6qm2 - Revision history

OCA at 23:13, 5 June 2019

OCA — Wed, 05 Jun 2019 23:13:16 GMT

←Older revision		Revision as of 23:13, 5 June 2019
Line 3:		Line 3:
	<StructureSection load='6qm2' size='340' side='right'caption='[[6qm2]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='6qm2' size='340' side='right'caption='[[6qm2]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qm2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QM2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qm2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"neisseria_lactamicus"_(sic)_hollis_et_al._1969 "neisseria lactamicus" (sic) hollis et al. 1969]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QM2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nlaIVR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=486 "Neisseria lactamicus" (sic) Hollis et al. 1969])</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='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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6qm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qm2 OCA], [http://pdbe.org/6qm2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qm2 RCSB], [http://www.ebi.ac.uk/pdbsum/6qm2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qm2 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=6qm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qm2 OCA], [http://pdbe.org/6qm2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qm2 RCSB], [http://www.ebi.ac.uk/pdbsum/6qm2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qm2 ProSAT]</span></td></tr>

OCA at 08:57, 1 May 2019

OCA — Wed, 01 May 2019 08:57:58 GMT

←Older revision		Revision as of 08:57, 1 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6qm2 is ~~ON HOLD~~	+	==NlaIV restriction endonuclease==
		+	<StructureSection load='6qm2' size='340' side='right'caption='[[6qm2]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6qm2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QM2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6qm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qm2 OCA], [http://pdbe.org/6qm2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qm2 RCSB], [http://www.ebi.ac.uk/pdbsum/6qm2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qm2 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/T2N4_NEILA T2N4_NEILA]] Recognizes the double-stranded sequence GGNNCC and cleaves after N-3.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Specificity engineering is challenging, and particularly difficult for enzymes that have the catalytic machinery and specificity determinants in close proximity. Restriction endonucleases have been used as a paradigm for protein engineering, but successful cases are rare. Here, we present the results of a directed evolution approach to the engineering of a dimeric, blunt end cutting restriction enzyme NlaIV (GGN/NCC). Based on the remote similarity to EcoRV endonuclease, regions for random mutagenesis and in vitro evolution were chosen. The obtained variants cleaved target sites with an up to 100-fold kcat/KM preference for AT or TA (GGW/WCC) over GC or CG (GGS/SCC) in the central dinucleotide step, compared to the only ~17-fold preference of the wild-type enzyme. To understand the basis of the increased specificity, we determined the crystal structure of NlaIV. Despite the presence of DNA in the crystallization mix, the enzyme crystallized in the free form. We therefore constructed a computational model of the NlaIV-DNA complex. According to the model, the mutagenesis of the regions that were in the proximity of DNA did not lead to the desired specificity change, which was instead conveyed in an indirect manner by substitutions in the more distant regions.

-	~~Authors: Czapinska~~, H., Siwek, W., Szczepanowski~~, R.H.~~, Bujnicki, J.M.~~, Bochtler, M~~., ~~Skowronek, K~~.	+	Crystal Structure and Directed Evolution of Specificity of NlaIV Restriction Endonuclease.,Czapinska H, Siwek W, Szczepanowski RH, Bujnicki JM, Bochtler M, Skowronek KJ J Mol Biol. 2019 Apr 14. pii: S0022-2836(19)30204-9. doi:, 10.1016/j.jmb.2019.04.010. PMID:30995450<ref>PMID:30995450</ref>

-	~~Description~~: ~~NlaIV restriction endonuclease~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6qm2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Type II site-specific deoxyribonuclease]]
	[[Category: Bochtler, M]]		[[Category: Bochtler, M]]
-	[[Category: Bujnicki, J.M]]	+	[[Category: Bujnicki, J M]]
	[[Category: Czapinska, H]]		[[Category: Czapinska, H]]
-	[[Category: Skowronek, K]]
	[[Category: Siwek, W]]		[[Category: Siwek, W]]
-	[[Category: Szczepanowski, R.H]]	+	[[Category: Skowronek, K]]
		+	[[Category: Szczepanowski, R H]]
		+	[[Category: Blunt end cutter]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nlaiv]]
		+	[[Category: Restriction endonuclease]]

OCA: Protected "6qm2" [edit=sysop:move=sysop]

OCA — Wed, 13 Feb 2019 08:05:06 GMT

Protected "6qm2" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:05, 13 February 2019

OCA: New page: '''Unreleased structure''' The entry 6qm2 is ON HOLD Authors: Czapinska, H., Siwek, W., Szczepanowski, R.H., Bujnicki, J.M., Bochtler, M., Skowronek, K. Description: NlaIV restriction ...

OCA — Wed, 13 Feb 2019 08:05:04 GMT

New page: '''Unreleased structure''' The entry 6qm2 is ON HOLD Authors: Czapinska, H., Siwek, W., Szczepanowski, R.H., Bujnicki, J.M., Bochtler, M., Skowronek, K. Description: NlaIV restriction ...

New page

'''Unreleased structure'''

The entry 6qm2 is ON HOLD

Authors: Czapinska, H., Siwek, W., Szczepanowski, R.H., Bujnicki, J.M., Bochtler, M., Skowronek, K.

Description: NlaIV restriction endonuclease
[[Category: Unreleased Structures]]
[[Category: Bochtler, M]]
[[Category: Bujnicki, J.M]]
[[Category: Czapinska, H]]
[[Category: Skowronek, K]]
[[Category: Siwek, W]]
[[Category: Szczepanowski, R.H]]