1yt3

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:59, 14 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1yt3.gif|left|200px]]
 
-
<!--
+
==Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing==
-
The line below this paragraph, containing "STRUCTURE_1yt3", creates the "Structure Box" on the page.
+
<StructureSection load='1yt3' size='340' side='right'caption='[[1yt3]], [[Resolution|resolution]] 1.60&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'>[[1yt3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YT3 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]] 1.6&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
{{STRUCTURE_1yt3| PDB=1yt3 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [https://pdbe.org/1yt3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB], [https://www.ebi.ac.uk/pdbsum/1yt3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yt3 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RND_ECOLI RND_ECOLI] Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides.<ref>PMID:3041371</ref> <ref>PMID:6263886</ref>
 +
== 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/yt/1yt3_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/main_output.php?pdb_ID=1yt3 ConSurf].
 +
<div style="clear:both"></div>
-
'''Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing'''
+
==See Also==
-
 
+
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-
 
+
== References ==
-
==Overview==
+
<references/>
-
RNase D (RND) is one of seven exoribonucleases identified in Escherichia coli. RNase D has homologs in many eubacteria and eukaryotes, and has been shown to contribute to the 3' maturation of several stable RNAs. Here, we report the 1.6 A resolution crystal structure of E. coli RNase D. The conserved DEDD residues of RNase D fold into an arrangement very similar to the Klenow fragment exonuclease domain. Besides the catalytic domain, RNase D also contains two structurally similar alpha-helical domains with no discernible sequence homology between them. These closely resemble the HRDC domain previously seen in RecQ-family helicases and several other proteins acting on nucleic acids. More interestingly, the DEDD catalytic domain and the two helical domains come together to form a ring-shaped structure. The ring-shaped architecture of E. coli RNase D and the HRDC domains likely play a major role in determining the substrate specificity of this exoribonuclease.
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
1YT3 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA].
+
-
 
+
-
==Reference==
+
-
Crystal structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing., Zuo Y, Wang Y, Malhotra A, Structure. 2005 Jul;13(7):973-84. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16004870 16004870]
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Ribonuclease III]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Malhotra A]]
-
[[Category: Malhotra, A.]]
+
[[Category: Wang Y]]
-
[[Category: Wang, Y.]]
+
[[Category: Zuo Y]]
-
[[Category: Zuo, Y.]]
+
-
[[Category: Exonuclease]]
+
-
[[Category: Exoribonuclease]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Nuclease]]
+
-
[[Category: Ribonuclease]]
+
-
[[Category: Rnase]]
+
-
[[Category: Trna processing]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 16:45:10 2008''
+

Current revision

Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing

PDB ID 1yt3

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/1yt3"
Personal tools