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.


1goc

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:25, 7 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1goc.gif|left|200px]]
 
-
<!--
+
==COOPERATIVE STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY INSERTION OF GLY-80B AND GLY-77-> ALA SUBSTITUTION==
-
The line below this paragraph, containing "STRUCTURE_1goc", creates the "Structure Box" on the page.
+
<StructureSection load='1goc' size='340' side='right'caption='[[1goc]], [[Resolution|resolution]] 2.00&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'>[[1goc]] 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=1GOC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GOC 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&#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=1goc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1goc OCA], [https://pdbe.org/1goc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1goc RCSB], [https://www.ebi.ac.uk/pdbsum/1goc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1goc ProSAT]</span></td></tr>
-
{{STRUCTURE_1goc| PDB=1goc | 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]
 +
== 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/go/1goc_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=1goc ConSurf].
 +
<div style="clear:both"></div>
-
'''COOPERATIVE STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY INSERTION OF GLY-80B AND GLY-77-> ALA SUBSTITUTION'''
+
==See Also==
-
 
+
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
The insertion of a Gly residue (designated as Gly-80b) between the C-cap of the alpha II-helix (Gln-80) and the N-cap of the alpha III-helix (Trp-81) in Escherichia coli ribonuclease HI enhances the protein stability by 0.4 kcal/mol in delta G (Kimura, S., Nakamura, H., Hashimoto, T., Oobatake, M., &amp; Kanaya, S. (1992) J. Biol. Chem. 267, 21535-21542). Another mutation within the alpha II-helix, Gly-77--&gt;Ala, reduces the stability by 0.9 kcal/mol. Simultaneous introduction of these mutations enhances the stability by 0.8 kcal/mol, indicating that the effects of these mutations are cooperative and not simply independent. We determined the crystal structures of these three mutant proteins (G80b-, A77-, and A77/G80b-RNase H) to investigate this cooperative mechanism of the protein stabilization. The structures revealed that the inserted Gly-80b assumes a left-handed helical conformation in both the G80b- and the A77/G80b-RNase H. This inserted glycine residue allows the formation of a "paperclip", which is a common motif at the C-termini of alpha-helices. Accompanying the formation of the paperclip motif, two intrahelical hydrogen bonds are formed between the backbone atoms (O78-N80b and O80b-N84). The stabilization caused by the insertion of Gly-80b can be ascribed to the formation of these hydrogen bonds. The Gly-77--&gt;Ala substitution destabilizes the protein due to the deformed packing interactions in the hydrophobic core around Ala-77 and the stress in the wedged indole ring of Trp-81. These effects are alleviated by the insertion of Gly-80b, which relaxes the backbone structure.(ABSTRACT TRUNCATED AT 250 WORDS)
+
-
 
+
-
==About this Structure==
+
-
1GOC 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=1GOC OCA].
+
-
 
+
-
==Reference==
+
-
Cooperative stabilization of Escherichia coli ribonuclease HI by insertion of Gly-80b and Gly-77--&gt;Ala substitution., Ishikawa K, Nakamura H, Morikawa K, Kimura S, Kanaya S, Biochemistry. 1993 Jul 20;32(28):7136-42. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8393706 8393706]
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Ribonuclease H]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Ishikawa K]]
-
[[Category: Ishikawa, K.]]
+
[[Category: Kanaya S]]
-
[[Category: Kanaya, S.]]
+
[[Category: Kimura S]]
-
[[Category: Kimura, S.]]
+
[[Category: Morikawa K]]
-
[[Category: Morikawa, K.]]
+
[[Category: Nakamura H]]
-
[[Category: Nakamura, H.]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 17:49:06 2008''
+

Current revision

COOPERATIVE STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY INSERTION OF GLY-80B AND GLY-77-> ALA SUBSTITUTION

PDB ID 1goc

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/1goc"
Personal tools