1v9p: Difference between revisions

Revision as of 07:33, 30 December 2020

Crystal Structure Of Nad+-Dependent DNA Ligase

Structural highlights

1v9p is a 2 chain structure with sequence from Atcc 43280. This structure supersedes the now removed PDB entry 1dgt. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	AMP, ZN
Related:	1dgt
Gene:	LIGA (ATCC 43280)
Activity:	DNA ligase (NAD(+)), with EC number 6.5.1.2
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DNLJ_THEFI] DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.^[1]

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 catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. Despite the difference in cofactor specificity and limited overall sequence similarity, the two classes of DNA ligase share basically the same catalytic mechanism. In this study, the crystal structure of an NAD(+)-dependent DNA ligase from Thermus filiformis, a 667 residue multidomain protein, has been determined by the multiwavelength anomalous diffraction (MAD) method. It reveals highly modular architecture and a unique circular arrangement of its four distinct domains. It also provides clues for protein flexibility and DNA-binding sites. A model for the multidomain ligase action involving large conformational changes is proposed.

Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.,Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW EMBO J. 2000 Mar 1;19(5):1119-29. PMID:10698952^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Jeon HJ, Shin HJ, Choi JJ, Hoe HS, Kim HK, Suh SW, Kwon ST. Mutational analyses of the thermostable NAD+-dependent DNA ligase from Thermus filiformis. FEMS Microbiol Lett. 2004 Aug 1;237(1):111-8. PMID:15268945 doi:https://dx.doi.org/10.1016/j.femsle.2004.06.018
↑ Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW. Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications. EMBO J. 2000 Mar 1;19(5):1119-29. PMID:10698952 doi:https://dx.doi.org/10.1093/emboj/19.5.1119

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Jeon HJ, Shin HJ, Choi JJ, Hoe HS, Kim HK, Suh SW, Kwon ST. Mutational analyses of the thermostable NAD+-dependent DNA ligase from Thermus filiformis. FEMS Microbiol Lett. 2004 Aug 1;237(1):111-8. PMID:15268945 doi:https://dx.doi.org/10.1016/j.femsle.2004.06.018

[2] Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW. Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications. EMBO J. 2000 Mar 1;19(5):1119-29. PMID:10698952 doi:https://dx.doi.org/10.1093/emboj/19.5.1119

[1]

[2]

@@ Line 1: / Line 1: @@
 ==Crystal Structure Of Nad+-Dependent DNA Ligase==
-<StructureSection load='1v9p' size='340' side='right' caption='[[1v9p]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='1v9p' size='340' side='right'caption='[[1v9p]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43280 Atcc 43280]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V9P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43280 Atcc 43280]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1V9P FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</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=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dgt|1dgt]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dgt|1dgt]]</div></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=276 ATCC 43280])</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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [http://pdbe.org/1v9p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [http://www.ebi.ac.uk/pdbsum/1v9p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9p 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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [http://pdbe.org/1v9p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [http://www.ebi.ac.uk/pdbsum/1v9p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9p ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 33: / Line 33: @@
 ==See Also==
-*[[DNA ligase|DNA ligase]]
+*[[DNA ligase 3D structures|DNA ligase 3D structures]]
 == References ==
 <references/>
@@ Line 39: / Line 39: @@
 </StructureSection>
 [[Category: Atcc 43280]]
+[[Category: Large Structures]]
 [[Category: Chang, C]]
 [[Category: Kim, H K]]

1v9p: Difference between revisions

Revision as of 07:33, 30 December 2020

Crystal Structure Of Nad+-Dependent DNA Ligase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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