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1ut5

From Proteopedia

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Divalent metal ions (manganese) bound to T5 5'-exonuclease

Structural highlights

1ut5 is a 2 chain structure with sequence from Escherichia virus T5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.75Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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]^[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 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^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Pickering TJ, Garforth S, Sayers JR, Grasby JA. Variation in the steady state kinetic parameters of wild type and mutant T5 5'-3'-exonuclease with pH. Protonation of Lys-83 is critical for DNA binding. J Biol Chem. 1999 Jun 18;274(25):17711-7. PMID:10364212
↑ Feng M, Patel D, Dervan JJ, Ceska T, Suck D, Haq I, Sayers JR. Roles of divalent metal ions in flap endonuclease-substrate interactions. Nat Struct Mol Biol. 2004 May;11(5):450-6. Epub 2004 Apr 11. PMID:15077103 doi:10.1038/nsmb754
↑ Garforth SJ, Ceska TA, Suck D, Sayers JR. Mutagenesis of conserved lysine residues in bacteriophage T5 5'-3' exonuclease suggests separate mechanisms of endo-and exonucleolytic cleavage. Proc Natl Acad Sci U S A. 1999 Jan 5;96(1):38-43. PMID:9874768
↑ Feng M, Patel D, Dervan JJ, Ceska T, Suck D, Haq I, Sayers JR. Roles of divalent metal ions in flap endonuclease-substrate interactions. Nat Struct Mol Biol. 2004 May;11(5):450-6. Epub 2004 Apr 11. PMID:15077103 doi:10.1038/nsmb754

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ut5"

Categories: Escherichia virus T5 | Large Structures | Ceska TA | Sayers JR | Suck D

@@ Line 3: / Line 3: @@
 <StructureSection load='1ut5' size='340' side='right'caption='[[1ut5]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ut5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpt5 Bpt5]. 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>
+<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='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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.75&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1exn|1exn]], [[1j5f|1j5f]], [[1ut8|1ut8]], [[1xo1|1xo1]]</div></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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </span></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]]
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Bpt5]]
+[[Category: Escherichia virus T5]]
 [[Category: Large Structures]]
-[[Category: Ceska, T A]]
+[[Category: Ceska TA]]
-[[Category: Sayers, J R]]
+[[Category: Sayers JR]]
-[[Category: Suck, D]]
+[[Category: Suck D]]
-[[Category: Exonuclease]]
-[[Category: Hydrolase]]
-[[Category: Nuclease]]

1ut5

From Proteopedia

Current revision

Divalent metal ions (manganese) bound to T5 5'-exonuclease

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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