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.


3cmq

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:30, 30 August 2023) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3cmq.png|left|200px]]
 
-
<!--
+
==Crystal structure of human mitochondrial phenylalanine tRNA synthetase==
-
The line below this paragraph, containing "STRUCTURE_3cmq", creates the "Structure Box" on the page.
+
<StructureSection load='3cmq' size='340' side='right'caption='[[3cmq]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3cmq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CMQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CMQ FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FA5:ADENOSINE-5-[PHENYLALANINYL-PHOSPHATE]'>FA5</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-
{{STRUCTURE_3cmq| PDB=3cmq | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3cmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmq OCA], [https://pdbe.org/3cmq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cmq RCSB], [https://www.ebi.ac.uk/pdbsum/3cmq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cmq ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/SYFM_HUMAN SYFM_HUMAN] Catalyzes direct attachment of p-Tyr (Tyr) to tRNAPhe. Permits also, with a lower efficiency, the attachment of m-Tyr to tRNAPhe, thereby opening the way for delivery of the misacylated tRNA to the ribosome and incorporation of ROS-damaged amino acid into proteins.<ref>PMID:19549855</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/cm/3cmq_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=3cmq ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
All class II aminoacyl-tRNA synthetases (aaRSs) are known to be active as functional homodimers, homotetramers, or heterotetramers. However, multimeric organization is not a prerequisite for phenylalanylation activity, as monomeric mitochondrial phenylalanyl-tRNA synthetase (PheRS) is also active. We herein report the structure, at 2.2 A resolution, of a human monomeric mitPheRS complexed with Phe-AMP. The smallest known aaRS, which is, in fact, 1/5 of a cytoplasmic analog, is a chimera of the catalytic module of the alpha and anticodon binding domain (ABD) of the bacterial beta subunit of (alphabeta)2 PheRS. We demonstrate that the ABD located at the C terminus of mitPheRS overlaps with the acceptor stem of phenylalanine transfer RNA (tRNAPhe) if the substrate is positioned in a manner similar to that seen in the binary Thermus thermophilus complex. Thus, formation of the PheRS-tRNAPhe complex in human mitochondria must be accompanied by considerable rearrangement (hinge-type rotation through approximately 160 degrees) of the ABD upon tRNA binding.
-
===Crystal structure of human mitochondrial phenylalanine tRNA synthetase===
+
The tRNA-induced conformational activation of human mitochondrial phenylalanyl-tRNA synthetase.,Klipcan L, Levin I, Kessler N, Moor N, Finarov I, Safro M Structure. 2008 Jul;16(7):1095-104. PMID:18611382<ref>PMID:18611382</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3cmq" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_18611382}}, adds the Publication Abstract to the page
+
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 18611382 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18611382}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
3CMQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CMQ OCA].
+
-
 
+
-
==Reference==
+
-
The tRNA-Induced Conformational Activation of Human Mitochondrial Phenylalanyl-tRNA Synthetase., Klipcan L, Levin I, Kessler N, Moor N, Finarov I, Safro M, Structure. 2008 Jul;16(7):1095-104. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18611382 18611382]
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Phenylalanine--tRNA ligase]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Finarov I]]
-
[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
+
[[Category: Kessler N]]
-
[[Category: Aminoacyl-trna synthetase]]
+
[[Category: Klipcan L]]
-
[[Category: Atp-binding]]
+
[[Category: Levin IL]]
-
[[Category: Classii aarss fold]]
+
[[Category: Moor N]]
-
[[Category: Ligase]]
+
[[Category: Safro M]]
-
[[Category: Mitochondrion]]
+
-
[[Category: Nucleotide-binding]]
+
-
[[Category: Protein biosynthesis]]
+
-
[[Category: Rna recogntion]]
+
-
[[Category: Rrm domain]]
+
-
[[Category: Transit peptide]]
+
-
[[Category: Trna]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 17 20:18:36 2008''
+

Current revision

Crystal structure of human mitochondrial phenylalanine tRNA synthetase

PDB ID 3cmq

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/3cmq"
Personal tools