1ydx

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{{Seed}}
 
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[[Image:1ydx.png|left|200px]]
 
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==Crystal structure of Type-I restriction-modification system S subunit from M. genitalium==
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The line below this paragraph, containing "STRUCTURE_1ydx", creates the "Structure Box" on the page.
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<StructureSection load='1ydx' size='340' side='right'caption='[[1ydx]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1ydx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycoplasma_genitalium Mycoplasma genitalium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YDX FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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{{STRUCTURE_1ydx| PDB=1ydx | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ydx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ydx OCA], [https://pdbe.org/1ydx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ydx RCSB], [https://www.ebi.ac.uk/pdbsum/1ydx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ydx ProSAT]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yd/1ydx_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1ydx ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structure of the eubacteria Mycoplasma genitalium ORF MG438 polypeptide, determined by multiple anomalous dispersion and refined at 2.3 A resolution, reveals the organization of S subunits from the Type I restriction and modification system. The structure consists of two globular domains, with about 150 residues each, separated by a pair of 40 residue long antiparallel alpha-helices. The globular domains correspond to the variable target recognition domains (TRDs), as previously defined for S subunits on sequence analysis, while the two helices correspond to the central (CR1) and C-terminal (CR2) conserved regions, respectively. The structure of the MG438 subunit presents an overall cyclic topology with an intramolecular 2-fold axis that superimposes the N and the C-half parts, each half containing a globular domain and a conserved helix. TRDs are found to be structurally related with the small domain of the Type II N6-adenine DNA MTase TaqI. These relationships together with the structural peculiarities of MG438, in particular the presence of the intramolecular quasi-symmetry, allow the proposal of a model for S subunits recognition of their DNA targets in agreement with previous experimental results. In the crystal, two subunits of MG438 related by a crystallographic 2-fold axis present a large contact area mainly involving the symmetric interactions of a cluster of exposed hydrophobic residues. Comparison with the recently reported structure of an S subunit from the archaea Methanococcus jannaschii highlights the structural features preserved despite a sequence identity below 20%, but also reveals important differences in the globular domains and in their disposition with respect to the conserved regions.
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===Crystal structure of Type-I restriction-modification system S subunit from M. genitalium===
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Crystal structure of a putative type I restriction-modification S subunit from Mycoplasma genitalium.,Calisto BM, Pich OQ, Pinol J, Fita I, Querol E, Carpena X J Mol Biol. 2005 Aug 26;351(4):749-62. PMID:16038930<ref>PMID:16038930</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_16038930}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1ydx" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 16038930 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16038930}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1YDX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycoplasma_genitalium Mycoplasma genitalium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YDX OCA].
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==Reference==
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Crystal structure of a putative type I restriction-modification S subunit from Mycoplasma genitalium., Calisto BM, Pich OQ, Pinol J, Fita I, Querol E, Carpena X, J Mol Biol. 2005 Aug 26;351(4):749-62. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16038930 16038930]
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[[Category: Mycoplasma genitalium]]
[[Category: Mycoplasma genitalium]]
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[[Category: Single protein]]
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[[Category: Carpena X]]
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[[Category: Carpena, X.]]
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[[Category: Fita I]]
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[[Category: Fita, I.]]
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[[Category: Machado B]]
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[[Category: Machado, B.]]
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[[Category: Pinol J]]
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[[Category: Pinol, J.]]
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[[Category: Querol E]]
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[[Category: Querol, E.]]
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[[Category: Quijada O]]
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[[Category: Quijada, O.]]
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[[Category: Type-i hsd]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 16:13:19 2008''
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Current revision

Crystal structure of Type-I restriction-modification system S subunit from M. genitalium

PDB ID 1ydx

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