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1g8t

From Proteopedia

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{{Seed}}
 
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[[Image:1g8t.png|left|200px]]
 
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==SM ENDONUCLEASE FROM SERATIA MARCENSCENS AT 1.1 A RESOLUTION==
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The line below this paragraph, containing "STRUCTURE_1g8t", creates the "Structure Box" on the page.
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<StructureSection load='1g8t' size='340' side='right'caption='[[1g8t]], [[Resolution|resolution]] 1.10&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'>[[1g8t]] 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=1G8T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G8T 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]] 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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_1g8t| PDB=1g8t | 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=1g8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g8t OCA], [https://pdbe.org/1g8t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g8t RCSB], [https://www.ebi.ac.uk/pdbsum/1g8t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g8t 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/g8/1g8t_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=1g8t 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 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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===SM ENDONUCLEASE FROM SERATIA MARCENSCENS AT 1.1 A RESOLUTION===
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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:10771425<ref>PMID:10771425</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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<div class="pdbe-citations 1g8t" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_10771425}}, adds the Publication Abstract to the page
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 10771425 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_10771425}}
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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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1G8T is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G8T OCA].
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==Reference==
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<ref group="xtra">PMID:10771425</ref><references group="xtra"/>
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[[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: Betzel, C H.]]
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[[Category: Lunin VV]]
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[[Category: Lunin, V V.]]
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[[Category: Mikhailov AM]]
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[[Category: Mikhailov, A M.]]
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[[Category: Perbandt M]]
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[[Category: Perbandt, M.]]
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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://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:11:54 2009''
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Current revision

SM ENDONUCLEASE FROM SERATIA MARCENSCENS AT 1.1 A RESOLUTION

PDB ID 1g8t

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