1ut5: Difference between revisions
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==Divalent metal ions (manganese) bound to T5 5'-exonuclease== | |||
<StructureSection load='1ut5' size='340' side='right'caption='[[1ut5]], [[Resolution|resolution]] 2.75Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1ut5]] 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=1UT5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UT5 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.75Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ut5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ut5 OCA], [https://pdbe.org/1ut5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ut5 RCSB], [https://www.ebi.ac.uk/pdbsum/1ut5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ut5 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[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> | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ut/1ut5_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</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=1ut5 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Flap endonucleases (FENs) have essential roles in DNA processing. They catalyze exonucleolytic and structure-specific endonucleolytic DNA cleavage reactions. Divalent metal ions are essential cofactors in both reactions. The crystal structure of FEN shows that the protein has two conserved metal-binding sites. Mutations in site I caused complete loss of catalytic activity. Mutation of crucial aspartates in site II abolished exonuclease action, but caused enzymes to retain structure-specific (flap endonuclease) activity. Isothermal titration calorimetry revealed that site I has a 30-fold higher affinity for cofactor than site II. Structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity site, whereas exonuclease activity requires that both the high- and low-affinity sites be occupied by divalent cofactor. The data suggest that a novel two-metal mechanism operates in the FEN-catalyzed exonucleolytic reaction. These results raise the possibility that local concentrations of free cofactor could influence the endo- or exonucleolytic pathway in vivo. | |||
Roles of divalent metal ions in flap endonuclease-substrate interactions.,Feng M, Patel D, Dervan JJ, Ceska T, Suck D, Haq I, Sayers JR Nat Struct Mol Biol. 2004 May;11(5):450-6. Epub 2004 Apr 11. PMID:15077103<ref>PMID:15077103</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1ut5" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Exonuclease 3D structures|Exonuclease 3D structures]] | |||
== References == | |||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: Ceska | </StructureSection> | ||
[[Category: Sayers | [[Category: Escherichia virus T5]] | ||
[[Category: Suck | [[Category: Large Structures]] | ||
[[Category: Ceska TA]] | |||
[[Category: Sayers JR]] | |||
[[Category: Suck D]] | |||
Latest revision as of 15:57, 13 December 2023
Divalent metal ions (manganese) bound to T5 5'-exonucleaseDivalent metal ions (manganese) bound to T5 5'-exonuclease
Structural highlights
FunctionFEN_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][1] [2] [3] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedFlap endonucleases (FENs) have essential roles in DNA processing. They catalyze exonucleolytic and structure-specific endonucleolytic DNA cleavage reactions. Divalent metal ions are essential cofactors in both reactions. The crystal structure of FEN shows that the protein has two conserved metal-binding sites. Mutations in site I caused complete loss of catalytic activity. Mutation of crucial aspartates in site II abolished exonuclease action, but caused enzymes to retain structure-specific (flap endonuclease) activity. Isothermal titration calorimetry revealed that site I has a 30-fold higher affinity for cofactor than site II. Structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity site, whereas exonuclease activity requires that both the high- and low-affinity sites be occupied by divalent cofactor. The data suggest that a novel two-metal mechanism operates in the FEN-catalyzed exonucleolytic reaction. These results raise the possibility that local concentrations of free cofactor could influence the endo- or exonucleolytic pathway in vivo. Roles of divalent metal ions in flap endonuclease-substrate interactions.,Feng M, Patel D, Dervan JJ, Ceska T, Suck D, Haq I, Sayers JR Nat Struct Mol Biol. 2004 May;11(5):450-6. Epub 2004 Apr 11. PMID:15077103[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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