4cxo: Difference between revisions
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==bifunctional endonuclease in complex with ssDNA== | ==bifunctional endonuclease in complex with ssDNA== | ||
<StructureSection load='4cxo' size='340' side='right' caption='[[4cxo]], [[Resolution|resolution]] 1.67Å' scene=''> | <StructureSection load='4cxo' size='340' side='right'caption='[[4cxo]], [[Resolution|resolution]] 1.67Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4cxo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CXO OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[4cxo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CXO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CXO FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=D5M:2-DEOXYADENOSINE-5-MONOPHOSPHATE'>D5M</scene>, <scene name='pdbligand= | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.67Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=D5M:2-DEOXYADENOSINE-5-MONOPHOSPHATE'>D5M</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | |||
<tr | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4cxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cxo OCA], [https://pdbe.org/4cxo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cxo RCSB], [https://www.ebi.ac.uk/pdbsum/4cxo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cxo ProSAT]</span></td></tr> | ||
</table> | |||
<table> | == Function == | ||
[https://www.uniprot.org/uniprot/ENDO2_ARATH ENDO2_ARATH] Probable endonuclease (By similarity). Can not hydrolyze single stranded DNA and does not cleave mismatches. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The multi S1/P1 nuclease AtBFN2 (EC 3.1.30.1) encoded by the Arabidopsis thaliana At1g68290 gene is a glycoprotein that digests RNA, ssDNA, and dsDNA. AtBFN2 depends on three zinc ions for cleaving DNA and RNA at 3'-OH to yield 5'-nucleotides. In addition, AtBFN2's enzymatic activity is strongly glycan dependent. Plant Zn(2+)-dependent endonucleases present a unique fold, and belong to the Phospholipase C (PLC)/P1 nuclease superfamily. In this work, we present the first complete, ligand-free, AtBFN2 crystal structure, along with sulfate, phosphate and ssDNA co-crystal structures. With these, we were able to provide better insight into the glycan structure and possible enzymatic mechanism. In comparison with other nucleases, the AtBFN2/ligand-free and AtBFN2/PO4 models suggest a similar, previously proposed, catalytic mechanism. Our data also confirm that the phosphate and vanadate can inhibit the enzyme activity by occupying the active site. More importantly, the AtBFN2/A5T structure reveals a novel and conserved secondary binding site, which seems to be important for plant Zn(2+)-dependent endonucleases. Based on these findings, we propose a rational ssDNA binding model, in which the ssDNA wraps itself around the protein and the attached surface glycan, in turn, reinforces the binding complex. | |||
Structural insights of the ssDNA binding site in the multifunctional endonuclease AtBFN2 from Arabidopsis thaliana.,Yu TF, Maestre-Reyna M, Ko CY, Ko TP, Sun YJ, Lin TY, Shaw JF, Wang AH PLoS One. 2014 Aug 26;9(8):e105821. doi: 10.1371/journal.pone.0105821., eCollection 2014. PMID:25157844<ref>PMID:25157844</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4cxo" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Endonuclease 3D structures|Endonuclease 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Ko | [[Category: Arabidopsis thaliana]] | ||
[[Category: Ko | [[Category: Large Structures]] | ||
[[Category: Lin | [[Category: Ko C-Y]] | ||
[[Category: Maestre-Reyna | [[Category: Ko T-P]] | ||
[[Category: Shaw | [[Category: Lin T-Y]] | ||
[[Category: Sun | [[Category: Maestre-Reyna M]] | ||
[[Category: Wang | [[Category: Shaw J-F]] | ||
[[Category: Yu | [[Category: Sun Y-J]] | ||
[[Category: Wang AH-J]] | |||
[[Category: Yu T-F]] | |||