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| | <StructureSection load='2p14' size='340' side='right'caption='[[2p14]], [[Resolution|resolution]] 1.50Å' scene=''> | | <StructureSection load='2p14' size='340' side='right'caption='[[2p14]], [[Resolution|resolution]] 1.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2p14]] 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=2P14 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P14 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2p14]] 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=2P14 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P14 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.5Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ewf|2ewf]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bspD6IR2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=127889 Bacillus sp. D6])</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=2p14 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p14 OCA], [https://pdbe.org/2p14 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p14 RCSB], [https://www.ebi.ac.uk/pdbsum/2p14 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p14 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=2p14 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p14 OCA], [https://pdbe.org/2p14 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p14 RCSB], [https://www.ebi.ac.uk/pdbsum/2p14 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p14 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A3FEV8_9BACI A3FEV8_9BACI] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus sp. d6]] | + | [[Category: Bacillus sp. D6]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Type II site-specific deoxyribonuclease]]
| + | [[Category: Artyukh RI]] |
| - | [[Category: Artyukh, R I]] | + | [[Category: Bartunik HD]] |
| - | [[Category: Bartunik, H D]] | + | [[Category: Kachalova GS]] |
| - | [[Category: Kachalova, G S]] | + | [[Category: Matvienko NI]] |
| - | [[Category: Matvienko, N I]] | + | [[Category: Rogulin EA]] |
| - | [[Category: Rogulin, E A]] | + | [[Category: Yunusova AK]] |
| - | [[Category: Yunusova, A K]] | + | [[Category: Zheleznaya LA]] |
| - | [[Category: Zheleznaya, L A]] | + | |
| - | [[Category: Heterodimeric restriction endonuclease]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
A3FEV8_9BACI
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kachalova GS, Rogulin EA, Yunusova AK, Artyukh RI, Perevyazova TA, Matvienko NI, Zheleznaya LA, Bartunik HD. 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. J Mol Biol. 2008 Dec 12;384(2):489-502. Epub 2008 Sep 21. PMID:18835275 doi:10.1016/j.jmb.2008.09.033
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