1gdr: Difference between revisions

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[[Image:1gdr.gif|left|200px]]


{{Structure
==MODEL FOR A DNA MEDIATED SYNAPTIC COMPLEX SUGGESTED BY CRYSTAL PACKING OF GAMMA DELTA RESOLVASE SUBUNITS==
|PDB= 1gdr |SIZE=350|CAPTION= <scene name='initialview01'>1gdr</scene>, resolution 3.5&Aring;
<StructureSection load='1gdr' size='340' side='right'caption='[[1gdr]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<table><tr><td colspan='2'>[[1gdr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GDR FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.5&#8491;</td></tr>
|GENE=  
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gdr OCA], [https://pdbe.org/1gdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gdr RCSB], [https://www.ebi.ac.uk/pdbsum/1gdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gdr ProSAT]</span></td></tr>
|DOMAIN=
</table>
|RELATEDENTRY=
== Function ==
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gdr OCA], [http://www.ebi.ac.uk/pdbsum/1gdr PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1gdr RCSB]</span>
[https://www.uniprot.org/uniprot/TNR1_ECOLI TNR1_ECOLI] This protein catalyzes the site-specific recombination of the transposon and also regulates its frequency of transposition.
}}
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gd/1gdr_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gdr ConSurf].
<div style="clear:both"></div>


'''MODEL FOR A DNA MEDIATED SYNAPTIC COMPLEX SUGGESTED BY CRYSTAL PACKING OF GAMMA DELTA RESOLVASE SUBUNITS'''
==See Also==
 
*[[Resolvase 3D structures|Resolvase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
The packing arrangement of the 12 subunits of intact gamma delta resolvase in the unit cell of a hexagonal crystal form suggests a model for site-specific recombination that involves a DNA-mediated synaptic intermediate. The crystal structure has been determined by molecular replacement and partially refined at 2.8/3.5 A resolution. Although the small DNA-binding domain is disordered in these crystals, packing considerations show that only a small region of space in the crystal could accommodate a domain of its size. A family of related models for a synaptic complex between two DNA duplexes and 12 monomers that are arranged as situated in the crystal is consistent with the known topology of the complex and the distances between the three resolvase dimer-binding sites per DNA; further, these models place the two DNA recombination sites in contact with each other between two resolvase dimers, implying that strand exchange is accomplished through direct DNA-DNA interaction. A major role postulated, then, for the resolvase protein assembly is to stabilize a res DNA structure that is close to the topological transition state of the reaction.
 
==About this Structure==
1GDR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GDR OCA].
 
==Reference==
Model for a DNA-mediated synaptic complex suggested by crystal packing of gamma delta resolvase subunits., Rice PA, Steitz TA, EMBO J. 1994 Apr 1;13(7):1514-24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8156989 8156989]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Rice, P A.]]
[[Category: Rice PA]]
[[Category: Steitz, T A.]]
[[Category: Steitz TA]]
[[Category: site-specific recombinase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:42:00 2008''

Latest revision as of 10:24, 7 February 2024

MODEL FOR A DNA MEDIATED SYNAPTIC COMPLEX SUGGESTED BY CRYSTAL PACKING OF GAMMA DELTA RESOLVASE SUBUNITSMODEL FOR A DNA MEDIATED SYNAPTIC COMPLEX SUGGESTED BY CRYSTAL PACKING OF GAMMA DELTA RESOLVASE SUBUNITS

Structural highlights

1gdr is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.5Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TNR1_ECOLI This protein catalyzes the site-specific recombination of the transposon and also regulates its frequency of transposition.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1gdr, resolution 3.50Å

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