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.


1f7v

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:11, 7 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1f7v.jpg|left|200px]]
 
-
{{Structure
+
==CRYSTAL STRUCTURE OF YEAST ARGINYL-TRNA SYNTHETASE COMPLEXED WITH THE TRNAARG==
-
|PDB= 1f7v |SIZE=350|CAPTION= <scene name='initialview01'>1f7v</scene>, resolution 2.90&Aring;
+
<StructureSection load='1f7v' size='340' side='right'caption='[[1f7v]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5&#39;-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5&#39;-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5&#39;-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5&#39;-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5&#39;-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5&#39;-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=I:INOSINIC+ACID'>I</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5&#39;-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5&#39;-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
+
<table><tr><td colspan='2'>[[1f7v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F7V FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginine--tRNA_ligase Arginine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.19 6.1.1.19] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1f7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7v OCA], [https://pdbe.org/1f7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f7v RCSB], [https://www.ebi.ac.uk/pdbsum/1f7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f7v ProSAT]</span></td></tr>
-
|RELATEDENTRY=[[1bs2|1BS2]], [[1f7u|1F7U]]
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7v OCA], [http://www.ebi.ac.uk/pdbsum/1f7v PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1f7v RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/SYRC_YEAST SYRC_YEAST] Forms part of a macromolecular complex that catalyzes the attachment of specific amino acids to cognate tRNAs during protein synthesis (By similarity).[HAMAP-Rule:MF_00123]
 +
== 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/f7/1f7v_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=1f7v ConSurf].
 +
<div style="clear:both"></div>
-
'''CRYSTAL STRUCTURE OF YEAST ARGINYL-TRNA SYNTHETASE COMPLEXED WITH THE TRNAARG'''
+
==See Also==
-
 
+
*[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]]
-
 
+
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-
==Overview==
+
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-
The 2.2 A crystal structure of a ternary complex formed by yeast arginyl-tRNA synthetase and its cognate tRNA(Arg) in the presence of the L-arginine substrate highlights new atomic features used for specific substrate recognition. This first example of an active complex formed by a class Ia aminoacyl-tRNA synthetase and its natural cognate tRNA illustrates additional strategies used for specific tRNA selection. The enzyme specifically recognizes the D-loop and the anticodon of the tRNA, and the mutually induced fit produces a conformation of the anticodon loop never seen before. Moreover, the anticodon binding triggers conformational changes in the catalytic center of the protein. The comparison with the 2.9 A structure of a binary complex formed by yeast arginyl-tRNA synthetase and tRNA(Arg) reveals that L-arginine binding controls the correct positioning of the CCA end of the tRNA(Arg). Important structural changes induced by substrate binding are observed in the enzyme. Several key residues of the active site play multiple roles in the catalytic pathway and thus highlight the structural dynamics of the aminoacylation reaction.
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
1F7V is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_servazzii Saccharomyces servazzii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7V OCA].
+
[[Category: Saccharomyces cerevisiae]]
-
 
+
[[Category: Cavarelli J]]
-
==Reference==
+
[[Category: Delagoutte B]]
-
tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding., Delagoutte B, Moras D, Cavarelli J, EMBO J. 2000 Nov 1;19(21):5599-610. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11060012 11060012]
+
[[Category: Moras D]]
-
[[Category: Arginine--tRNA ligase]]
+
-
[[Category: Saccharomyces servazzii]]
+
-
[[Category: Single protein]]
+
-
[[Category: Cavarelli, J.]]
+
-
[[Category: Delagoutte, B.]]
+
-
[[Category: Moras, D.]]
+
-
[[Category: aminoacylation]]
+
-
[[Category: arginyl-trna synthetase]]
+
-
[[Category: trna-protein complex]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:17:47 2008''
+

Current revision

CRYSTAL STRUCTURE OF YEAST ARGINYL-TRNA SYNTHETASE COMPLEXED WITH THE TRNAARG

PDB ID 1f7v

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/1f7v"
Personal tools