1smn

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[[Image:1smn.gif|left|200px]]
 
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{{Structure
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==IDENTIFICATION OF THE SERRATIA ENDONUCLEASE DIMER: STRUCTURAL BASIS AND IMPLICATIONS FOR CATALYSIS==
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|PDB= 1smn |SIZE=350|CAPTION= <scene name='initialview01'>1smn</scene>, resolution 2.04&Aring;
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<StructureSection load='1smn' size='340' side='right'caption='[[1smn]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<table><tr><td colspan='2'>[[1smn]] 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=1SMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SMN FirstGlance]. <br>
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|ACTIVITY= [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]
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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]] 2.04&#8491;</td></tr>
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|GENE= NUCA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=615 Serratia marcescens])
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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=1smn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1smn OCA], [https://pdbe.org/1smn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1smn RCSB], [https://www.ebi.ac.uk/pdbsum/1smn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1smn ProSAT]</span></td></tr>
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}}
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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/sm/1smn_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=1smn 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 Serratia endonuclease is an extracellularly secreted enzyme capable of cleaving both single- and double-stranded forms of DNA and RNA. It is the first member of a large class of related and usually dimeric endonucleases for which a structure is known. Using X-ray crystallography, the structure of monomer of this enzyme was reported by us previously (Miller MD et al., 1994, Nature Struct Biol 1:461-468). We now confirm the dimeric nature of this enzyme through light-scattering experiments and identify the physiologic dimer interface through crystal packing analysis. This dimerization occurs through an isologous twofold interaction localized to the carboxy-terminal subdomain of the enzyme. The dimer is a prolate ellipsoid with dimensions 30 A x 35 A x 90 A. The dimer interface is flat and contains four salt links, several hydrogen bonds, and nonpolar interactions. Buried water is prominent in this interface and it includes an unusual "cubic" water cluster. The position of the two active sites in the dimer suggests that they can act independently in their cleavage of DNA, but have a geometrical advantage in attacking substrate relative to the monomer.
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'''IDENTIFICATION OF THE SERRATIA ENDONUCLEASE DIMER: STRUCTURAL BASIS AND IMPLICATIONS FOR CATALYSIS'''
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Identification of the Serratia endonuclease dimer: structural basis and implications for catalysis.,Miller MD, Krause KL Protein Sci. 1996 Jan;5(1):24-33. PMID:8771193<ref>PMID:8771193</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 1smn" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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The Serratia endonuclease is an extracellularly secreted enzyme capable of cleaving both single- and double-stranded forms of DNA and RNA. It is the first member of a large class of related and usually dimeric endonucleases for which a structure is known. Using X-ray crystallography, the structure of monomer of this enzyme was reported by us previously (Miller MD et al., 1994, Nature Struct Biol 1:461-468). We now confirm the dimeric nature of this enzyme through light-scattering experiments and identify the physiologic dimer interface through crystal packing analysis. This dimerization occurs through an isologous twofold interaction localized to the carboxy-terminal subdomain of the enzyme. The dimer is a prolate ellipsoid with dimensions 30 A x 35 A x 90 A. The dimer interface is flat and contains four salt links, several hydrogen bonds, and nonpolar interactions. Buried water is prominent in this interface and it includes an unusual "cubic" water cluster. The position of the two active sites in the dimer suggests that they can act independently in their cleavage of DNA, but have a geometrical advantage in attacking substrate relative to the monomer.
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1SMN is a [[Single protein]] structure of sequence 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=1SMN OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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Identification of the Serratia endonuclease dimer: structural basis and implications for catalysis., Miller MD, Krause KL, Protein Sci. 1996 Jan;5(1):24-33. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8771193 8771193]
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[[Category: Serratia marcescens]]
[[Category: Serratia marcescens]]
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[[Category: Serratia marcescens nuclease]]
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[[Category: Krause KL]]
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[[Category: Single protein]]
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[[Category: Miller MD]]
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[[Category: Krause, K L.]]
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[[Category: Miller, M D.]]
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[[Category: dnase]]
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[[Category: nuclease]]
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[[Category: rnase]]
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[[Category: sugar-nonspecific nuclease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:06:58 2008''
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Current revision

IDENTIFICATION OF THE SERRATIA ENDONUCLEASE DIMER: STRUCTURAL BASIS AND IMPLICATIONS FOR CATALYSIS

PDB ID 1smn

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