View source for RecG Bound to Three-Way DNA Junction

[[Image:1gm5 showing chains ADP.png|left|270px]]

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===STRUCTURE OF RECG BOUND TO THREE-WAY DNA JUNCTION===


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==About this Structure==
{{STRUCTURE_1gm5|  PDB=1gm5  |  SCENE=1gm5/1gm5_default/3  |CAPTION= 1gm5, resolution 3.24&Aring; (<scene name='1gm5/1gm5_default/3'>default scene</scene>).}}
1GM5 is a 4 chains structure (1 protein chain and 3 nucleic acid chains) of sequences from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GM5 OCA]. 


The <scene name='1gm5/1gm5_drums/1'>structure of RecG bound to a three-way junction</scene> is a '''<font color="#a09060">monomeric protein</font>''' bound to 3 '''<font color="#ae00fe">DNA chains</font>''' and '''<font color="#48e018">adenosinediphosphate</font>'''. <nowiki>[</nowiki>This scene uses the [[DRuMS]] color scheme. <nowiki>]</nowiki> {{Link Toggle FancyCartoonHighQualityView}}
 

<scene name='1gm5/1gm5_domains/3'>RecG has three structural domains</scene>:
*The N-terminal domain, <font color="green">Domain 1</font>, is about half the protein and extensively contacts the DNA junction.
*<font color="gold">Domain 2</font> is one of the two RecA-like domains common to helicases/translocases; '''<font color="cyan">ADP</font>''' is bound here.
*<font color="crimson">Domain 3</font> is the other of the two RecA-like domains common to helicases/translocases.


Schematic of the DNA fork seen in the structure:<br>
[[Image:Dna three way junction sequence.jpg|200px]]


<scene name='1gm5/1gm5_domain1/2'>Structural motifs of domain 1</scene>:
*<font color="pink">N-terminal helical subdomain</font>.
*The <font color="purple">wedge subdomain</font>, <scene name='1gm5/1gm5_domain1/3'>this orientation</scene> better shows how this subdomain splits the arms of the junction. Grooves on the sides of the wedge are too narrow to accommodate duplex DNA
*The <font color="cyan">remainder</font> of domain 1.


<scene name='1gm5/1gm5_junction/6'>Further details of the interaction between the protein and junction</scene>:
*The protein is shown in silver to enable highlighting of significant features.
*<font color="orange">Phe204</font> and <font color="orange">Tyr208</font> stack on the <font color="orange">orphan bases</font> to stabilize and cap the helical regions at the junction.
*A <font color="magenta">base that was paired in the original substrate is flipped out</font> in the structure as it seems to be caught in the middle of switching between duplexes of the fork and presumably this base isn't stabilized in keeping with it being a transient state.


<scene name='1gm5/1gm5_surface/2'>Surface representation of the interaction with the DNA substrate</scene>. <nowiki>[</nowiki>Note: this view generates a substantial surface which may take several minutes to calculate. Be patient.<nowiki>]</nowiki>
*This scene probably most clearly shows that grooves on the sides of the wedge are too narrow to accommodate duplex DNA.
*Presumably if the template duplex arm were longer as it would be in vivo, it would interact with domains 2 and 3, perhaps in the cleft between them.

==Additional Resources==
For additional information, see: [[DNA Replication, Repair, and Recombination]]
<br />

==Reference==
<ref group="xtra">PMID:11595187</ref><references group="xtra"/>
[[Category: Thermotoga maritima]]
[[Category: Extremophile]]
[[Category: Thermophile]]
[[Category: Scaife, S.]]
[[Category: Singleton, M R.]]
[[Category: Wigley, D B.]]
[[Category: Helicase]]
[[Category: Replication restart]]
[[Category: Recombination]]
[[Category: Adp]]
[[Category: Atp-binding]]
[[Category: Atpase]]
[[Category: DNA-binding]]
[[Category: Topic Page]]

''Page originally seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 22:17:57 2009''