This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1jl2

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:42, 16 August 2023) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1jl2.png|left|200px]]
 
-
<!--
+
==Crystal structure of TCEO RNase H-a chimera combining the folding core from T. thermophilus RNase H and the remaining region of E. coli RNase H==
-
The line below this paragraph, containing "STRUCTURE_1jl2", creates the "Structure Box" on the page.
+
<StructureSection load='1jl2' size='340' side='right'caption='[[1jl2]], [[Resolution|resolution]] 1.76&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'>[[1jl2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JL2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JL2 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]] 1.76&#8491;</td></tr>
-
-->
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jl2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jl2 OCA], [https://pdbe.org/1jl2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jl2 RCSB], [https://www.ebi.ac.uk/pdbsum/1jl2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jl2 ProSAT]</span></td></tr>
-
{{STRUCTURE_1jl2| PDB=1jl2 | SCENE= }}
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RNH_ECOLI RNH_ECOLI] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042][https://www.uniprot.org/uniprot/RNH_THET8 RNH_THET8] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
 +
== 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/jl/1jl2_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=1jl2 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
To investigate the contribution of the folding cores to the thermodynamic stability of RNases H, we used rational design to create two chimeras composed of parts of a thermophilic and a mesophilic RNase H. Each chimera combines the folding core from one parent protein and the remaining parts of the other. Both chimeras form active, well-folded RNases H. Stability curves, based on CD-monitored chemical denaturations, show that the chimera with the thermophilic core is more stable, has a higher midpoint of thermal denaturation, and a lower change in heat capacity (DeltaCp) upon unfolding than the chimera with the mesophilic core. A possible explanation for the low DeltaCp of both the parent thermophilic RNase H and the chimera with the thermophilic core is the residual structure in the denatured state. On the basis of the studied parameters, the chimera with the thermophilic core resembles a true thermophilic protein. Our results suggest that the folding core plays an essential role in conferring thermodynamic parameters to RNases H.
-
===Crystal structure of TCEO RNase H-a chimera combining the folding core from T. thermophilus RNase H and the remaining region of E. coli RNase H===
+
Contributions of folding cores to the thermostabilities of two ribonucleases H.,Robic S, Berger JM, Marqusee S Protein Sci. 2002 Feb;11(2):381-9. PMID:11790848<ref>PMID:11790848</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1jl2" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_11790848}}, adds the Publication Abstract to the page
+
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 11790848 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_11790848}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Escherichia coli K-12]]
-
1JL2 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli_and_thermus_thermophilus Escherichia coli and thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JL2 OCA].
+
[[Category: Large Structures]]
-
 
+
[[Category: Thermus thermophilus HB8]]
-
==Reference==
+
[[Category: Berger JM]]
-
<ref group="xtra">PMID:11790848</ref><references group="xtra"/>
+
[[Category: Marqusee S]]
-
[[Category: Escherichia coli and thermus thermophilus]]
+
[[Category: Robic S]]
-
[[Category: Ribonuclease H]]
+
-
[[Category: Berger, J M.]]
+
-
[[Category: Marqusee, S.]]
+
-
[[Category: Robic, S.]]
+
-
[[Category: Mixed alpha-beta protein]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:08:42 2009''
+

Current revision

Crystal structure of TCEO RNase H-a chimera combining the folding core from T. thermophilus RNase H and the remaining region of E. coli RNase H

PDB ID 1jl2

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/1jl2"
Personal tools