1xo1

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[[Image:1xo1.jpg|left|200px]]
 
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{{Structure
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==T5 5'-EXONUCLEASE MUTANT K83A==
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|PDB= 1xo1 |SIZE=350|CAPTION= <scene name='initialview01'>1xo1</scene>, resolution 2.5&Aring;
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<StructureSection load='1xo1' size='340' side='right'caption='[[1xo1]], [[Resolution|resolution]] 2.50&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'>[[1xo1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T5 Escherichia virus T5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XO1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XO1 FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </span>
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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]] 2.5&#8491;</td></tr>
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|GENE= D15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10726 Enterobacteria phage T5])
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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=1xo1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xo1 OCA], [https://pdbe.org/1xo1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xo1 RCSB], [https://www.ebi.ac.uk/pdbsum/1xo1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xo1 ProSAT]</span></td></tr>
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|DOMAIN=
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</table>
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|RELATEDENTRY=
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== Function ==
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xo1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xo1 OCA], [http://www.ebi.ac.uk/pdbsum/1xo1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xo1 RCSB]</span>
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[https://www.uniprot.org/uniprot/FEN_BPT5 FEN_BPT5] Catalyzes both the 5'-exonucleolytic and structure-specific endonucleolytic hydrolysis of DNA branched nucleic acid molecules and probably plays a role in viral genome replication (PubMed:9874768, PubMed:15077103, PubMed:10364212). Active on flap (branched duplex DNA containing a free single-stranded 5'-end), 5'overhangs and pseudo-Y structures (PubMed:9874768, PubMed:15077103, PubMed:10364212). The substrates require a free, single-stranded 5' end, with endonucleolytic hydrolysis occurring at the junction of double- and single-stranded DNA (PubMed:9874768). This function may be used for example to trim such branched molecules generated by Okazaki fragments synthesis during replication.[HAMAP-Rule:MF_04140]<ref>PMID:10364212</ref> <ref>PMID:15077103</ref> <ref>PMID:9874768</ref>
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}}
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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'''T5 5'-EXONUCLEASE MUTANT K83A'''
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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/xo/1xo1_consurf.spt"</scriptWhenChecked>
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==Overview==
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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=1xo1 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 ==
Efficient cellular DNA replication requires the activity of a 5'-3' exonuclease. These enzymes are able to hydrolyze DNA.DNA and RNA.DNA substrates exonucleolytically, and they are structure-specific endonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. Crystal structures of three representative enzymes identify two divalent-metal-binding sites typically separated by 8-10 A. Site-directed mutagenesis was used to investigate the roles of three lysine residues (K83, K196, and K215) situated near two metal-binding sites in bacteriophage T5 5'-3' exonuclease. Neither K196 nor K215 was essential for either the exo- or the endonuclease activity, but mutation of these residues increased the dissociation constant for the substrate from 5 nM to 200 nM (K196A) and 50 nM (K215A). Biochemical analysis demonstrated that K83 is absolutely required for exonucleolytic activity on single-stranded DNA but is not required for endonucleolytic cleavage of flap structures. Structural analysis of this mutant by x-ray crystallography showed no significant perturbations around the metal-binding sites in the active site. The wild-type protein has different pH optima for endonuclease and exonuclease activities. Taken together, these results suggest that different mechanisms for endo- and exonucleolytic hydrolysis are used by this multifunctional enzyme.
Efficient cellular DNA replication requires the activity of a 5'-3' exonuclease. These enzymes are able to hydrolyze DNA.DNA and RNA.DNA substrates exonucleolytically, and they are structure-specific endonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. Crystal structures of three representative enzymes identify two divalent-metal-binding sites typically separated by 8-10 A. Site-directed mutagenesis was used to investigate the roles of three lysine residues (K83, K196, and K215) situated near two metal-binding sites in bacteriophage T5 5'-3' exonuclease. Neither K196 nor K215 was essential for either the exo- or the endonuclease activity, but mutation of these residues increased the dissociation constant for the substrate from 5 nM to 200 nM (K196A) and 50 nM (K215A). Biochemical analysis demonstrated that K83 is absolutely required for exonucleolytic activity on single-stranded DNA but is not required for endonucleolytic cleavage of flap structures. Structural analysis of this mutant by x-ray crystallography showed no significant perturbations around the metal-binding sites in the active site. The wild-type protein has different pH optima for endonuclease and exonuclease activities. Taken together, these results suggest that different mechanisms for endo- and exonucleolytic hydrolysis are used by this multifunctional enzyme.
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==About this Structure==
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Mutagenesis of conserved lysine residues in bacteriophage T5 5'-3' exonuclease suggests separate mechanisms of endo-and exonucleolytic cleavage.,Garforth SJ, Ceska TA, Suck D, Sayers JR Proc Natl Acad Sci U S A. 1999 Jan 5;96(1):38-43. PMID:9874768<ref>PMID:9874768</ref>
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1XO1 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t5 Enterobacteria phage t5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XO1 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Mutagenesis of conserved lysine residues in bacteriophage T5 5'-3' exonuclease suggests separate mechanisms of endo-and exonucleolytic cleavage., Garforth SJ, Ceska TA, Suck D, Sayers JR, Proc Natl Acad Sci U S A. 1999 Jan 5;96(1):38-43. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9874768 9874768]
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</div>
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[[Category: Enterobacteria phage t5]]
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<div class="pdbe-citations 1xo1" style="background-color:#fffaf0;"></div>
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[[Category: Exodeoxyribonuclease (lambda-induced)]]
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[[Category: Single protein]]
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[[Category: Ceska, T A.]]
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[[Category: Sayers, J R.]]
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[[Category: Suck, D.]]
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[[Category: exonuclease]]
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[[Category: hydrolase]]
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[[Category: nuclease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:52:18 2008''
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==See Also==
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*[[Exonuclease 3D structures|Exonuclease 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Escherichia virus T5]]
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[[Category: Large Structures]]
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[[Category: Ceska TA]]
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[[Category: Sayers JR]]
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[[Category: Suck D]]

Current revision

T5 5'-EXONUCLEASE MUTANT K83A

PDB ID 1xo1

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