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==Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus==
==Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus==
<StructureSection load='3jsl' size='340' side='right' caption='[[3jsl]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='3jsl' size='340' side='right'caption='[[3jsl]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3jsl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JSL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JSL FirstGlance]. <br>
<table><tr><td colspan='2'>[[3jsl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JSL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JSL FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 1.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3jsn|3jsn]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</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=3jsl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jsl OCA], [https://pdbe.org/3jsl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jsl RCSB], [https://www.ebi.ac.uk/pdbsum/3jsl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jsl ProSAT]</span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2] </span></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=3jsl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jsl OCA], [http://pdbe.org/3jsl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jsl RCSB], [http://www.ebi.ac.uk/pdbsum/3jsl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jsl ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DNLJ_STAAU DNLJ_STAAU]
== 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=3jsl 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=3jsl ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DNA ligase catalyzes phosphodiester-bond formation between immediately adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA and plays a central role in many cellular and biochemical processes, including DNA replication, repair and recombination. Bacterial NAD(+)-dependent DNA ligases have been extensively characterized as potential antibacterial targets because of their essentiality and their structural distinction from human ATP-dependent DNA ligases. The high-resolution structure of the adenylation domain of Staphylococcus aureus NAD(+)-dependent DNA ligase establishes the conserved domain architecture with other bacterial adenylation domains. Two apo crystal structures revealed that the active site possesses the preformed NAD(+)-binding pocket and the 'C2 tunnel' lined with hydrophobic residues: Leu80, Phe224, Leu287, Phe295 and Trp302. The C2 tunnel is unique to bacterial DNA ligases and the Leu80 side chain at the mouth of the tunnel points inside the tunnel and forms a narrow funnel in the S. aureus DNA ligase structure. Taken together with other DNA ligase structures, the S. aureus DNA ligase structure provides a basis for a more integrated understanding of substrate recognition and catalysis and will be also be of help in the development of small-molecule inhibitors.
Structure of the adenylation domain of NAD(+)-dependent DNA ligase from Staphylococcus aureus.,Han S, Chang JS, Griffor M Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Nov 1;65(Pt, 11):1078-82. Epub 2009 Oct 13. PMID:19923722<ref>PMID:19923722</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3jsl" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[DNA ligase|DNA ligase]]
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Chang, J S]]
[[Category: Large Structures]]
[[Category: Griffor, M]]
[[Category: Han, S]]
[[Category: Dna damage]]
[[Category: Dna ligase]]
[[Category: Dna repair]]
[[Category: Dna replication]]
[[Category: Ligase]]
[[Category: Magnesium]]
[[Category: Manganese]]
[[Category: Metal-binding]]
[[Category: Nad]]
[[Category: Nad+-dependent]]
[[Category: Staphylococcus aureus]]
[[Category: Staphylococcus aureus]]
[[Category: Zinc]]
[[Category: Chang JS]]
[[Category: Griffor M]]
[[Category: Han S]]

Latest revision as of 10:13, 21 February 2024

Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus

3jsl, resolution 1.80Å

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