1wki

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:36, 1 May 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1wki.gif|left|200px]]
 
-
{{Structure
+
==solution structure of ribosomal protein L16 from thermus thermophilus HB8==
-
|PDB= 1wki |SIZE=350|CAPTION= <scene name='initialview01'>1wki</scene>
+
<StructureSection load='1wki' size='340' side='right'caption='[[1wki]]' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND=
+
<table><tr><td colspan='2'>[[1wki]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WKI FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-
|GENE= RPLP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wki OCA], [https://pdbe.org/1wki PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wki RCSB], [https://www.ebi.ac.uk/pdbsum/1wki PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wki ProSAT], [https://www.topsan.org/Proteins/RSGI/1wki TOPSAN]</span></td></tr>
-
|DOMAIN=
+
</table>
-
|RELATEDENTRY=
+
== Function ==
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wki OCA], [http://www.ebi.ac.uk/pdbsum/1wki PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1wki RCSB]</span>
+
[https://www.uniprot.org/uniprot/RL16_THET8 RL16_THET8] This protein binds directly to 23S rRNA. Interacts with the A site tRNA.[HAMAP-Rule:MF_01342]
-
}}
+
== 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/wk/1wki_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=1wki ConSurf].
 +
<div style="clear:both"></div>
-
'''solution structure of ribosomal protein L16 from thermus thermophilus HB8'''
+
==See Also==
-
 
+
*[[Ribosomal protein L16|Ribosomal protein L16]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
Ribosomal protein L16 is an essential component of the bacterial ribosome. It organizes the architecture of aminoacyl tRNA binding site in the ribosome 50S subunit. The three-dimensional structure of L16 from Thermus thermophilus HB8 was determined by NMR. In solution, L16 forms an alpha+beta sandwich structure combined with two additional beta sheets located at the loop regions connecting the two layers. The terminal regions and a central loop region did not show any specific secondary structure. The structured part of L16 could be superimposed well on the C(alpha) model of L16 determined in the crystal structure of the ribosome 50S subunit. By overlaying the L16 solution structure onto the coordinates of the ribosome crystal structure, we constructed the combined model that represents the ribosome-bound state of L16 in the detailed structure. The model showed that L16 possesses residues in contact with helices 38, 39, 42, 43 and 89 of 23S rRNA and helix 4 of 5S rRNA. This suggests its broad effect on the ribosome architecture. Comparison of L16 with the L10e protein, which is the archaeal counterpart, showed that they share a common fold, but differ in some regions of functional importance, especially in the N-terminal region. All known mutation sites in L16 that confer resistance to avilamycin and evernimicin were positioned so that their side-chains were exposed to solvent in the internal cavity of the ribosome. This suggests the direct participation of L16 as a part of the binding site for antibiotics.
+
[[Category: Large Structures]]
-
 
+
[[Category: Thermus thermophilus HB8]]
-
==About this Structure==
+
[[Category: Kobayashi Y]]
-
1WKI is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKI OCA].
+
[[Category: Kuramitsu S]]
-
 
+
[[Category: Nishimura M]]
-
==Reference==
+
[[Category: Ohkubo T]]
-
Solution structure of ribosomal protein L16 from Thermus thermophilus HB8., Nishimura M, Yoshida T, Shirouzu M, Terada T, Kuramitsu S, Yokoyama S, Ohkubo T, Kobayashi Y, J Mol Biol. 2004 Dec 10;344(5):1369-83. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15561149 15561149]
+
[[Category: Shirouzu M]]
-
[[Category: Protein complex]]
+
[[Category: Terada T]]
-
[[Category: Thermus thermophilus]]
+
[[Category: Yokoyama S]]
-
[[Category: Kobayashi, Y.]]
+
[[Category: Yoshida T]]
-
[[Category: Kuramitsu, S.]]
+
-
[[Category: Nishimura, M.]]
+
-
[[Category: Ohkubo, T.]]
+
-
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+
-
[[Category: Shirouzu, M.]]
+
-
[[Category: Terada, T.]]
+
-
[[Category: Yokoyama, S.]]
+
-
[[Category: Yoshida, T.]]
+
-
[[Category: mixed alpha/beta]]
+
-
[[Category: ribosome]]
+
-
[[Category: riken structural genomics/proteomics initiative]]
+
-
[[Category: rsgi]]
+
-
[[Category: structural genomic]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:37:32 2008''
+

Current revision

solution structure of ribosomal protein L16 from thermus thermophilus HB8

PDB ID 1wki

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/1wki"
Personal tools