5a0m

From Proteopedia

(Difference between revisions)

Current revision

THE CRYSTAL STRUCTURE OF I-SCEI IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF MN

Structural highlights

5a0m is a 10 chain structure with sequence from Saccharomyces cerevisiae and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SCE1_YEAST Mitochondrial DNA endonuclease involved in intron homing. It introduces a specific double-strand break in the DNA of the 21S rRNA gene and thus mediates the insertion of an intron, containing its own coding sequence (group I intron), into an intronless gene. Specifically recognizes and cleaves the sequence 5'-TAGGGATAACAGGGTAAT-3'.

Publication Abstract from PubMed

Homing endonucleases are highly specific DNA-cleaving enzymes that recognize and cleave long stretches of DNA. The engineering of these enzymes provides instruments for genome modification in a wide range of fields, including gene targeting. The homing endonuclease I-SceI from the yeast Saccharomyces cerevisiae has been purified after overexpression in Escherichia coli and its crystal structure has been determined in complex with its target DNA. In order to evaluate the number of ions that are involved in the cleavage process, thus determining the catalytic mechanism, crystallization experiments were performed in the presence of Mn(2+), yielding crystals that were suitable for X-ray diffraction analysis. The crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 80.11, b = 80.57, c = 130.87 A, alpha = beta = gamma = 90 degrees . The self-rotation function and the Matthews coefficient suggested the presence of two protein-DNA complexes in the asymmetric unit. The crystals diffracted to a resolution limit of 2.9 A using synchrotron radiation. From the anomalous data, it was determined that three cations are involved in catalysis and it was confirmed that I-SceI follows a two-metal-ion DNA-strand cleavage mechanism.

Structure of the I-SceI nuclease complexed with its dsDNA target and three catalytic metal ions.,Prieto J, Redondo P, Merino N, Villate M, Montoya G, Blanco FJ, Molina R Acta Crystallogr F Struct Biol Commun. 2016 Jun 1;72(Pt 6):473-9. doi:, 10.1107/S2053230X16007512. Epub 2016 May 23. PMID:27303901^[1]

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

References

↑ Prieto J, Redondo P, Merino N, Villate M, Montoya G, Blanco FJ, Molina R. Structure of the I-SceI nuclease complexed with its dsDNA target and three catalytic metal ions. Acta Crystallogr F Struct Biol Commun. 2016 Jun 1;72(Pt 6):473-9. doi:, 10.1107/S2053230X16007512. Epub 2016 May 23. PMID:27303901 doi:http://dx.doi.org/10.1107/S2053230X16007512

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5a0m"

@@ Line 1: / Line 1: @@
 ==THE CRYSTAL STRUCTURE OF I-SCEI IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF MN==
-<StructureSection load='5a0m' size='340' side='right' caption='[[5a0m]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='5a0m' size='340' side='right'caption='[[5a0m]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5a0m]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5A0M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5a0m]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5A0M FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.9&#8491;</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=5a0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a0m OCA], [http://pdbe.org/5a0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5a0m RCSB], [http://www.ebi.ac.uk/pdbsum/5a0m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5a0m ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=5a0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a0m OCA], [https://pdbe.org/5a0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5a0m RCSB], [https://www.ebi.ac.uk/pdbsum/5a0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5a0m ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SCE1_YEAST SCE1_YEAST]] Mitochondrial DNA endonuclease involved in intron homing. It introduces a specific double-strand break in the DNA of the 21S rRNA gene and thus mediates the insertion of an intron, containing its own coding sequence (group I intron), into an intronless gene. Specifically recognizes and cleaves the sequence 5'-TAGGGATAACAGGGTAAT-3'.
+[https://www.uniprot.org/uniprot/SCE1_YEAST SCE1_YEAST] Mitochondrial DNA endonuclease involved in intron homing. It introduces a specific double-strand break in the DNA of the 21S rRNA gene and thus mediates the insertion of an intron, containing its own coding sequence (group I intron), into an intronless gene. Specifically recognizes and cleaves the sequence 5'-TAGGGATAACAGGGTAAT-3'.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 5a0m" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Blanco, F J]]
+[[Category: Large Structures]]
-[[Category: Merino, N]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Molina, R]]
+[[Category: Synthetic construct]]
-[[Category: Prieto, J]]
+[[Category: Blanco FJ]]
-[[Category: Redondo, P]]
+[[Category: Merino N]]
-[[Category: Villate, M]]
+[[Category: Molina R]]
-[[Category: Gene targeting]]
+[[Category: Prieto J]]
-[[Category: Genetic]]
+[[Category: Redondo P]]
-[[Category: Homing endonuclease]]
+[[Category: Villate M]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Protein-dna interaction]]

5a0m

From Proteopedia

Current revision

THE CRYSTAL STRUCTURE OF I-SCEI IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF MN

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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