1a76: Difference between revisions

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==FLAP ENDONUCLEASE-1 FROM METHANOCOCCUS JANNASCHII==
==FLAP ENDONUCLEASE-1 FROM METHANOCOCCUS JANNASCHII==
<StructureSection load='1a76' size='340' side='right' caption='[[1a76]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='1a76' size='340' side='right'caption='[[1a76]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1a76]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A76 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1A76 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1a76]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A76 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A76 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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&#8491;</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=1a76 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a76 OCA], [http://pdbe.org/1a76 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1a76 RCSB], [http://www.ebi.ac.uk/pdbsum/1a76 PDBsum]</span></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=1a76 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a76 OCA], [https://pdbe.org/1a76 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a76 RCSB], [https://www.ebi.ac.uk/pdbsum/1a76 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a76 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/FEN_METJA FEN_METJA]] 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.  
[https://www.uniprot.org/uniprot/FEN_METJA FEN_METJA] 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.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a7/1a76_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a7/1a76_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 18: Line 20:
</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=1a76 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=1a76 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), a structure specific nuclease, is an essential enzyme for eukaryotic DNA replication and repair. The crystal structure of FEN-1 from Methanococcus jannaschii, determined at 2.0 A resolution, reveals an active site with two metal ions residing on top of a deep cleft where several conserved acidic residues are clustered. Near the active site, a long flexible loop comprised of many basic and aromatic residues forms a hole large enough to accommodate the DNA substrate. Deletion mutations in this loop significantly decreased the nuclease activity and specificity of FEN-1, suggesting that the loop is critical for recognition and cleavage of the junction between single and double-stranded regions of flap DNA.
The crystal structure of flap endonuclease-1 from Methanococcus jannaschii.,Hwang KY, Baek K, Kim HY, Cho Y Nat Struct Biol. 1998 Aug;5(8):707-13. PMID:9699635<ref>PMID:9699635</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1a76" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Endonuclease|Endonuclease]]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Baek, K]]
[[Category: Baek K]]
[[Category: Cho, Y]]
[[Category: Cho Y]]
[[Category: Hwang, K Y]]
[[Category: Hwang KY]]
[[Category: Kim, H]]
[[Category: Kim H]]
[[Category: 5'-3' exo-endo nuclease complex]]
[[Category: 5'-3' exo/endo nuclease]]
[[Category: Dna repair]]
[[Category: Dna replication]]
[[Category: Rad27]]
[[Category: Rth]]

Latest revision as of 09:28, 7 February 2024

FLAP ENDONUCLEASE-1 FROM METHANOCOCCUS JANNASCHIIFLAP ENDONUCLEASE-1 FROM METHANOCOCCUS JANNASCHII

Structural highlights

1a76 is a 1 chain structure with sequence from Methanocaldococcus jannaschii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FEN_METJA 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.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1a76, resolution 2.00Å

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