2iy5: Difference between revisions

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-{{Seed}}
-[[Image:2iy5.png|left|200px]]
-<!--
+==PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog==
-The line below this paragraph, containing "STRUCTURE_2iy5", creates the "Structure Box" on the page.
+<StructureSection load='2iy5' size='340' side='right'caption='[[2iy5]], [[Resolution|resolution]] 3.10&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'>[[2iy5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IY5 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]] 3.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FYA:ADENOSINE-5-[PHENYLALANINOL-PHOSPHATE]'>FYA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_2iy5|  PDB=2iy5  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2iy5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iy5 OCA], [https://pdbe.org/2iy5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iy5 RCSB], [https://www.ebi.ac.uk/pdbsum/2iy5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iy5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYFA_THET8 SYFA_THET8]
+== 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/iy/2iy5_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=2iy5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of the ternary complex of (alphabeta)(2) heterotetrameric phenylalanyl-tRNA synthetase (PheRS) from Thermus thermophilus with cognate tRNA(Phe) and a nonhydrolyzable phenylalanyl-adenylate analogue (PheOH-AMP) has been determined at 3.1 A resolution. It reveals conformational changes in tRNA(Phe) induced by the PheOH-AMP binding. The single-stranded 3' end exhibits a hairpin conformation in contrast to the partial unwinding observed previously in the binary PheRS.tRNA(Phe) complex. The CCA end orientation is stabilized by extensive base-specific interactions of A76 and C75 with the protein and by intra-RNA interactions of A73 with adjacent nucleotides. The 4-amino group of the "bulged out" C75 is trapped by two negatively charged residues of the beta subunit (Glubeta31 and Aspbeta33), highly conserved in eubacterial PheRSs. The position of the A76 base is stabilized by interactions with Hisalpha212 of motif 2 (universally conserved in PheRSs) and class II-invariant Argalpha321 of motif 3. Important conformational changes induced by the binding of tRNA(Phe) and PheOH-AMP are observed in the catalytic domain: the motif 2 loop and a "helical" loop (residues 139-152 of the alpha subunit) undergo coordinated displacement; Metalpha148 of the helical loop adopts a conformation preventing the 2'-OH group of A76 from approaching the alpha-carbonyl carbon of PheOH-AMP. The unfavorable position of the terminal ribose stems from the absence of the alpha-carbonyl oxygen in the analogue. Our data suggest that the idiosyncratic feature of PheRS, which aminoacylates the 2'-OH group of the terminal ribose, is dictated by the system-specific topology of the CCA end-binding site.
-===PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH TRNA AND A PHENYLALANYL-ADENYLATE ANALOG===
+The crystal structure of the ternary complex of phenylalanyl-tRNA synthetase with tRNAPhe and a phenylalanyl-adenylate analogue reveals a conformational switch of the CCA end.,Moor N, Kotik-Kogan O, Tworowski D, Sukhanova M, Safro M Biochemistry. 2006 Sep 5;45(35):10572-83. PMID:16939209<ref>PMID:16939209</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2iy5" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16939209}}, 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 16939209 is the PubMed ID number.
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
--->
+== References ==
-{{ABSTRACT_PUBMED_16939209}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-IY5 is a 3 chains 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=2IY5 OCA].
+[[Category: Large Structures]]
+[[Category: Thermus thermophilus HB8]]
-==Reference==
+[[Category: Kotik-Kogan O]]
-<ref group="xtra">PMID:16939209</ref><references group="xtra"/>
+[[Category: Moor N]]
-[[Category: Phenylalanine--tRNA ligase]]
+[[Category: Safro M]]
-[[Category: Thermus thermophilus]]
+[[Category: Sukhanova M]]
-[[Category: Kotik-Kogan, O.]]
+[[Category: Tworowski D]]
-[[Category: Moor, N.]]
-[[Category: Safro, M.]]
-[[Category: Sukhanova, M.]]
-[[Category: Tworowski, D.]]
-[[Category: Aminoacyl-trna synthetase]]
-[[Category: Atp-binding]]
-[[Category: Class ii aminoacyl-trna synthetase]]
-[[Category: Helix-turn-helix motif]]
-[[Category: Ligase]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
-[[Category: Nucleotide-binding]]
-[[Category: Phenylalanyl-trna synthetase]]
-[[Category: Protein biosynthesis]]
-[[Category: Rbd domin]]
-[[Category: Rna-binding]]
-[[Category: Sh3 domain]]
-[[Category: Thermus thermophilus]]
-[[Category: Trna-binding]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 15:54:44 2009''