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.


1n9w

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:54, 14 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1n9w.jpg|left|200px]]
 
-
{{Structure
+
==Crystal structure of the non-discriminating and archaeal-type aspartyl-tRNA synthetase from Thermus thermophilus==
-
|PDB= 1n9w |SIZE=350|CAPTION= <scene name='initialview01'>1n9w</scene>, resolution 2.3&Aring;
+
<StructureSection load='1n9w' size='340' side='right'caption='[[1n9w]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND=
+
<table><tr><td colspan='2'>[[1n9w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N9W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N9W 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]] 2.3&#8491;</td></tr>
-
|GENE=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1n9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n9w OCA], [https://pdbe.org/1n9w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n9w RCSB], [https://www.ebi.ac.uk/pdbsum/1n9w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n9w ProSAT]</span></td></tr>
-
|DOMAIN=
+
</table>
-
|RELATEDENTRY=
+
== Function ==
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n9w OCA], [http://www.ebi.ac.uk/pdbsum/1n9w PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1n9w RCSB]</span>
+
[https://www.uniprot.org/uniprot/SYDND_THET8 SYDND_THET8] Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn) with similar efficiencies. Reaction proceeds in two steps: aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn).<ref>PMID:10727213</ref> <ref>PMID:9220965</ref>
-
}}
+
== 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/n9/1n9w_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=1n9w ConSurf].
 +
<div style="clear:both"></div>
-
'''Crystal structure of the non-discriminating and archaeal-type aspartyl-tRNA synthetase from Thermus thermophilus'''
+
==See Also==
-
 
+
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-
 
+
== References ==
-
==Overview==
+
<references/>
-
In most organisms, tRNA aminoacylation is ensured by 20 aminoacyl-tRNA synthetases (aaRSs). In eubacteria, however, synthetases can be duplicated as in Thermus thermophilus, which contains two distinct AspRSs. While AspRS-1 is specific, AspRS-2 is non-discriminating and aspartylates tRNA(Asp) and tRNA(Asn). The structure at 2.3 A resolution of AspRS-2, the first of a non-discriminating synthetase, was solved. It differs from that of AspRS-1 but has resemblance to that of discriminating and archaeal AspRS from Pyrococcus kodakaraensis. The protein presents non-conventional features in its OB-fold anticodon-binding domain, namely the absence of a helix inserted between two beta-strands of this fold and a peculiar L1 loop differing from the large loops known to interact with tRNA(Asp) identity determinant C36 in conventional AspRSs. In AspRS-2, this loop is small and structurally homologous to that in AsnRSs, including conservation of a proline. In discriminating Pyrococcus AspRS, the L1 loop, although small, lacks this proline and is not superimposable with that of AspRS-2 or AsnRS. Its particular status is demonstrated by a loop-exchange experiment that renders the Pyrococcus AspRS non-discriminating.
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
1N9W is a [[Single protein]] structure of sequence 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=1N9W OCA].
+
-
 
+
-
==Reference==
+
-
Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain., Charron C, Roy H, Blaise M, Giege R, Kern D, EMBO J. 2003 Apr 1;22(7):1632-43. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12660169 12660169]
+
-
[[Category: Single protein]]
+
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
-
[[Category: Blaise, M.]]
+
[[Category: Blaise M]]
-
[[Category: Charron, C.]]
+
[[Category: Charron C]]
-
[[Category: Giege, R.]]
+
[[Category: Giege R]]
-
[[Category: Kern, D.]]
+
[[Category: Kern D]]
-
[[Category: Roy, H.]]
+
[[Category: Roy H]]
-
[[Category: biosynthetic protein]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:27:26 2008''
+

Current revision

Crystal structure of the non-discriminating and archaeal-type aspartyl-tRNA synthetase from Thermus thermophilus

PDB ID 1n9w

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/1n9w"
Personal tools