2g88: Difference between revisions

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{{Seed}}
[[Image:2g88.png|left|200px]]


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==MSRECA-dATP COMPLEX==
The line below this paragraph, containing "STRUCTURE_2g88", creates the "Structure Box" on the page.
<StructureSection load='2g88' size='340' side='right'caption='[[2g88]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2g88]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G88 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G88 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
{{STRUCTURE_2g88|  PDB=2g88  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2g88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g88 OCA], [https://pdbe.org/2g88 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g88 RCSB], [https://www.ebi.ac.uk/pdbsum/2g88 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g88 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q7X416_MYCSM Q7X416_MYCSM] Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs.[RuleBase:RU000526]
== 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/g8/2g88_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=2g88 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
RecA protein is a crucial and central component of the homologous recombination and DNA repair machinery. Despite numerous studies on the protein, several issues concerning its action, including the allosteric regulation mechanism have remained unclear. Here we report, for the first time, a crystal structure of a complex of Mycobacterium smegmatis RecA (MsRecA) with dATP, which exhibits a fully ordered C-terminal domain, with a second dATP molecule bound to it. ATP binding is an essential step for all activities of RecA, since it triggers the formation of active nucleoprotein filaments. In the crystal filament, dATP at the first site communicates with a dATP of the second site of an adjacent subunit, through conserved residues, suggesting a new route for allosteric regulation. In addition, subtle but definite changes observed in the orientation of the nucleotide at the first site and in the positions of the segment preceding loop L2 as well as in the segment 102-105 situated between the 2 nt, all appear to be concerted and suggestive of a biological role for the second bound nucleotide.


===MSRECA-dATP COMPLEX===
Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery.,Krishna R, Manjunath GP, Kumar P, Surolia A, Chandra NR, Muniyappa K, Vijayan M Nucleic Acids Res. 2006 Apr 28;34(8):2186-95. Print 2006. PMID:16648362<ref>PMID:16648362</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2g88" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_16648362}}, adds the Publication Abstract to the page
*[[3D structures of recombinase A|3D structures of recombinase A]]
(as it appears on PubMed at http://www.pubmed.gov), where 16648362 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_16648362}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2G88 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G88 OCA].
[[Category: Mycolicibacterium smegmatis]]
 
[[Category: Chandra NR]]
==Reference==
[[Category: Krishna R]]
Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery., Krishna R, Manjunath GP, Kumar P, Surolia A, Chandra NR, Muniyappa K, Vijayan M, Nucleic Acids Res. 2006 Apr 28;34(8):2186-95. Print 2006. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16648362 16648362]
[[Category: Kumar P]]
 
[[Category: Manjunath GP]]
Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation., Datta S, Prabu MM, Vaze MB, Ganesh N, Chandra NR, Muniyappa K, Vijayan M, Nucleic Acids Res. 2000 Dec 15;28(24):4964-73. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11121488 11121488]
[[Category: Muniyappa K]]
 
[[Category: Surolia A]]
Structural studies on MtRecA-nucleotide complexes: insights into DNA and nucleotide binding and the structural signature of NTP recognition., Datta S, Ganesh N, Chandra NR, Muniyappa K, Vijayan M, Proteins. 2003 Feb 15;50(3):474-85. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12557189 12557189]
[[Category: Vijayan M]]
 
Crystal structures of Mycobacterium smegmatis RecA and its nucleotide complexes., Datta S, Krishna R, Ganesh N, Chandra NR, Muniyappa K, Vijayan M, J Bacteriol. 2003 Jul;185(14):4280-4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12837805 12837805]
[[Category: Mycobacterium smegmatis]]
[[Category: Single protein]]
[[Category: Chandra, N R.]]
[[Category: Krishna, R.]]
[[Category: Kumar, P.]]
[[Category: Manjunath, G P.]]
[[Category: Muniyappa, K.]]
[[Category: Surolia, A.]]
[[Category: Vijayan, M.]]
[[Category: Dna-repair]]
[[Category: Recombination]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 15:34:31 2008''

Latest revision as of 12:36, 30 August 2023

MSRECA-dATP COMPLEXMSRECA-dATP COMPLEX

Structural highlights

2g88 is a 1 chain structure with sequence from Mycolicibacterium smegmatis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.2Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q7X416_MYCSM Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs.[RuleBase:RU000526]

Evolutionary Conservation

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

Publication Abstract from PubMed

RecA protein is a crucial and central component of the homologous recombination and DNA repair machinery. Despite numerous studies on the protein, several issues concerning its action, including the allosteric regulation mechanism have remained unclear. Here we report, for the first time, a crystal structure of a complex of Mycobacterium smegmatis RecA (MsRecA) with dATP, which exhibits a fully ordered C-terminal domain, with a second dATP molecule bound to it. ATP binding is an essential step for all activities of RecA, since it triggers the formation of active nucleoprotein filaments. In the crystal filament, dATP at the first site communicates with a dATP of the second site of an adjacent subunit, through conserved residues, suggesting a new route for allosteric regulation. In addition, subtle but definite changes observed in the orientation of the nucleotide at the first site and in the positions of the segment preceding loop L2 as well as in the segment 102-105 situated between the 2 nt, all appear to be concerted and suggestive of a biological role for the second bound nucleotide.

Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery.,Krishna R, Manjunath GP, Kumar P, Surolia A, Chandra NR, Muniyappa K, Vijayan M Nucleic Acids Res. 2006 Apr 28;34(8):2186-95. Print 2006. PMID:16648362[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Krishna R, Manjunath GP, Kumar P, Surolia A, Chandra NR, Muniyappa K, Vijayan M. Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery. Nucleic Acids Res. 2006 Apr 28;34(8):2186-95. Print 2006. PMID:16648362 doi:http://dx.doi.org/34/8/2186

2g88, resolution 3.20Å

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