalabeled/5'>Each monomer of Vasa in the structure is bound to RNA and an ATP analog; this is presumed to represent the biological molecule.</scene>
-<scene name='2db3/Vasadomains/3'>Each monomer of Vasa has an N-terminal domain that binds the 3' side of the RNA and a C-terminal domain that binds the 5' side of the RNA</scene>.
-<scene name='2db3/Vasaconservedmotifs/5'>The 11 conserved motifs colored</scene> according to [http://www.sciencedirect.com/science?_ob=MiamiCaptionURL&_method=retrieve&_udi=B6WSN-4JS75DF-H&_image=fig1&_ba=1&_user=10&_rdoc=1&_fmt=full&_orig=search&_cdi=7051&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=ddca6b04cb5c204e01dd48186897bfc6 figure 1] of [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4JS75DF-H&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=4fc4ed285ab82e6628b1ffcc86eed0d7 the paper] describing the structure. {{Link Toggle FancyCartoonHighQualityView}}.
-<scene name='2db3/Vasawedgehelix/1'>The wedge helix (overlapping with Motif Ib) clashes with the RNA continuing on in normal helix and forces a bend between nucleotide 5 and 6 in the structure.</scene> <nowiki>[</nowiki>Note: this view generates a surface area which may take half a minute to calculate.<nowiki>]</nowiki><br>
-Motifs I and II bind the triphosphate of the ATP analog directly and through <scene name='2db3/Vasamg/3'>a magnesium ion</scene> and water. A <scene name='2db3/Vasamgwater/3'>red broken line connects the gamma-phosphorous atom and a well-ordered water</scene> located ~3.25&Aring; away, situated ideally for a nucleophilic in-line attack. <scene name='2db3/Vasashielding/3'>Two arginines and a histidine shield the active site</scene> from the negative charge of the phosphates. <scene name='2db3/Vasaadenospec/4'>Gln272 recognizes the adenosine base moiety</scene>, specifying ATP vs. GTP.