2odn: Difference between revisions

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-{{Seed}}
-[[Image:2odn.png|left|200px]]
-<!--
+==MSRECA-dATP complex==
-The line below this paragraph, containing "STRUCTURE_2odn", creates the "Structure Box" on the page.
+<StructureSection load='2odn' size='340' side='right'caption='[[2odn]], [[Resolution|resolution]] 3.10&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'>[[2odn]] 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=2ODN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ODN 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]] 3.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene></td></tr>
-{{STRUCTURE_2odn|  PDB=2odn  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2odn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2odn OCA], [https://pdbe.org/2odn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2odn RCSB], [https://www.ebi.ac.uk/pdbsum/2odn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2odn 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/od/2odn_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=2odn ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Mycobacterium smegmatis RecA and its nucleotide complexes crystallize in three different, but closely related, forms characterized by specific ranges of unit cell dimensions. The six crystals reported here and five reported earlier, all grown under the same or very similar conditions, belong to these three forms, all in space group P6(1). They include one obtained by reducing relative humidity around the crystal. In all crystals, RecA monomers form filaments around a 6(1) screw axis. Thus, the c-dimension of the crystal corresponds to the pitch of the RecA filament. As reported for Escherichia coli RecA, the variation in the pitch among the three forms correlates well with the motion of the C-terminal domain of the RecA monomers with respect to the main domain. The domain motion is compatible with formation of inactive as well as active RecA filaments involving monomers with a fully ordered C domain. It does not appear to influence the movement upon nucleotide-binding of the switch residue, which is believed to provide the trigger for transmitting the effect of nucleotide binding to the DNA-binding region. Interestingly, partial dehydration of the crystal results in the movement of the residue similar to that caused by nucleotide binding. The ordering of the DNA-binding loops, which present ensembles of conformations, is also unaffected by domain motion. The conformation of loop L2 appears to depend upon nucleotide binding, presumably on account of the movement of the switch residue that forms part of the loop. The conformations of loops L1 and L2 are correlated and have implications for intermolecular communications within the RecA filament. The structures resulting from different orientations of the C domain and different conformations of the DNA-binding loops appear to represent snapshots of the RecA at different phases of activity, and provide insights into the mechanism of action of RecA.
-===MSRECA-dATP complex===
+Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: crystallographic and comparative analysis of 11 structures of Mycobacterium smegmatis RecA.,Krishna R, Prabu JR, Manjunath GP, Datta S, Chandra NR, Muniyappa K, Vijayan M J Mol Biol. 2007 Apr 6;367(4):1130-44. Epub 2007 Jan 26. PMID:17306300<ref>PMID:17306300</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2odn" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17306300}}, 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 17306300 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17306300}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-ODN 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=2ODN OCA].
+[[Category: Mycolicibacterium smegmatis]]
+[[Category: Chandra NR]]
-==Reference==
+[[Category: Datta S]]
-Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: crystallographic and comparative analysis of 11 structures of Mycobacterium smegmatis RecA., Krishna R, Prabu JR, Manjunath GP, Datta S, Chandra NR, Muniyappa K, Vijayan M, J Mol Biol. 2007 Apr 6;367(4):1130-44. Epub 2007 Jan 26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17306300 17306300]
+[[Category: Krishna R]]
+[[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: Rajan Prabu J]]
-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]
-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: Deleted entry]]
-[[Category: Mycobacterium smegmatis]]
-[[Category: Single protein]]
-[[Category: Chandra, N R.]]
-[[Category: Datta, S.]]
-[[Category: Krishna, R.]]
-[[Category: Manjunath, G P.]]
-[[Category: Muniyappa, K.]]
-[[Category: Prabu, J Rajan.]]
-[[Category: Vijayan, M.]]
-[[Category: Dna-repair]]
-[[Category: Recombination]]
-[[Category: Sos responce]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 16:09:28 2008''