2z70

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (05:38, 17 October 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2z70.png|left|200px]]
 
-
<!--
+
==E.coli RNase 1 in complex with d(CGCGATCGCG)==
-
The line below this paragraph, containing "STRUCTURE_2z70", creates the "Structure Box" on the page.
+
<StructureSection load='2z70' size='340' side='right'caption='[[2z70]], [[Resolution|resolution]] 1.70&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'>[[2z70]] is a 2 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=2Z70 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z70 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]] 1.7&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-
{{STRUCTURE_2z70| PDB=2z70 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2z70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z70 OCA], [https://pdbe.org/2z70 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z70 RCSB], [https://www.ebi.ac.uk/pdbsum/2z70 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z70 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RNI_ECOLI RNI_ECOLI] One of the few RNases that cleaves the phosphodiester bond between any two nucleotide. Shows a preference for cytidylic or guanylic acid.
 +
== 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/z7/2z70_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=2z70 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The crystal structure of Escherichia coli ribonuclease I (EcRNase I) reveals an RNase T2-type fold consisting of a conserved core of six beta-strands and three alpha-helices. The overall architecture of the catalytic residues is very similar to the plant and fungal RNase T2 family members, but the perimeter surrounding the active site is characterized by structural elements specific for E. coli. In the structure of EcRNase I in complex with a substrate-mimicking decadeoxynucleotide d(CGCGATCGCG), we observe a cytosine bound in the B2 base binding site and mixed binding of thymine and guanine in the B1 base binding site. The active site residues His55, His133, and Glu129 interact with the phosphodiester linkage only through a set of water molecules. Residues forming the B2 base recognition site are well conserved among bacterial homologs and may generate limited base specificity. On the other hand, the B1 binding cleft acquires true base aspecificity by combining hydrophobic van der Waals contacts at its sides with a water-mediated hydrogen-bonding network at the bottom. This B1 base recognition site is highly variable among bacterial sequences and the observed interactions are unique to EcRNaseI and a few close relatives.
-
===E.coli RNase 1 in complex with d(CGCGATCGCG)===
+
Nonspecific base recognition mediated by water bridges and hydrophobic stacking in ribonuclease I from Escherichia coli.,Rodriguez SM, Panjikar S, Van Belle K, Wyns L, Messens J, Loris R Protein Sci. 2008 Apr;17(4):681-90. Epub 2008 Feb 27. PMID:18305191<ref>PMID:18305191</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 2z70" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_18305191}}, adds the Publication Abstract to the page
+
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 18305191 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18305191}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
2Z70 is a 2 chains structure of sequences 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=2Z70 OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:18305191</ref><references group="xtra"/>
+
-
[[Category: Enterobacter ribonuclease]]
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Loris, R.]]
+
[[Category: Large Structures]]
-
[[Category: Martinez-Rodriguez, S.]]
+
[[Category: Loris R]]
-
[[Category: Messens, J.]]
+
[[Category: Martinez-Rodriguez S]]
-
[[Category: Cytoplasm]]
+
[[Category: Messens J]]
-
[[Category: Endonuclease]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Periplasm]]
+
-
[[Category: Ribonuclease]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 11:19:08 2009''
+

Current revision

E.coli RNase 1 in complex with d(CGCGATCGCG)

PDB ID 2z70

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/2z70"
Personal tools