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.

1sn8

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:32, 14 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1sn8.jpg|left|200px]]
 
-
{{Structure
+
==Crystal structure of the S1 domain of RNase E from E. coli (Pb derivative)==
-
|PDB= 1sn8 |SIZE=350|CAPTION= <scene name='initialview01'>1sn8</scene>, resolution 2.00&Aring;
+
<StructureSection load='1sn8' size='340' side='right'caption='[[1sn8]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=PB:LEAD (II) ION'>PB</scene>
+
<table><tr><td colspan='2'>[[1sn8]] 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=1SN8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SN8 FirstGlance]. <br>
-
|ACTIVITY=
+
</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>
-
|GENE= RNE, AMS, HMP1, B1084 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene></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=1sn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sn8 OCA], [https://pdbe.org/1sn8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sn8 RCSB], [https://www.ebi.ac.uk/pdbsum/1sn8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sn8 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RNE_ECOLI RNE_ECOLI] Matures 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of colE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in E.coli. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process.
 +
== 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/sn/1sn8_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=1sn8 ConSurf].
 +
<div style="clear:both"></div>
-
'''Crystal structure of the S1 domain of RNase E from E. coli (Pb derivative)'''
+
==See Also==
-
 
+
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
S1 domains occur in four of the major enzymes of mRNA decay in Escherichia coli: RNase E, PNPase, RNase II, and RNase G. Here, we report the structure of the S1 domain of RNase E, determined by both X-ray crystallography and NMR spectroscopy. The RNase E S1 domain adopts an OB-fold, very similar to that found with PNPase and the major cold shock proteins, in which flexible loops are appended to a well-ordered five-stranded beta-barrel core. Within the crystal lattice, the protein forms a dimer stabilized primarily by intermolecular hydrophobic packing. Consistent with this observation, light-scattering, chemical crosslinking, and NMR spectroscopic measurements confirm that the isolated RNase E S1 domain undergoes a specific monomer-dimer equilibrium in solution with a K(D) value in the millimolar range. The substitution of glycine 66 with serine dramatically destabilizes the folded structure of this domain, thereby providing an explanation for the temperature-sensitive phenotype associated with this mutation in full-length RNase E. Based on amide chemical shift perturbation mapping, the binding surface for a single-stranded DNA dodecamer (K(D)=160(+/-40)microM) was identified as a groove of positive electrostatic potential containing several exposed aromatic side-chains. This surface, which corresponds to the conserved ligand-binding cleft found in numerous OB-fold proteins, lies distal to the dimerization interface, such that two independent oligonucleotide-binding sites can exist in the dimeric form of the RNase E S1 domain. Based on these data, we propose that the S1 domain serves a dual role of dimerization to aid in the formation of the tetrameric quaternary structure of RNase E as described by Callaghan et al. in 2003 and of substrate binding to facilitate RNA hydrolysis by the adjacent catalytic domains within this multimeric enzyme.
+
-
 
+
-
==About this Structure==
+
-
1SN8 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=1SN8 OCA].
+
-
 
+
-
==Reference==
+
-
Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces., Schubert M, Edge RE, Lario P, Cook MA, Strynadka NC, Mackie GA, McIntosh LP, J Mol Biol. 2004 Jul 30;341(1):37-54. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15312761 15312761]
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Cook, M A.]]
+
[[Category: Cook MA]]
-
[[Category: Edge, R E.]]
+
[[Category: Edge RE]]
-
[[Category: Lario, P.]]
+
[[Category: Lario P]]
-
[[Category: Mackie, G A.]]
+
[[Category: Mackie GA]]
-
[[Category: McIntosh, L P.]]
+
[[Category: McIntosh LP]]
-
[[Category: Schubert, M.]]
+
[[Category: Schubert M]]
-
[[Category: Strynadka, N C.J.]]
+
[[Category: Strynadka NCJ]]
-
[[Category: PB]]
+
-
[[Category: ob-fold]]
+
-
[[Category: rna-binding]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:07:12 2008''
+

Current revision

Crystal structure of the S1 domain of RNase E from E. coli (Pb derivative)

PDB ID 1sn8

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/1sn8"
Personal tools