3h1t: Difference between revisions
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[[Image: | ==The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016== | ||
<StructureSection load='3h1t' size='340' side='right' caption='[[3h1t]], [[Resolution|resolution]] 2.30Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3h1t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_vulnificus Vibrio vulnificus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H1T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3H1T FirstGlance]. <br> | |||
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VV0265 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=672 Vibrio vulnificus])</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=3h1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h1t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3h1t RCSB], [http://www.ebi.ac.uk/pdbsum/3h1t PDBsum]</span></td></tr> | |||
</table> | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h1/3h1t_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</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/chain_selection.php?pdb_ID=2ata ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Among four types of bacterial restriction enzymes that cleave a foreign DNA depending on its methylation status, type I enzymes composed of three subunits are interesting because of their unique DNA cleavage and translocation mechanisms performed by the restriction subunit (HsdR). The elucidated N-terminal fragment structure of a putative HsdR subunit from Vibrio vulnificus YJ016 reveals three globular domains. The nucleolytic core within an N-terminal nuclease domain (NTD) is composed of one basic and three acidic residues, which include a metal-binding site. An ATP hydrolase (ATPase) site at the interface of two RecA-like domains (RDs) is located close to the probable DNA-binding site for translocation, which is far from the NTD nucleolytic core. Comparison of relative domain arrangements with other functionally related ATP and/or DNA complex structures suggests a possible translocation and restriction mechanism of the HsdR subunit. Furthermore, careful analysis of its sequence and structure implies that a linker helix connecting two RDs and an extended region within the nuclease domain may play a central role in switching the DNA translocation into the restriction activity. | |||
The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity.,Uyen NT, Park SY, Choi JW, Lee HJ, Nishi K, Kim JS Nucleic Acids Res. 2009 Nov;37(20):6960-9. Epub 2009 Jul 22. PMID:19625490<ref>PMID:19625490</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
< | |||
[[Category: Vibrio vulnificus]] | [[Category: Vibrio vulnificus]] | ||
[[Category: Kim, J S | [[Category: Kim, J S]] | ||
[[Category: Lee, H J | [[Category: Lee, H J]] | ||
[[Category: Park, S Y | [[Category: Park, S Y]] | ||
[[Category: Atp-binding]] | [[Category: Atp-binding]] | ||
[[Category: Hydrolase]] | [[Category: Hydrolase]] | ||
[[Category: Nucleotide-binding]] | [[Category: Nucleotide-binding]] | ||
[[Category: Restriction enzyme hsdr]] | [[Category: Restriction enzyme hsdr]] | ||
Revision as of 09:41, 8 December 2014
The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016
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