3ory

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Current revision (11:18, 21 February 2024) (edit) (undo)
 
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<StructureSection load='3ory' size='340' side='right'caption='[[3ory]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3ory' size='340' side='right'caption='[[3ory]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3ory]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desam Desam]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ORY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ORY FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3ory]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfurococcus_amylolyticus Desulfurococcus amylolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ORY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ORY FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=3ory FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ory OCA], [https://pdbe.org/3ory PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ory RCSB], [https://www.ebi.ac.uk/pdbsum/3ory PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ory ProSAT]</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=3ory FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ory OCA], [https://pdbe.org/3ory PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ory RCSB], [https://www.ebi.ac.uk/pdbsum/3ory PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ory ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/F2Z289_DESAM F2Z289_DESAM] 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 structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA.[HAMAP-Rule:MF_00614]
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Flap endonuclease 1 (FEN1) is a key enzyme in DNA repair and DNA replication. It is a structure-specific nuclease that removes 5'-overhanging flaps and the RNA/DNA primer during maturation of the Okazaki fragment. Homologues of FEN1 exist in a wide range of bacteria, archaea and eukaryotes. In order to further understand the structural basis of the DNA recognition, binding and cleavage mechanism of FEN1, the structure of FEN1 from the hyperthermophilic archaeon Desulfurococcus amylolyticus (DaFEN1) was determined at 2.00 A resolution. The overall fold of DaFEN1 was similar to those of other archaeal FEN1 proteins; however, the helical clamp and the flexible loop exhibited a putative substrate-binding pocket with a unique conformation.
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Structure of flap endonuclease 1 from the hyperthermophilic archaeon Desulfurococcus amylolyticus.,Mase T, Kubota K, Miyazono K, Kawarabayasi Y, Tanokura M Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Feb 1;67(Pt, 2):209-13. Epub 2011 Jan 21. PMID:21301087<ref>PMID:21301087</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3ory" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Desam]]
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[[Category: Desulfurococcus amylolyticus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Kawarabayashii, Y]]
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[[Category: Kawarabayashii Y]]
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[[Category: Kubota, K]]
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[[Category: Kubota K]]
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[[Category: Mase, T]]
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[[Category: Mase T]]
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[[Category: Miyazono, K]]
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[[Category: Miyazono K]]
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[[Category: Tanokura, M]]
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[[Category: Tanokura M]]
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[[Category: Endonuclease]]
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[[Category: Hydrolase]]
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Current revision

Crystal structure of Flap endonuclease 1 from hyperthermophilic archaeon Desulfurococcus amylolyticus

PDB ID 3ory

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