PcrA helicase

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(→Structure of Pcr4 DNA Helicase)
Current revision (11:46, 31 January 2012) (edit) (undo)
 
(67 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1pjr.png|left|200px]]
+
[[Image:1jprto3jpr.png|left|300px]]
<!--
<!--
Line 7: Line 7:
or leave the SCENE parameter empty for the default display.
or leave the SCENE parameter empty for the default display.
-->
-->
-
{{STRUCTURE_1pjr| PDB=1pjr | SCENE='User:Luis_E_Ramirez-Tapia/Sandbox_1/1pjrglobular/1'}}
+
<!--The line below this paragraph, {{ABSTRACT_PUBMED_8934527}}, adds the Publication Abstract to the page
-
 
+
-
 
+
-
===Structure of Pcr4 DNA Helicase===
+
-
 
+
-
<!--
+
-
The line below this paragraph, {{ABSTRACT_PUBMED_8934527}}, adds the Publication Abstract to the page
+
(as it appears on PubMed at http://www.pubmed.gov), where 8934527 is the PubMed ID number.
(as it appears on PubMed at http://www.pubmed.gov), where 8934527 is the PubMed ID number.
-->
-->
-
{{ABSTRACT_PUBMED_8934527}}
+
<!--{{ABSTRACT_PUBMED_8934527}} -->
'''
'''
-
<scene name='User:Luis_E_Ramirez-Tapia/Sandbox_1/1pjrglobular/1'>TextToBeDisplayed</scene>
 
-
Helicases are nucleic acid–dependent ATP-ases that are capable of unwinding DNA [http://en.wikipedia.org/wiki/DNA] or RNA [http://en.wikipedia.org/wiki/RNA] 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 is part of the helicase superfamily I. A monomeric protein that is mainly alfa helical
 
-
<scene name='User:Luis_E_Ramirez-Tapia/Sandbox_1/Initial/1'>secondary structure</scene>
 
-
Repressors are proteins that inhibit the expression of DNA]; that is, they inhibit the transcription of [http://en.wikipedia.org/wiki/Messenger_rna messenger RNA] from their target genes. Each repressor targets a specific co-regulated group of genes by recognizing a specific sequence of DNA, called the ''operator'' in [http://en.wikipedia.org/wiki/Bacteria bacteria]. Repressor proteins are coded for by ''regulatory'' genes.
+
== What is a Helicase? ==
-
The lactose ("lac") repressor controls the expression of bacterial enzymes involved in the metabolism of of the sugar lactose. When the lac repressor binds lactose, it changes to an inactive conformation that cannot repress the production of these enzymes. Thus, the enzymes needed to use lactose are made only when lactose is available. The lac repressor, and the group of genes it controls, which is called an [http://en.wikipedia.org/wiki/Operon operon], were the first such gene regulatory system to be discovered. The operon was described in 1960<ref>L'opéron: groupe de gènes à expression coordonée par un opérateur. [Operon: a group of genes with the expression coordinated by an operator.] C R Hebd Seances Acad Sci., 250:1727-9, 1960. [http://www.ncbi.nlm.nih.gov/pubmed/14406329 PubMed 14406329]</ref> by François Jacob ''et al.'', who also correctly proposed the general mechanism of regulation by the lac repressor. The [http://nobelprize.org/nobel_prizes/medicine/laureates/1965/ 1965 Nobel Prize in Physiology or Medicine] was awarded to François Jacob, André Lwoff, and Jacques Monod "for their discoveries concerning genetic control of enzyme and virus synthesis".
+
{{STRUCTURE_1pjr| PDB=1pjr | SIZE=400| SCENE= |right|CAPTION=PcrA , [[1pjr]] }}
-
 
+
<scene name='User:Luis_E_Ramirez-Tapia/Sandbox_1/1pjrglobular/1'>Spacefill</scene>
-
For a general introduction to the lac repressor, please see David Goodsell's [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb39_1.html Introduction to the lac repressor] in his series [[Molecule of the Month]], and the article in Wikipedia on the [http://en.wikipedia.org/wiki/Lac_repressor lac repressor]. Mitchell Lewis published a detailed review in 2005<ref name='lewis'>The lac repressor. Lewis, M. C R Biol. 328:521-48, 2005. [http://www.ncbi.nlm.nih.gov/pubmed/15950160 PubMed 15950160]</ref>.
+
Helicases are nucleic acid–dependent ATP-ases that are capable of unwinding DNA [http://en.wikipedia.org/wiki/DNA] or RNA [http://en.wikipedia.org/wiki/RNA] 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).
-
 
+
-
==Structure of the lac repressor==
+
-
<applet load='1lbg' size='450' frame='true' align='right' scene='Lac_repressor/1lbg_lac_repressor_with_dna/9' />
+
-
 
+
-
The lac repressor protein (<scene name='Lac_repressor/1lbg_lac_repressor_with_dna/9'>initial labeled scene</scene> showing chain A in [[1lbg]], [[Resolution|resolution]] 4.8 &Aring;), starting at the N-terminus, begins with a <font color='red'><b>DNA-binding "headpiece"</b></font>, followed by a <font color='orange'><b>hinge region</b></font>, then an <font color='#00e080'><b>N-terminal ligand-binding subdomain</b></font> and a <font color='#20d0f0'><b>C-terminal ligand binding subdomain</b></font>, a <font color='#ff8080'><b>linker</b></font>, and a C-terminal <font color='#6060ff'><b>tetramerization helix</b></font><ref name='domaincolors'>This domain coloring scheme is adapted from Fig. 6 in the review by Lewis (''C. R. Biol.'' 328:521, 2005). Domains are <font color='red'><b>1-45</b></font>, <font color='orange'><b>46-62</b></font>, <font color='#00e080'><b>(63-162,291-320)</b></font>, <font color='#20d0f0'><b>(163-290,321-332)</b></font>, <font color='#ff8080'><b>330-339</b></font>, and <font color='#6060ff'><b>340-357</b></font>.</ref>. (<scene name='Lac_repressor/1lbg_lac_repressor_with_dna/10'>Hide labels</scene>.) In the absence of DNA, the <font color='orange'><b>hinge region</b></font> does not form the alpha helix shown here.
+
-
 
+
-
As can be seen when the chain is <scene name='Lac_repressor/1lbg_lac_repressor_with_dna/2'>colored with an N to C rainbow scheme</scene>
+
-
{{Template:ColorKey_N2CRainbow}}
+
-
each of the ligand-binding subdomains is made up of two discontinuous segments.
+
-
 
+
-
The lac repressor forms <scene name='Lac_repressor/1lbg_lac_repressor_with_dna/3'>homo-dimers</scene>. Dimerization buries 2,200 &Aring;<sup>2</sup> of surface, including a <scene name='Lac_repressor/1lbi_apo_lac_repressor/3'>hydrophobic patch on each chain</scene>,
+
-
<center><big>{{Template:ColorKey_Hydrophobic}}, {{Template:ColorKey_Polar}}</big></center>
+
-
forming a hydrophobic core (shown with [[1lbi]], [[resolution]] 2.7 &Aring;, lacking the DNA-binding domain due to [[Disorder|disorder]]).
+
 +
==PcrA a Simple Model for Helicases==
 +
[[Image:Pcr4_structures.jpg|thumb|350px|left|PcrA_Structure]]
 +
PcrA is part of the replication machinery of the [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]a gram (+) bacteria, This helicase is part of the superfamily I of Helicases. Monomeric protein that is mainly <scene name='User:Luis_E_Ramirez-Tapia/Sandbox_1/Initial/1'>alfa helical</scene> has the <scene name='User:Luis_E_Ramirez-Tapia/Sandbox_2/1pjrconser/2'>highly conserved</scene> Rec domians. This helicase was reported as a mutation in the gen PcrA from [http://en.wikipedia.org/wiki/staphylococcu "Stapphylococcus aerous"], this mutation was related to a deficiency in the replication of a reporter plasmid.[http://www.ncbi.nlm.nih.gov/pubmed/8232203?ordinalpos=81&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum]
<table align='right'><tr><td>&nbsp;</td><td>{{Template:ColorKey_ConSurf}}</td></tr></table>
<table align='right'><tr><td>&nbsp;</td><td>{{Template:ColorKey_ConSurf}}</td></tr></table>
-
The most highly <scene name='Lac_repressor/1lbg_lac_repressor_with_dna/8'>conserved surface on the lac repressor</scene> is the surface that contacts {{Template:ColorKey_Composition_DNA}}<ref>Conservation results for [[1lbg]] are from the precalculated [http://consurfdb.tau.ac.il ConSurf Database], using 103 sequences from Swiss-Prot with an average pairwise distance of 2.4.</ref>. (Only alpha carbon atoms are shown here, without sidechains, because sidechains were not resolved in the 4.8 &Aring; [[1lbg]] model.) The dimerization surfaces are the <scene name='Lac_repressor/1lbi_apo_lac_repressor/4'>most conserved sides</scene> of the ligand-binding domains<ref>Conservation results for [[1lbi]] are from the [http://consurf.tau.ac.il ConSurf Server], using 100 sequences from Uniprot with an average pairwise distance of 1.3.</ref>. (This scene shows sidechains, using the 2.7 &Aring; model in [[1lbi]], which lacks the DNA-binding domain due to disorder.)
+
{{clear}}
-
<--! scene with translucent :a is #11, but I didn't like it. -->
+
==PcrA Biochemistry==
-
The C-terminal tetramerization helices tether two dimers, and thus the functional form of <scene name='Lac_repressor/1lbg_lac_repressor_with_dna/7'>lac repressor is a homo-tetramer</scene> with two {{Template:ColorKey_Composition_DNA}}-binding sites.
+
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.[http://www.icnet.uk/labs/wigley/projects/helicase/35.html]
 +
[[Image:Wigleypcr4.jpg]]
-
==DNA Binding: Bending the Operator==
+
==PcrA Helicase Mechanism : The Mexican Wave==
-
====Non-Specific Binding====
 
-
<!--
 
-
<table width='350' align='right' cellpadding='5'><tr><td rowspan='2'>&nbsp;</td><td bgcolor='#d0d0d0'>
 
-
-->
 
-
<applet load='Image:1osl_ca.pdb' size='450' frame='true' align='right' scene='Lac_repressor/1osl_ca_dot_pdb/2' />
 
-
<!--
 
-
</td></tr><tr><td bgcolor='#d0d0d0'>[[Morphs|Morph]] of the lac repressor bending DNA as binding changes from non-specific ([[1osl]]) to specific recognition of the operator sequence ([[1l1m]]).</td></tr></table>
 
-
-->
 
-
Lac repressor binds to DNA non-specifically (<scene name='Lac_repressor/1osl_ca_dot_pdb/2'>initial scene</scene> derived <ref name='alphac'>For these scenes, the 20-model [[PDB file|PDB files]] for [[1osl]] and [[1l1m]] were reduced in size, to avoid exceeding the java memory available to the Jmol applet. All atoms except amino acid alpha carbons and DNA phosphorus atoms were removed using the free program ''alphac.exe'' from [http://www.umass.edu/microbio/rasmol/pdbtools.htm PDBTools]. Secondary structure HELIX records from the original PDB file header were retained. The results are [[Image:1osl_ca.pdb|1osl_ca.pdb]] and [[Image:1l1m_ca.pdb]].</ref> from [[1osl]], 20 [[NMR Ensembles of Models|NMR models]]), enabling it to slide rapidly along the DNA double helix until it encounters the lac operator sequence. The DNA-binding domain employs a [[Helix-turn-helix motif|helix-turn-helix motif]] ({{Template:ColorKey_Helix}}, {{Template:ColorKey_Turn}}). During non-specific binding, the <font color='orange'><b>hinge region</b></font> is disordered (indicated by the range of positions of the 20 models), and the <font color='#ae00ff'><b>DNA double helix</b></font> is straight. The model shown at right ([[1osl]]) has two copies of the DNA-binding domain and <font color='orange'><b>hinge region</b></font> (<scene name='Lac_repressor/1osl_ca_dot_pdb/3'>Apply green color</scene> to distinguish the <font color='#00a060'><b>chain B hinge</b></font>). <scene name='Lac_repressor/1osl_ca_dot_pdb/8'>Animating</scene> these 20 [[NMR Ensembles of Models|NMR models]] simulates thermal motion of the disordered hinge regions. {{Template:Button Toggle Animation}}
+
{{STRUCTURE_3pjr| PDB=3pjr | SIZE=400| SCENE= |right|CAPTION=PcrA complex with DNA and ATP, [[3pjr]] }}
-
====Specific Binding====
+
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. [http://www.ncbi.nlm.nih.gov/pubmed/10199404ordinalpos=39&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum]
 +
Two crystal form of the enzyma, one couple with a 10 mer DNA and a non hydrolizable form of ATP (ATPnP) (pdb id: 3pjr [[3pjr]], <scene name='User:Luis_E_Ramirez-Tapia/Sandbox_2/3pjrinitial/1'>(Enzyme Subtrate Structure) </scene>and another a truncated form embebed in sulfate (pdb id: 2pjr [[2pjr]]<scene name='User:Luis_E_Ramirez-Tapia/Sandbox_2/2pjrinitial/1'>(Enzyme Product Structure)</scene>, 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.[http://www.icnet.uk/labs/wigley/projects/helicase/35.html]
 +
[[Image:Mexicanwave.jpg|thumb|170px|left|Inchworm or Mexicanwave model]]
 +
[[Image:Snapshot_2008-12-03_14-11-31.jpg|thumb|400px|left|PcrA Movie]]
-
Upon recognizing the specific operator sequence, the non-specific binding converts to <scene name='Lac_repressor/1l1m_ca_specific_bindiing/3'>specific binding</scene> (derived<ref name='alphac' /> from [[1l1m]], 20 [[NMR Ensembles of Models|NMR models]]). During this conversion, the hinge region changes from disordered loops to {{Template:ColorKey_Helix}} (<scene name='Lac_repressor/1l1m_ca_specific_bindiing/4'>highlight new helices</scene>), which bind in the minor groove of the DNA. This binding opens the minor groove, bending the <font color='#ae00ff'><b>DNA double helix</b></font>. <scene name='Lac_repressor/1l1m_ca_specific_bindiing/6'>Animating</scene> these can be compared with the animation of the non-specific binding. {{Template:Button Toggle Animation}}
 
-
====Morph of Conversion====
 
-
The <scene name='Morphs/1osl_19_1l1m_9_morph/4'>changes during conversion from non-specific to specific binding</scene> can be seen more easily when they are animated smoothly by [[Morphs|morphing]]. (The methods used to create this morph are given in [[Lac repressor morph methods]].) Note the bending of the DNA, with the widening of the central minor groove on the convex aspect. Also note the conversion of the disulfide-bonded hinge region loops to alpha helices. (The displayed secondary structure is calculated for each model in the morph interpolation.)
+
'''The link below show a movie with the principal characteristics of this protein as long with the inchworm model'''. [http://www.youtube.com/watch?v=fDwaWCkhgZI Pcr4 Helicase and Mexican Wave]
 +
{{Clear}}
-
The specific recognition of the lac operator sequence in the DNA occurs largely though [[Hydrogen bonds|hydrogen bonds]]. <scene name='Lac_repressor/1osl_14_1l1m_9_morph_hbonds/1'>Formation of hydrogen bonds that recognize the operator sequence</scene> is illustrated in this rendering of the morph. Shown are hydrogen bonds involving Arg22.N-eta2 and Tyr18.OH interacting with DNA base oxygens in the major groove, and Ala53.O interacting with a DNA base nitrogen in the minor groove. (Not all of the relevant hydrogen bonds are shown; see [[Lac repressor morph methods|Methods]].) {{Template:Button Toggle Animation}}
+
==The Superfamily 1 (SF1)==
 +
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.
-
Test: <scene name='Lac_repressor/1osl_19_1l1m_9_morph/1'>bad morph scene</scene>
+
{{STRUCTURE_2is1| PDB=2is1 | SIZE=300| SCENE= |left|CAPTION=UVRD complex with DNA and sulfate, [[2is1]] }}
 +
{{STRUCTURE_1uaa| PDB=1uaa | SIZE=300| SCENE= |center|CAPTION=REP complex with DNA, [[1uaa]] }}
-
==Animation for Powerpoint&reg; Slides==
+
{{clear}}
-
Here is an animated multi-gif [[Morphs#True_Movies|true movie]] of the above morph, ready to insert into a Powerpoint&reg;<ref>''Powerpoint'' is a registered trademark for a software package licensed by [http://microsoft.com Microsoft Corp.].</ref> slide.
+
-
[[Image:Lacrep_anim_large.gif|center]]
+
-
* In Windows, simply drag the movie and drop it into the Powerpoint slide. You can then resize it and position it. The movie should play when you change the View to Slide Show ("project") the slide.
 
-
* In Mac OSX, Ctrl-Click on the movie, then Save Image. In Mac Powerpoint, at the desired slide, use the Insert menu (at the top) and select Movie ..., then insert the saved .gif movie file. After inserting the movie, make sure the Toolbox is showing (controlled with an icon-button at the top of the window). Now you can resize and reposition the movie. Click in the movie in the slide to select it. Now, in the Toolbox/Formatting Palette, under Movie, check Loop Until Stopped. Now the movie should play when you change the View to Slide Show ("project") the slide.
 
-
==Challenge Your Understanding==
 
-
Here are some questions to challenge your understanding.
 
-
#Why does the lac repressor bind to DNA non-specifically?
 
-
#When the lac repressor binds non-specifically to DNA, what part of the DNA double helix does it bind to?
 
-
#Does DNA have a net charge, and if so, is it negative or positive in aqueous solution at pH 7?
 
-
#What kinds of chemical bonds are likely to be involved in non-specific binding of the repressor protein to DNA?
 
-
#Does specific binding of lac repressor to DNA disrupt any of the Watson-Crick hydrogen bonds between the base pairs in the DNA strands?
 
-
#How do proteins such as the lac repressor recognize specific nucleotide sequences in a DNA double helix?
 
-
#What kinds of chemical bonds are involved in specific binding of the repressor protein to DNA?
 
-
#Does the lac repressor recognize specific bases in the major or minor grooves of the DNA?
 
-
#Why does the lac repressor bend the DNA double helix when it recognizes its specific nucleotide sequence?
 
-
Answers are available on request to {{Template:Contact}}. If you would like us to make the answers publically available within Proteopedia, please let us know. When contacting us, please give your full name, your position, institution or school, and location.
+
==About this Structure==
 +
1PJR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PJR OCA].
-
==Content Attribution==
+
==3D structures of helicase==
-
The morphs displayed here were originally prepared by [[User:Eric Martz|Eric Martz]] in 2004 for the page [http://atlas.proteinexplorer.org/morphs/lacrep Lac Repressor Binding to DNA], within [http://proteinexplorer.org ProteinExplorer.Org].
+
[[Helicase]]
-
==See Also==
+
==Additional Resources==
-
 
+
For additional information, see: [[DNA Replication, Repair, and Recombination]]
-
*[[:Category: Lac repressor]] and [[:Category: Lac Repressor]], automatically-generated pages that list [[PDB codes]] for lac repressor models.
+
<br />
-
*[[Morphs]] where the morph of the lac repressor is used as an example.
+
-
 
+
-
==References & Notes==
+
-
<references />
+
-
 
+
-
== History of DNA Helicase Discovery ==
+
-
 
+
-
==About this Structure==
+
-
1PJR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PJR OCA].
+
==Reference==
==Reference==
Line 128: Line 82:
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 01:38:49 2008''
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 01:38:49 2008''
 +
 +
^ 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.

Current revision

Contents

What is a Helicase?

PDB ID 1pjr

Drag the structure with the mouse to rotate
PcrA , 1pjr
Gene: PCRA (Geobacillus stearothermophilus)
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


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_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 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]

 Image:Consurf_key_small.gif

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] Image:Wigleypcr4.jpg

PcrA Helicase Mechanism : The Mexican Wave

PDB ID 3pjr

Drag the structure with the mouse to rotate
PcrA complex with DNA and ATP, 3pjr
Ligands:
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml



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 3pjr, and another a truncated form embebed in sulfate (pdb id: 2pjr 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]

Inchworm or Mexicanwave model
Inchworm or Mexicanwave model
PcrA Movie
PcrA Movie


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

The Superfamily 1 (SF1)

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.


PDB ID 2is1

Drag the structure with the mouse to rotate
UVRD complex with DNA and sulfate, 2is1
Ligands: , ,
Gene: uvrD (Escherichia coli)
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml



PDB ID 1uaa

Drag the structure with the mouse to rotate
REP complex with DNA, 1uaa
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml





About this Structure

1PJR is a Single protein structure of sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA.

3D structures of helicase

Helicase

Additional Resources

For additional information, see: DNA Replication, Repair, and Recombination

Reference

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

Page seeded by OCA on Mon Jul 28 01:38:49 2008

^ 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.

Proteopedia Page Contributors and Editors (what is this?)

Luis E Ramirez-Tapia, Michal Harel, Eran Hodis, David Canner

Retrieved from "http://52.214.119.220/wiki/index.php/PcrA_helicase"
Personal tools