1fvi: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1fvi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlorella_virus Chlorella virus]. The July 2004 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''DNA Ligase''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2004_7 10.2210/rcsb_pdb/mom_2004_7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FVI FirstGlance]. <br>
<table><tr><td colspan='2'>[[1fvi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlorella_virus Chlorella virus]. The July 2004 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''DNA Ligase''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2004_7 10.2210/rcsb_pdb/mom_2004_7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FVI FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1fvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fvi OCA], [https://pdbe.org/1fvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fvi RCSB], [https://www.ebi.ac.uk/pdbsum/1fvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fvi 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=1fvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fvi OCA], [https://pdbe.org/1fvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fvi RCSB], [https://www.ebi.ac.uk/pdbsum/1fvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fvi ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/A7RCB1_PBCVA A7RCB1_PBCVA]
== 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=1fvi 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=1fvi ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Chlorella virus DNA ligase is the smallest eukaryotic ATP-dependent ligase known; it has an intrinsic nick-sensing function and suffices for yeast cell growth. Here, we report the 2.0 A crystal structure of the covalent ligase-AMP reaction intermediate. The conformation of the adenosine nucleoside and contacts between the enzyme and the ribose sugar have undergone a significant change compared to complexes of T7 ligase with ATP or mRNA capping enzyme with GTP. The conformational switch allows the 3' OH of AMP to coordinate directly the 5' PO(4) of the nick. The structure explains why nick sensing is restricted to adenylated ligase and why the 5' phosphate is required for DNA binding. We identify a metal binding site on ligase-adenylate and propose a mechanism of nick recognition and catalysis supported by mutational data.
Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining.,Odell M, Sriskanda V, Shuman S, Nikolov DB Mol Cell. 2000 Nov;6(5):1183-93. PMID:11106756<ref>PMID:11106756</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1fvi" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Nikolov, D B]]
[[Category: Nikolov DB]]
[[Category: Odell, M]]
[[Category: Odell M]]
[[Category: Shuman, S]]
[[Category: Shuman S]]
[[Category: Sriskanda, V]]
[[Category: Sriskanda V]]
[[Category: Adenylated dna ligase]]
[[Category: Ligase]]

Revision as of 11:17, 27 March 2024

CRYSTAL STRUCTURE OF CHLORELLA VIRUS DNA LIGASE-ADENYLATE

1fvi, resolution 2.00Å

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