4aag

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the mutant D75N I-CreI in complex with its wild- type target in presence of Ca at the active site (The four central bases, 2NN region, are composed by GTAC from 5' to 3')

Structural highlights

4aag is a 4 chain structure with sequence from Chlamydomonas reinhardtii 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 2.8Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DNE1_CHLRE Endonuclease involved in group I intron homing. Recognizes and cleaves a 19-24 bp palindromic DNA site.

Publication Abstract from PubMed

Homing endonucleases represent protein scaffolds that provide powerful tools for genome manipulation, as these enzymes possess a very low frequency of DNA cleavage in eukaryotic genomes due to their high specificity. The basis of protein-DNA recognition must be understood to generate tailored enzymes that target the DNA at sites of interest. Protein-DNA interaction engineering of homing endonucleases has demonstrated the potential of these approaches to create new specific instruments to target genes for inactivation or repair. Protein-DNA interface studies have been focused mostly on specific contacts between amino acid side chains and bases to redesign the binding interface. However, it has been shown that 4 bp in the central DNA sequence of the 22-bp substrate of a homing endonuclease (I-CreI), which do not show specific protein-DNA interactions, is not devoid of content information. Here, we analyze the mechanism of target discrimination in this substrate region by the I-CreI protein, determining how it can occur independently of the specific protein-DNA interactions. Our data suggest the important role of indirect readout in this substrate region, opening the possibility for a fully rational search of new target sequences, thus improving the development of redesigned enzymes for therapeutic and biotechnological applications.

Non-specific protein-DNA interactions control I-CreI target binding and cleavage.,Molina R, Redondo P, Stella S, Marenchino M, D'Abramo M, Gervasio FL, Charles Epinat J, Valton J, Grizot S, Duchateau P, Prieto J, Montoya G Nucleic Acids Res. 2012 Apr 11. PMID:22495931^[1]

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

References

↑ Molina R, Redondo P, Stella S, Marenchino M, D'Abramo M, Gervasio FL, Charles Epinat J, Valton J, Grizot S, Duchateau P, Prieto J, Montoya G. Non-specific protein-DNA interactions control I-CreI target binding and cleavage. Nucleic Acids Res. 2012 Apr 11. PMID:22495931 doi:10.1093/nar/gks320

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/4aag"

@@ Line 3: / Line 3: @@
 <StructureSection load='4aag' size='340' side='right'caption='[[4aag]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4aag]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlre Chlre]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AAG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4aag]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii] 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=4AAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AAG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4aaf|4aaf]], [[1g9z|1g9z]], [[1bp7|1bp7]], [[2vbl|2vbl]], [[4aae|4aae]], [[2vbo|2vbo]], [[1mow|1mow]], [[1t9i|1t9i]], [[4aad|4aad]], [[1u0d|1u0d]], [[1t9j|1t9j]], [[1n3e|1n3e]], [[1af5|1af5]], [[4aab|4aab]], [[2vbj|2vbj]], [[1g9y|1g9y]], [[2vbn|2vbn]], [[1n3f|1n3f]], [[1u0c|1u0c]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=4aag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aag OCA], [https://pdbe.org/4aag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4aag RCSB], [https://www.ebi.ac.uk/pdbsum/4aag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4aag ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DNE1_CHLRE DNE1_CHLRE]] Endonuclease involved in group I intron homing. Recognizes and cleaves a 19-24 bp palindromic DNA site.
+[https://www.uniprot.org/uniprot/DNE1_CHLRE DNE1_CHLRE] Endonuclease involved in group I intron homing. Recognizes and cleaves a 19-24 bp palindromic DNA site.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Chlre]]
+[[Category: Chlamydomonas reinhardtii]]
 [[Category: Large Structures]]
-[[Category: Abramo, M D]]
+[[Category: Synthetic construct]]
-[[Category: Duchateau, P]]
+[[Category: D'Abramo M]]
-[[Category: Epinat, J C]]
+[[Category: Duchateau P]]
-[[Category: Gervasio, F]]
+[[Category: Epinat JC]]
-[[Category: Grizot, S]]
+[[Category: Gervasio F]]
-[[Category: Marenchino, M]]
+[[Category: Grizot S]]
-[[Category: Molina, R]]
+[[Category: Marenchino M]]
-[[Category: Montoya, G]]
+[[Category: Molina R]]
-[[Category: Prieto, J]]
+[[Category: Montoya G]]
-[[Category: Redondo, P]]
+[[Category: Prieto J]]
-[[Category: Stella, S]]
+[[Category: Redondo P]]
-[[Category: Valton, J]]
+[[Category: Stella S]]
-[[Category: Gene targeting]]
+[[Category: Valton J]]
-[[Category: Homing endonuclease]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Protein-dna interaction]]

4aag

From Proteopedia

Current revision

Crystal structure of the mutant D75N I-CreI in complex with its wild- type target in presence of Ca at the active site (The four central bases, 2NN region, are composed by GTAC from 5' to 3')

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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