2ewf: Difference between revisions

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<StructureSection load='2ewf' size='340' side='right'caption='[[2ewf]], [[Resolution|resolution]] 1.84&Aring;' scene=''>
<StructureSection load='2ewf' size='340' side='right'caption='[[2ewf]], [[Resolution|resolution]] 1.84&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2ewf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._d6 Bacillus sp. d6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EWF FirstGlance]. <br>
<table><tr><td colspan='2'>[[2ewf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._D6 Bacillus sp. D6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EWF FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</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]] 1.84&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</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=2ewf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ewf OCA], [https://pdbe.org/2ewf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ewf RCSB], [https://www.ebi.ac.uk/pdbsum/2ewf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ewf 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=2ewf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ewf OCA], [https://pdbe.org/2ewf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ewf RCSB], [https://www.ebi.ac.uk/pdbsum/2ewf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ewf ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/A3FEV7_9BACI A3FEV7_9BACI]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ewf ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ewf ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The heterodimeric restriction endonuclease R.BspD6I from Bacillus species D6 recognizes a pseudosymmetric sequence and cuts both DNA strands outside the recognition sequence. The large subunit, Nt.BspD6I, acts as a type IIS site-specific monomeric nicking endonuclease. The isolated small subunit, ss.BspD6I, does not bind DNA and is not catalytically active. We solved the crystal structures of Nt.BspD6I and ss.BspD6I at high resolution. Nt.BspD6I consists of three domains, two of which exhibit structural similarity to the recognition and cleavage domains of FokI. ss.BspD6I has a fold similar to that of the cleavage domain of Nt.BspD6I, each containing a PD-(D/E)XK motif and a histidine as an additional putative catalytic residue. In contrast to the DNA-bound FokI structure, in which the cleavage domain is rotated away from the DNA, the crystal structure of Nt.BspD6I shows the recognition and cleavage domains in favorable orientations for interactions with DNA. Docking models of complexes of Nt.BspD6I and R.BspD6I with cognate DNA were constructed on the basis of structural similarity to individual domains of FokI, R.BpuJI and HindIII. A three-helix bundle forming an interdomain linker in Nt.BspD6I acts as a rigid spacer adjusting the orientations of the spatially separated domains to match the distance between the recognition and cleavage sites accurately.
Structural analysis of the heterodimeric type IIS restriction endonuclease R.BspD6I acting as a complex between a monomeric site-specific nickase and a catalytic subunit.,Kachalova GS, Rogulin EA, Yunusova AK, Artyukh RI, Perevyazova TA, Matvienko NI, Zheleznaya LA, Bartunik HD J Mol Biol. 2008 Dec 12;384(2):489-502. Epub 2008 Sep 21. PMID:18835275<ref>PMID:18835275</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2ewf" 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: Bacillus sp. d6]]
[[Category: Bacillus sp. D6]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Artyukh, R I]]
[[Category: Artyukh RI]]
[[Category: Bartunik, H D]]
[[Category: Bartunik HD]]
[[Category: Kachalova, G S]]
[[Category: Kachalova GS]]
[[Category: Matvienko, N I]]
[[Category: Matvienko NI]]
[[Category: Perevyazova, T A]]
[[Category: Perevyazova TA]]
[[Category: Rogulin, E A]]
[[Category: Rogulin EA]]
[[Category: Zheleznaya, L A]]
[[Category: Zheleznaya LA]]
[[Category: Beta-alpha-barrel]]
[[Category: Helix-turn-helix]]
[[Category: Hydrolase]]

Latest revision as of 12:19, 14 February 2024

Crystal structure of the site-specific DNA nickase N.BspD6ICrystal structure of the site-specific DNA nickase N.BspD6I

Structural highlights

2ewf is a 1 chain structure with sequence from Bacillus sp. D6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.84Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A3FEV7_9BACI

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2ewf, resolution 1.84Å

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OCA
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