|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==T5 5'-EXONUCLEASE MUTANT K83A== | | ==T5 5'-EXONUCLEASE MUTANT K83A== |
| - | <StructureSection load='1xo1' size='340' side='right' caption='[[1xo1]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='1xo1' size='340' side='right'caption='[[1xo1]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1xo1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt5 Bpt5]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XO1 FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">D15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10726 BPT5])</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]] 2.5Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></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=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> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/1xo1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xo1 RCSB], [http://www.ebi.ac.uk/pdbsum/1xo1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xo1 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/EXO5_BPT5 EXO5_BPT5]] 5'-exonucleolytic degradation of double-stranded (ds) DNA. Can also cleave bifurcated nucleic acids such as flap and pseudo-Y substrates in a structure-specific manner. This requires free 5' single-stranded (ss) ends and cleaves at the ds/ss junction. Binds DNA pseudo-Y substrates with a dissociation constant of 5 nM. | + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 31: |
Line 30: |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Exonuclease|Exonuclease]] | + | *[[Exonuclease 3D structures|Exonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bpt5]] | + | [[Category: Escherichia virus T5]] |
| - | [[Category: Ceska, T A]] | + | [[Category: Large Structures]] |
| - | [[Category: Sayers, J R]] | + | [[Category: Ceska TA]] |
| - | [[Category: Suck, D]] | + | [[Category: Sayers JR]] |
| - | [[Category: Exonuclease]] | + | [[Category: Suck D]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Nuclease]]
| + | |
| Structural highlights
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
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.
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[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
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
- ↑ 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
|
