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| | <StructureSection load='2cfm' size='340' side='right'caption='[[2cfm]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='2cfm' size='340' side='right'caption='[[2cfm]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2cfm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CFM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2CFM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2cfm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CFM 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=MG:MAGNESIUM+ION'>MG</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]] 1.8Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cfm OCA], [https://pdbe.org/2cfm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cfm RCSB], [https://www.ebi.ac.uk/pdbsum/2cfm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cfm ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2cfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cfm OCA], [http://pdbe.org/2cfm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2cfm RCSB], [http://www.ebi.ac.uk/pdbsum/2cfm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2cfm ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DNLI_PYRFU DNLI_PYRFU]] DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.[HAMAP-Rule:MF_00407] | + | [https://www.uniprot.org/uniprot/DNLI_PYRFU DNLI_PYRFU] DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.[HAMAP-Rule:MF_00407] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 43587]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ishino, Y]] | + | [[Category: Pyrococcus furiosus]] |
| - | [[Category: Morikawa, K]] | + | [[Category: Ishino Y]] |
| - | [[Category: Nishida, H]] | + | [[Category: Morikawa K]] |
| - | [[Category: Cell cycle]] | + | [[Category: Nishida H]] |
| - | [[Category: Cell division]]
| + | |
| - | [[Category: Dna damage]]
| + | |
| - | [[Category: Dna recombination]]
| + | |
| - | [[Category: Dna repair]]
| + | |
| - | [[Category: Dna replication]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Nucleotide-binding]]
| + | |
| - | [[Category: Protein-nucleotide complex]]
| + | |
| Structural highlights
Function
DNLI_PYRFU DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.[HAMAP-Rule:MF_00407]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
DNA ligases join single-strand breaks in double-stranded DNA, and are essential to maintain genome integrity in DNA metabolism. Here, we report the 1.8 A resolution structure of Pyrococcus furiosus DNA ligase (PfuLig), which represents the first full-length atomic view of an ATP-dependent eukaryotic-type DNA ligase. The enzyme comprises the N-terminal DNA-binding domain, the middle adenylation domain, and the C-terminal OB-fold domain. The architecture of each domain resembles those of human DNA ligase I, but the domain arrangements differ strikingly between the two enzymes. The closed conformation of the two "catalytic core" domains at the carboxyl terminus in PfuLig creates a small compartment, which holds a non-covalently bound AMP molecule. This domain rearrangement results from the "domain-connecting" role of the helical extension conserved at the C termini in archaeal and eukaryotic DNA ligases. The DNA substrate in the human open-ligase is replaced by motif VI in the Pfu closed-ligase. Both the shapes and electrostatic distributions are similar between motif VI and the DNA substrate, suggesting that motif VI in the closed state mimics the incoming substrate DNA. Two basic residues (R531 and K534) in motif VI reside within the active site pocket and interact with the phosphate group of the bound AMP. The crystallographic and functional analyses of mutant enzymes revealed that these two residues within the RxDK sequence play essential and complementary roles in ATP processing. This sequence is also conserved exclusively among the covalent nucleotidyltransferases, even including mRNA-capping enzymes with similar helical extensions at the C termini.
The closed structure of an archaeal DNA ligase from Pyrococcus furiosus.,Nishida H, Kiyonari S, Ishino Y, Morikawa K J Mol Biol. 2006 Jul 28;360(5):956-67. Epub 2006 Jun 12. PMID:16820169[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Nishida H, Kiyonari S, Ishino Y, Morikawa K. The closed structure of an archaeal DNA ligase from Pyrococcus furiosus. J Mol Biol. 2006 Jul 28;360(5):956-67. Epub 2006 Jun 12. PMID:16820169 doi:10.1016/j.jmb.2006.05.062
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