1rxv: Difference between revisions

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<StructureSection load='1rxv' size='340' side='right'caption='[[1rxv]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='1rxv' size='340' side='right'caption='[[1rxv]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1rxv]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RXV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1RXV FirstGlance]. <br>
<table><tr><td colspan='2'>[[1rxv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RXV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RXV FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1rwz|1rwz]], [[1rxq|1rxq]], [[1rxw|1rxw]], [[1rxz|1rxz]]</div></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]] 2.5&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">FEN, AF0264 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</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=1rxv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxv OCA], [https://pdbe.org/1rxv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rxv RCSB], [https://www.ebi.ac.uk/pdbsum/1rxv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rxv ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1rxv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxv OCA], [http://pdbe.org/1rxv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rxv RCSB], [http://www.ebi.ac.uk/pdbsum/1rxv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rxv ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/FEN_ARCFU FEN_ARCFU]] 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_ARCFU FEN_ARCFU] 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]]
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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=1rxv ConSurf].
</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=1rxv ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Flap EndoNuclease-1 (FEN-1) and the processivity factor proliferating cell nuclear antigen (PCNA) are central to DNA replication and repair. To clarify the molecular basis of FEN-1 specificity and PCNA activation, we report here structures of FEN-1:DNA and PCNA:FEN-1-peptide complexes, along with fluorescence resonance energy transfer (FRET) and mutational results. FEN-1 binds the unpaired 3' DNA end (3' flap), opens and kinks the DNA, and promotes conformational closing of a flexible helical clamp to facilitate 5' cleavage specificity. Ordering of unstructured C-terminal regions in FEN-1 and PCNA creates an intermolecular beta sheet interface that directly links adjacent PCNA and DNA binding regions of FEN-1 and suggests how PCNA stimulates FEN-1 activity. The DNA and protein conformational changes, composite complex structures, FRET, and mutational results support enzyme-PCNA alignments and a kinked DNA pivot point that appear suitable to coordinate rotary handoffs of kinked DNA intermediates among enzymes localized by the three PCNA binding sites.
Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair.,Chapados BR, Hosfield DJ, Han S, Qiu J, Yelent B, Shen B, Tainer JA Cell. 2004 Jan 9;116(1):39-50. PMID:14718165<ref>PMID:14718165</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1rxv" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Arcfl]]
[[Category: Archaeoglobus fulgidus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Chapados, B R]]
[[Category: Chapados BR]]
[[Category: Han, S]]
[[Category: Han S]]
[[Category: Hosfield, D J]]
[[Category: Hosfield DJ]]
[[Category: Qiu, J]]
[[Category: Qiu J]]
[[Category: Shen, B]]
[[Category: Shen B]]
[[Category: Tainer, J A]]
[[Category: Tainer JA]]
[[Category: Yelent, B]]
[[Category: Yelent B]]
[[Category: 3' flap binding site]]
[[Category: Dna repair]]
[[Category: Dna replication]]
[[Category: Helical clamp]]
[[Category: Helix-3 turn-helix]]
[[Category: Hydrolase-dna complex]]
[[Category: Protein-dna complex]]
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