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1ql0

From Proteopedia

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(New page: 200px<br /><applet load="1ql0" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ql0, resolution 1.1&Aring;" /> '''SM ENDONUCLEASE FROM ...)
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[[Image:1ql0.jpg|left|200px]]<br /><applet load="1ql0" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ql0, resolution 1.1&Aring;" />
 
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'''SM ENDONUCLEASE FROM SERATIA MARCENSCENS AT ATOMIC RESOLUTION'''<br />
 
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==Overview==
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==Sm Endonuclease from Seratia marcenscens at atomic resolution==
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The three-dimensional crystal structure of Serratia marcescens, endonuclease has been refined at 1.1 A resolution to an R factor of 12.9%, and an R(free) of 15.6% with the use of anisotropic temperature factors., The model contains 3694 non-H atoms, 715 water molecules, four sulfate, ions and two Mg(2+)-binding sites at the active sites of the homodimeric, protein. It is shown that the magnesium ion linked to the active-site, Asn119 of each monomer is surrounded by five water molecules and shows an, octahedral coordination geometry. The temperature factors for the bound, Mg(2+) ions in the A and B subunits are 7.08 and 4.60 A(2), respectively, and the average temperature factors for the surrounding water molecules, are 12.13 and 10.3 A(2), respectively. In comparison with earlier, structures, alternative side-chain conformations are defined for 51, residues of the dimer, including the essential active-site residue Arg57., A plausible mechanism of enzyme function is proposed based on the, high-resolution S. marcescens nuclease structure, the functional, characteristics of the natural and mutational forms of the enzyme and, consideration of its structural analogy with homing endo-nuclease I-PpoI.
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<StructureSection load='1ql0' size='340' side='right'caption='[[1ql0]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ql0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QL0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QL0 FirstGlance]. <br>
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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]] 1.1&#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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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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=1ql0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ql0 OCA], [https://pdbe.org/1ql0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ql0 RCSB], [https://www.ebi.ac.uk/pdbsum/1ql0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ql0 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NUCA_SERMA NUCA_SERMA] Catalyzes the hydrolysis of both DNA and RNA, double- or single-stranded, at the 3'position of the phosphodiester bond to produce 5'-phosphorylated mono-, di-, tri- and tetranucleotides. DNA is a slightly better substrate than RNA.
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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/ql/1ql0_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1ql0 ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1QL0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Serratia_marcescens_nuclease Serratia marcescens nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.30.2 3.1.30.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1QL0 OCA].
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Atomic structure of the Serratia marcescens endonuclease at 1.1 A resolution and the enzyme reaction mechanism., Shlyapnikov SV, Lunin VV, Perbandt M, Polyakov KM, Lunin VY, Levdikov VM, Betzel C, Mikhailov AM, Acta Crystallogr D Biol Crystallogr. 2000 May;56(Pt 5):567-72. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10771425 10771425]
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[[Category: Large Structures]]
[[Category: Serratia marcescens]]
[[Category: Serratia marcescens]]
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[[Category: Serratia marcescens nuclease]]
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[[Category: Betzel CH]]
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[[Category: Single protein]]
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[[Category: Mikhailov AM]]
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[[Category: Betzel, C.H.]]
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[[Category: Perbandt M]]
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[[Category: Mikhailov, A.M.]]
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[[Category: Perbandt, M.]]
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[[Category: MG]]
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[[Category: endonuclease]]
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[[Category: hydrolase]]
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[[Category: magnesium]]
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[[Category: nuclease]]
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[[Category: signal]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:47:07 2007''
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Current revision

Sm Endonuclease from Seratia marcenscens at atomic resolution

PDB ID 1ql0

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