1a0i: Difference between revisions

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 <StructureSection load='1a0i' size='340' side='right'caption='[[1a0i]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1a0i]] is a 1 chain structure. The July 2004 RCSB PDB [http://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 [http://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=1A0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1A0I FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1a0i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7]. 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=1A0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A0I FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</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]] 2.6&#8491;</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_(ATP) DNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.1 6.5.1.1] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene></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=1a0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a0i OCA], [http://pdbe.org/1a0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1a0i RCSB], [http://www.ebi.ac.uk/pdbsum/1a0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1a0i 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=1a0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a0i OCA], [https://pdbe.org/1a0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a0i RCSB], [https://www.ebi.ac.uk/pdbsum/1a0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a0i ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DNLI_BPT7 DNLI_BPT7]] DNA ligase, which is expressed in the early stage of lytic development, has been implicated in T7 DNA synthesis and genetic recombination. It may also play a role in T7 DNA repair.
+[https://www.uniprot.org/uniprot/DNLI_BPT7 DNLI_BPT7] DNA ligase, which is expressed in the early stage of lytic development, has been implicated in T7 DNA synthesis and genetic recombination. It may also play a role in T7 DNA repair.
 == Evolutionary Conservation ==
 [[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=1a0i ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The crystal structure of the ATP-dependent DNA ligase from bacteriophage T7 has been solved at 2.6 A resolution. The protein comprises two domains with a deep cleft running between them. The structure of a complex with ATP reveals that the nucleotide binding pocket is situated on the larger N-terminal domain, at the base of the cleft between the two domains of the enzyme. Comparison of the overall domain structure with that of DNA methyltransferases, coupled with other evidence, suggests that DNA also binds in this cleft. Since this structure is the first of the nucleotidyltransferase superfamily, which includes the eukaryotic mRNA capping enzymes, the relationship between the structure of DNA ligase and that of other nucleotidyltransferases is also discussed.
-Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.,Subramanya HS, Doherty AJ, Ashford SR, Wigley DB Cell. 1996 May 17;85(4):607-15. PMID:8653795<ref>PMID:8653795</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1a0i" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[ATP-Dependent DNA Ligase (Bacteriophage T7)|ATP-Dependent DNA Ligase (Bacteriophage T7)]]
+*[[DNA ligase 3D structures|DNA ligase 3D structures]]
-*[[ATP-dependent DNA ligase from bacteriophage T7|ATP-dependent DNA ligase from bacteriophage T7]]
-*[[DNA ligase|DNA ligase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: DNA Ligase]]
+[[Category: Escherichia phage T7]]
 [[Category: Large Structures]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Ashford, S R]]
+[[Category: Ashford SR]]
-[[Category: Doherty, A J]]
+[[Category: Doherty AJ]]
-[[Category: Subramanya, H S]]
+[[Category: Subramanya HS]]
-[[Category: Wigley, D B]]
+[[Category: Wigley DB]]
-[[Category: Dna replication]]
-[[Category: Ligase]]