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.


2cyb

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:45, 13 March 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2cyb.gif|left|200px]]<br /><applet load="2cyb" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2cyb, resolution 1.80&Aring;" />
 
-
'''Crystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyrosine from Archaeoglobus fulgidus'''<br />
 
-
==Overview==
+
==Crystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyrosine from Archaeoglobus fulgidus==
-
Tyrosyl-tRNA synthetase (TyrRS) catalyzes the tyrosylation of tRNA(Tyr) in a two-step reaction. TyrRS has the "HIGH" and "KMSKS" motifs, which play essential roles in the formation of the tyrosyl-adenylate from tyrosine and ATP. Here, we determined the crystal structures of Archaeoglobus fulgidus and Pyrococcus horikoshii TyrRSs in the l-tyrosine-bound form at 1.8A and 2.2A resolutions, respectively, and that of Aeropyrum pernix TyrRS in the substrate-free form at 2.2 A. The conformation of the KMSKS motif differs among the three TyrRSs. In the A.pernix TyrRS, the KMSKS loop conformation corresponds to the ATP-bound "closed" form. In contrast, the KMSKS loop of the P.horikoshii TyrRS forms a novel 3(10) helix, which appears to correspond to the "semi-closed" form. This conformation enlarges the entrance to the tyrosine-binding pocket, which facilitates the pyrophosphate ion release after the tyrosyl-adenylate formation, and probably is involved in the initial tRNA binding. The KMSSS loop of the A.fulgidus TyrRS is somewhat farther from the active site and is stabilized by hydrogen bonds. Based on the three structures, possible structural changes of the KMSKS motif during the tyrosine activation reaction are discussed. We suggest that the insertion sequence just before the KMSKS motif, which exists in some archaeal species, enhances the binding affinity of the TyrRS for its cognate tRNA. In addition, a non-proline cis peptide bond, which is involved in the tRNA binding, is conserved among the archaeal TyrRSs.
+
<StructureSection load='2cyb' size='340' side='right'caption='[[2cyb]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2cyb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CYB FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TYR:TYROSINE'>TYR</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=2cyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cyb OCA], [https://pdbe.org/2cyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cyb RCSB], [https://www.ebi.ac.uk/pdbsum/2cyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cyb ProSAT], [https://www.topsan.org/Proteins/RSGI/2cyb TOPSAN]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/SYY_ARCFU SYY_ARCFU] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr) (By similarity).[HAMAP-Rule:MF_02008]
 +
== 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/cy/2cyb_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=2cyb ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
2CYB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus] with <scene name='pdbligand=TYR:'>TYR</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYB OCA].
+
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Crystal structures of tyrosyl-tRNA synthetases from Archaea., Kuratani M, Sakai H, Takahashi M, Yanagisawa T, Kobayashi T, Murayama K, Chen L, Liu ZJ, Wang BC, Kuroishi C, Kuramitsu S, Terada T, Bessho Y, Shirouzu M, Sekine S, Yokoyama S, J Mol Biol. 2006 Jan 20;355(3):395-408. Epub 2005 Nov 14. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16325203 16325203]
+
[[Category: Archaeoglobus fulgidus]]
[[Category: Archaeoglobus fulgidus]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Tyrosine--tRNA ligase]]
+
[[Category: Kobayashi T]]
-
[[Category: Kobayashi, T.]]
+
[[Category: Kuratani M]]
-
[[Category: Kuratani, M.]]
+
[[Category: Sakai H]]
-
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+
[[Category: Shirouzu M]]
-
[[Category: Sakai, H.]]
+
[[Category: Takahashi M]]
-
[[Category: Shirouzu, M.]]
+
[[Category: Terada T]]
-
[[Category: Takahashi, M.]]
+
[[Category: Yanagisawa T]]
-
[[Category: Terada, T.]]
+
[[Category: Yokoyama S]]
-
[[Category: Yanagisawa, T.]]
+
-
[[Category: Yokoyama, S.]]
+
-
[[Category: TYR]]
+
-
[[Category: national project on protein structural and functional analyses]]
+
-
[[Category: nppsfa]]
+
-
[[Category: riken structural genomics/proteomics initiative]]
+
-
[[Category: rossmann-fold]]
+
-
[[Category: rsgi]]
+
-
[[Category: structural genomics]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:53:43 2008''
+

Current revision

Crystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyrosine from Archaeoglobus fulgidus

PDB ID 2cyb

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/2cyb"
Personal tools