Wayne Decatur: /* About this Structure */

Wayne Decatur — Fri, 05 Oct 2012 16:14:23 GMT

About this Structure

←Older revision		Revision as of 16:14, 5 October 2012
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	==About this Structure==		==About this Structure==
	{{STRUCTURE_1gm5\| PDB=1gm5 \| SCENE=1gm5/1gm5_default/3 \|CAPTION= 1gm5, resolution 3.24Å (<scene name='1gm5/1gm5_default/3'>default scene</scene>).}}		{{STRUCTURE_1gm5\| PDB=1gm5 \| SCENE=1gm5/1gm5_default/3 \|CAPTION= 1gm5, resolution 3.24Å (<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].	+	[[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].

Jaime Prilusky at 08:49, 29 July 2012

Jaime Prilusky — Sun, 29 Jul 2012 08:49:41 GMT

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	[[Category: Atpase]]		[[Category: Atpase]]
	[[Category: DNA-binding]]		[[Category: DNA-binding]]
-	[[~~Categor~~: Topic Page]]	+	[[Category: Topic Page]]

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Wayne Decatur at 17:37, 12 July 2011

Wayne Decatur — Tue, 12 Jul 2011 17:37:32 GMT

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	[[Category: Atpase]]		[[Category: Atpase]]
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Wayne Decatur: started page

Wayne Decatur — Tue, 12 Jul 2011 17:33:14 GMT

started page

New page

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



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


{{ABSTRACT_PUBMED_11595187}}

==About this Structure==
{{STRUCTURE_1gm5| PDB=1gm5 | SCENE=1gm5/1gm5_default/3 |CAPTION= 1gm5, resolution 3.24Å (<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 '''monomeric protein''' bound to 3 '''DNA chains''' and '''adenosinediphosphate'''. <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, Domain 1, is about half the protein and extensively contacts the DNA junction.
*Domain 2 is one of the two RecA-like domains common to helicases/translocases; '''ADP''' is bound here.
*Domain 3 is the other of the two RecA-like domains common to helicases/translocases.

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

<scene name='1gm5/1gm5_domain1/2'>Structural motifs of domain 1</scene>:
*N-terminal helical subdomain.
*The wedge subdomain, <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 remainder 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.
*Phe204 and Tyr208 stack on the orphan bases to stabilize and cap the helical regions at the junction.
*A base that was paired in the original substrate is flipped out 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]]
 

==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]]

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

RecG Bound to Three-Way DNA Junction - Revision history

Wayne Decatur: /* About this Structure */

Jaime Prilusky at 08:49, 29 July 2012

Wayne Decatur at 17:37, 12 July 2011

Wayne Decatur: started page