3v21: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
Line 3: Line 3:
<StructureSection load='3v21' size='340' side='right'caption='[[3v21]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
<StructureSection load='3v21' size='340' side='right'caption='[[3v21]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3v21]] is a 22 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V21 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V21 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3v21]] is a 22 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V21 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V21 FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3v1z|3v1z]], [[3v20|3v20]]</div></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]] 2.7&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bse634IR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [https://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=3v21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v21 OCA], [https://pdbe.org/3v21 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v21 RCSB], [https://www.ebi.ac.uk/pdbsum/3v21 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v21 ProSAT]</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=3v21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v21 OCA], [https://pdbe.org/3v21 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v21 RCSB], [https://www.ebi.ac.uk/pdbsum/3v21 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v21 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/Q8RT53_GEOSE Q8RT53_GEOSE]
Restriction endonuclease Bse634I recognizes and cleaves the degenerate DNA sequence 5'-R/CCGGY-3' (R stands for A or G; Y for T or C, '/' indicates a cleavage position). Here, we report the crystal structures of the Bse634I R226A mutant complexed with cognate oligoduplexes containing ACCGGT and GCCGGC sites, respectively. In the crystal, all potential H-bond donor and acceptor atoms on the base edges of the conserved CCGG core are engaged in the interactions with Bse634I amino acid residues located on the alpha6 helix. In contrast, direct contacts between the protein and outer base pairs are limited to van der Waals contact between the purine nucleobase and Pro203 residue in the major groove and a single H-bond between the O2 atom of the outer pyrimidine and the side chain of the Asn73 residue in the minor groove. Structural data coupled with biochemical experiments suggest that both van der Waals interactions and indirect readout contribute to the discrimination of the degenerate base pair by Bse634I. Structure comparison between related enzymes Bse634I (R/CCGGY), NgoMIV (G/CCGGC) and SgrAI (CR/CCGGYG) reveals how different specificities are achieved within a conserved structural core.
 
Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease.,Manakova E, Grazulis S, Zaremba M, Tamulaitiene G, Golovenko D, Siksnys V Nucleic Acids Res. 2012 Apr 11. PMID:22495930<ref>PMID:22495930</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3v21" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 12980]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Type II site-specific deoxyribonuclease]]
[[Category: Golovenko D]]
[[Category: Golovenko, D]]
[[Category: Grazulis S]]
[[Category: Grazulis, S]]
[[Category: Manakova EN]]
[[Category: Manakova, E N]]
[[Category: Tamulaitiene G]]
[[Category: Tamulaitiene, G]]
[[Category: Dna binding protein]]
[[Category: Hydrolase]]
[[Category: Hydrolase-dna complex]]
[[Category: Protein-dna complex]]
[[Category: Restriction endonuclease]]

Latest revision as of 17:15, 14 March 2024

Crystal structure of Type IIF restriction endonuclease Bse634I with cognate DNACrystal structure of Type IIF restriction endonuclease Bse634I with cognate DNA

Structural highlights

3v21 is a 22 chain structure with sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.7Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q8RT53_GEOSE

See Also

3v21, resolution 2.70Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=3v21&oldid=4099287"