2q7h: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /><applet load="2q7h" size="350" color="white" frame="true" align="right" spinBox="true" caption="2q7h, resolution 2.10Å" /> '''pyrrolysyl-tRNA synt...
 
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2q7h.gif|left|200px]]<br /><applet load="2q7h" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2q7h, resolution 2.10&Aring;" />
'''pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate'''<br />


==Overview==
==Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate==
Pyrrolysine (Pyl), the 22nd natural amino acid and genetically encoded by, UAG, becomes attached to its cognate tRNA by pyrrolysyl-tRNA synthetase, (PylRS). We have determined three crystal structures of the Methanosarcina, mazei PylRS complexed with either AMP-PNP, Pyl-AMP plus pyrophosphate, or, the Pyl analogue N-epsilon-[(cylopentyloxy)carbonyl]-l-lysine plus ATP., The structures reveal that PylRS utilizes a deep hydrophobic pocket for, recognition of the Pyl side chain. A comparison of these structures with, previously determined class II tRNA synthetase complexes illustrates that, different substrate specificities derive from changes in a small number of, residues that form the substrate side-chain-binding pocket. The knowledge, of these structures allowed the placement of PylRS in the aminoacyl-tRNA, synthetase (aaRS) tree as the last known synthetase that evolved for, genetic code expansion, as well as the finding that Pyl arose before the, last universal common ancestral state. The PylRS structure provides an, excellent framework for designing new aaRSs with altered amino acid, specificity.
<StructureSection load='2q7h' size='340' side='right'caption='[[2q7h]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2q7h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q7H 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]] 2.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=YLY:(2R)-2-AMINO-6-({[(2S,3R)-3-METHYLPYRROLIDIN-2-YL]CARBONYL}AMINO)HEXANOYL+[(2S,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+HYDROGEN+(R)-PHOSPHATE'>YLY</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=2q7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q7h OCA], [https://pdbe.org/2q7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q7h RCSB], [https://www.ebi.ac.uk/pdbsum/2q7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q7h ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PYLS_METMA PYLS_METMA] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG (By similarity).
== 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/q7/2q7h_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=2q7h ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2Q7H is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei] with <scene name='pdbligand=EDO:'>EDO</scene>, <scene name='pdbligand=YLY:'>YLY</scene> and <scene name='pdbligand=POP:'>POP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q7H OCA].
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation., Kavran JM, Gundllapalli S, O'donoghue P, Englert M, Soll D, Steitz TA, Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11268-73. Epub 2007 Jun 25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17592110 17592110]
[[Category: Large Structures]]
[[Category: Methanosarcina mazei]]
[[Category: Methanosarcina mazei]]
[[Category: Single protein]]
[[Category: Kavran JM]]
[[Category: Kavran, J.M.]]
[[Category: Steitz TA]]
[[Category: Steitz, T.A.]]
[[Category: EDO]]
[[Category: POP]]
[[Category: YLY]]
[[Category: pyrrolysine]]
[[Category: pyrrolysyl-trna synthetase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 14:26:36 2008''

Latest revision as of 12:14, 21 February 2024

Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphatePyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate

Structural highlights

2q7h is a 1 chain structure with sequence from Methanosarcina mazei. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PYLS_METMA Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2q7h, resolution 2.10Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2q7h&oldid=4062691"