3ebc: Difference between revisions

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==Structure of N141A HincII with Cognate DNA==
==Structure of N141A HincII with Cognate DNA==
<StructureSection load='3ebc' size='340' side='right' caption='[[3ebc]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
<StructureSection load='3ebc' size='340' side='right'caption='[[3ebc]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ebc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EBC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EBC FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ebc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EBC 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]] 2.55&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hincIIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </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=3ebc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ebc OCA], [https://pdbe.org/3ebc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ebc RCSB], [https://www.ebi.ac.uk/pdbsum/3ebc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ebc ProSAT]</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=3ebc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ebc OCA], [http://pdbe.org/3ebc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ebc RCSB], [http://www.ebi.ac.uk/pdbsum/3ebc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ebc ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/T2C2_HAEIF T2C2_HAEIF]] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.  
[https://www.uniprot.org/uniprot/T2C2_HAEIF T2C2_HAEIF] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Control of replication, transcription, recombination and repair requires proteins capable of finding particular DNA sequences in a background of a large excess of nonspecific sequences. Such recognition can involve direct readout, with direct contacts to the bases of DNA, or in some cases through the less well-characterized indirect readout mechanisms. In order to measure the relative contributions of direct and indirect readout by a sequence specific endonuclease, HincII, a mutant enzyme deficient in a direct contact, was characterized, and surprisingly showed no loss of sequence specificity. The three dimensional crystal structure shows the loss of most of the direct readout contacts to the DNA, possibly capturing an early stage in target site recognition using predominately indirect readout to prescreen sites before full sequence interrogation.
 
Early interrogation and recognition of DNA sequence by indirect readout.,Little EJ, Babic AC, Horton NC Structure. 2008 Dec 12;16(12):1828-37. PMID:19081059<ref>PMID:19081059</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ebc" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Endonuclease|Endonuclease]]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacterium influenzae lehmann and neumann 1896]]
[[Category: Haemophilus influenzae]]
[[Category: Type II site-specific deoxyribonuclease]]
[[Category: Large Structures]]
[[Category: Babic, A C]]
[[Category: Babic AC]]
[[Category: Horton, N C]]
[[Category: Horton NC]]
[[Category: Little, E J]]
[[Category: Little EJ]]
[[Category: Dimerization]]
[[Category: Endonuclease]]
[[Category: Hydrolase]]
[[Category: Hydrolase-dna complex]]
[[Category: Intermediate]]
[[Category: Mutant]]
[[Category: Nuclease]]
[[Category: R-loop]]
[[Category: Restriction system]]

Latest revision as of 12:46, 21 February 2024

Structure of N141A HincII with Cognate DNAStructure of N141A HincII with Cognate DNA

Structural highlights

3ebc is a 4 chain structure with sequence from Haemophilus influenzae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.55Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

T2C2_HAEIF Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.

See Also

3ebc, resolution 2.55Å

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