|
|
| (2 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal Structure of Flap Endonuclease-1 R42E mutant from Pyrococcus horikoshii== | | ==Crystal Structure of Flap Endonuclease-1 R42E mutant from Pyrococcus horikoshii== |
| - | <StructureSection load='1mc8' size='340' side='right' caption='[[1mc8]], [[Resolution|resolution]] 3.10Å' scene=''> | + | <StructureSection load='1mc8' size='340' side='right'caption='[[1mc8]], [[Resolution|resolution]] 3.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1mc8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MC8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MC8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1mc8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MC8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MC8 FirstGlance]. <br> |
| - | </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=1mc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mc8 OCA], [http://pdbe.org/1mc8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mc8 RCSB], [http://www.ebi.ac.uk/pdbsum/1mc8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1mc8 ProSAT]</span></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]] 3.1Å</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=1mc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mc8 OCA], [https://pdbe.org/1mc8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mc8 RCSB], [https://www.ebi.ac.uk/pdbsum/1mc8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mc8 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/FEN_PYRHO FEN_PYRHO]] Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Binds the unpaired 3'-DNA end and kinks the DNA to facilitate 5' cleavage specificity. Cleaves one nucleotide into the double-stranded DNA from the junction in flap DNA, leaving a nick for ligation. Also involved in the base excision repair (BER) pathway. Acts as a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA (By similarity). | + | [https://www.uniprot.org/uniprot/FEN_PYRHO FEN_PYRHO] Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Binds the unpaired 3'-DNA end and kinks the DNA to facilitate 5' cleavage specificity. Cleaves one nucleotide into the double-stranded DNA from the junction in flap DNA, leaving a nick for ligation. Also involved in the base excision repair (BER) pathway. Acts as a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA (By similarity). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 27: |
Line 28: |
| | </div> | | </div> |
| | <div class="pdbe-citations 1mc8" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 1mc8" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pyrococcus shinkaii]] | + | [[Category: Large Structures]] |
| - | [[Category: Abe, J]] | + | [[Category: Pyrococcus horikoshii]] |
| - | [[Category: Harata, K]] | + | [[Category: Abe J]] |
| - | [[Category: Matsui, E]] | + | [[Category: Harata K]] |
| - | [[Category: Matsui, I]] | + | [[Category: Matsui E]] |
| - | [[Category: Musti, K V]] | + | [[Category: Matsui I]] |
| - | [[Category: Yamazaki, K]] | + | [[Category: Musti KV]] |
| - | [[Category: Flexible loop]]
| + | [[Category: Yamazaki K]] |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
FEN_PYRHO Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Binds the unpaired 3'-DNA end and kinks the DNA to facilitate 5' cleavage specificity. Cleaves one nucleotide into the double-stranded DNA from the junction in flap DNA, leaving a nick for ligation. Also involved in the base excision repair (BER) pathway. Acts as a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA (By similarity).
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
The crystal structure of flap endonuclease-1 from Pyrococcus horikoshii (phFEN-1) was determined to a resolution of 3.1 A. The active cleft of the phFEN-1 molecule is formed with one large loop and four small loops. We examined the function of the conserved residues and positively charged clusters on these loops by kinetic analysis with 45 different mutants. Arg(40) and Arg(42) on small loop 1, a cluster Lys(193)-Lys(195) on small loop 2, and two sites, Arg(94) and Arg(118)-Lys(119), on the large loop were identified as binding sites. Lys(87) on the large loop may play significant roles in catalytic reaction. Furthermore, we successfully elucidated the function of the four DNA binding sites that form productive ES complexes specific for each endo- or exo-type hydrolysis, probably by bending the substrates. For the endo-activity, Arg(94) and Lys(193)-Lys(195) located at the top and bottom of the molecule were key determinants. For the exo-activity, all four sites were needed, but Arg(118)-Lys(119) was dominant. The major binding sites for both the nick substrate and double-stranded DNA might be the same.
Molecular structure and novel DNA binding sites located in loops of flap endonuclease-1 from Pyrococcus horikoshii.,Matsui E, Musti KV, Abe J, Yamasaki K, Matsui I, Harata K J Biol Chem. 2002 Oct 4;277(40):37840-7. Epub 2002 Jul 29. PMID:12147694[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Matsui E, Musti KV, Abe J, Yamasaki K, Matsui I, Harata K. Molecular structure and novel DNA binding sites located in loops of flap endonuclease-1 from Pyrococcus horikoshii. J Biol Chem. 2002 Oct 4;277(40):37840-7. Epub 2002 Jul 29. PMID:12147694 doi:10.1074/jbc.M205235200
|
