We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

3h1t

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (01:52, 21 November 2024) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3h1t.jpg|left|200px]]
 
-
<!--
+
==The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016==
-
The line below this paragraph, containing "STRUCTURE_3h1t", creates the "Structure Box" on the page.
+
<StructureSection load='3h1t' size='340' side='right'caption='[[3h1t]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3h1t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_vulnificus_YJ016 Vibrio vulnificus YJ016]. 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 [https://proteopedia.org/fgij/fg.htm?mol=3H1T FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-
{{STRUCTURE_3h1t| PDB=3h1t | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3h1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h1t OCA], [https://pdbe.org/3h1t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3h1t RCSB], [https://www.ebi.ac.uk/pdbsum/3h1t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3h1t ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q7MPU7_VIBVY Q7MPU7_VIBVY]
 +
== 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/initialview03.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/main_output.php?pdb_ID=3h1t 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===
+
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_19625490}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 3h1t" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 19625490 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_19625490}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
3H1T is a 1 chain structure of 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].
+
[[Category: Vibrio vulnificus YJ016]]
-
 
+
[[Category: Kim JS]]
-
==Reference==
+
[[Category: Lee HJ]]
-
<ref group="xtra">PMID:19625490</ref><references group="xtra"/>
+
[[Category: Park SY]]
-
[[Category: Vibrio vulnificus]]
+
-
[[Category: Kim, J S.]]
+
-
[[Category: Lee, H J.]]
+
-
[[Category: Park, S Y.]]
+
-
[[Category: Atp-binding]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Nucleotide-binding]]
+
-
[[Category: Restriction enzyme hsdr]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 21 10:24:36 2009''
+

Current revision

The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016

PDB ID 3h1t

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3h1t"
Personal tools