1nj2: Difference between revisions

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New page: left|200px<br /><applet load="1nj2" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nj2, resolution 3.11Å" /> '''Crystal structure of...
 
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[[Image:1nj2.gif|left|200px]]<br /><applet load="1nj2" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1nj2, resolution 3.11&Aring;" />
'''Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus'''<br />


==Overview==
==Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus==
Cysteinyl-tRNA synthetase is an essential enzyme required for protein, synthesis. Genes encoding this protein have not been identified in, Methanocaldococcus jannaschii, Methanothermobacter thermautotrophicus, or, Methanopyrus kandleri. It has previously been proposed that the, prolyl-tRNA synthetase (ProRS) enzymes in these organisms recognize either, proline or cysteine and can aminoacylate their cognate tRNAs through a, dual-specificity mechanism. We report five crystal structures at, resolutions between 2.6 and 3.2 A: apo M. jannaschii ProRS, and M., thermautotrophicus ProRS in apo form and in complex with, cysteinyl-sulfamoyl-, prolyl-sulfamoyl-, and alanyl-sulfamoyl-adenylates., These aminoacyl-adenylate analogues bind to a single active-site pocket, and induce an identical set of conformational changes in loops around the, active site when compared with the ligand-free conformation of ProRS. The, cysteinyl- and prolyl-adenylate analogues have similar, nanomolar, affinities for M. thermautotrophicus ProRS. Homology modeling of tRNA onto, these adenylate complexes places the 3'-OH of A76 in an appropriate, position for the transfer of any of the three amino acids to tRNA. Thus, these structures explain recent biochemical experiments showing that M., jannaschii ProRS misacylates tRNA(Pro) with cysteine, and argue against, the proposal that these archaeal ProRS enzymes possess the dual capacity, to aminoacylate both tRNA(Pro) and tRNA(Cys) with their cognate amino, acids.
<StructureSection load='1nj2' size='340' side='right'caption='[[1nj2]], [[Resolution|resolution]] 3.11&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1nj2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._Delta_H Methanothermobacter thermautotrophicus str. Delta H]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NJ2 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]] 3.11&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1nj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj2 OCA], [https://pdbe.org/1nj2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nj2 RCSB], [https://www.ebi.ac.uk/pdbsum/1nj2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nj2 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SYP_METTH SYP_METTH] Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). Can inadvertently accommodate and process cysteine.[HAMAP-Rule:MF_01571]
== 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/nj/1nj2_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=1nj2 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1NJ2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus] with ZN and MG as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Proline--tRNA_ligase Proline--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.15 6.1.1.15] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NJ2 OCA].
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases., Kamtekar S, Kennedy WD, Wang J, Stathopoulos C, Soll D, Steitz TA, Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):1673-8. Epub 2003 Feb 10. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12578991 12578991]
[[Category: Large Structures]]
[[Category: Methanothermobacter thermautotrophicus]]
[[Category: Methanothermobacter thermautotrophicus str. Delta H]]
[[Category: Proline--tRNA ligase]]
[[Category: Kamtekar S]]
[[Category: Single protein]]
[[Category: Kennedy WD]]
[[Category: Kamtekar, S.]]
[[Category: Soll D]]
[[Category: Kennedy, W.D.]]
[[Category: Stathopoulos C]]
[[Category: Soll, D.]]
[[Category: Steitz TA]]
[[Category: Stathopoulos, C.]]
[[Category: Wang J]]
[[Category: Steitz, T.A.]]
[[Category: Wang, J.]]
[[Category: MG]]
[[Category: ZN]]
[[Category: class-ii trna synthetase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:18:35 2007''

Latest revision as of 10:57, 14 February 2024

Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicusCrystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus

Structural highlights

1nj2 is a 1 chain structure with sequence from Methanothermobacter thermautotrophicus str. Delta H. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.11Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SYP_METTH Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). Can inadvertently accommodate and process cysteine.[HAMAP-Rule:MF_01571]

Evolutionary Conservation

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

See Also

1nj2, resolution 3.11Å

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