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<StructureSection load='1nj5' size='340' side='right'caption='[[1nj5]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='1nj5' size='340' side='right'caption='[[1nj5]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1nj5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NJ5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1nj5]] 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=1NJ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NJ5 FirstGlance]. <br>
</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=P5A:5-O-(N-(L-PROLYL)-SULFAMOYL)ADENOSINE'>P5A</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1nj1|1nj1]], [[1nj2|1nj2]], [[1nj6|1nj6]], [[1nj8|1nj8]]</div></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=P5A:5-O-(N-(L-PROLYL)-SULFAMOYL)ADENOSINE'>P5A</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MTH611 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</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=1nj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj5 OCA], [https://pdbe.org/1nj5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nj5 RCSB], [https://www.ebi.ac.uk/pdbsum/1nj5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nj5 ProSAT]</span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1nj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj5 OCA], [http://pdbe.org/1nj5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nj5 RCSB], [http://www.ebi.ac.uk/pdbsum/1nj5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nj5 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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]  
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1nj5 ConSurf].
</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=1nj5 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:12578991<ref>PMID:12578991</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1nj5" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Metth]]
[[Category: Methanothermobacter thermautotrophicus str. Delta H]]
[[Category: Proline--tRNA ligase]]
[[Category: Kamtekar S]]
[[Category: Kamtekar, S]]
[[Category: Kennedy WD]]
[[Category: Kennedy, W D]]
[[Category: Soll D]]
[[Category: Soll, D]]
[[Category: Stathopoulos C]]
[[Category: Stathopoulos, C]]
[[Category: Steitz TA]]
[[Category: Steitz, T A]]
[[Category: Wang J]]
[[Category: Wang, J]]
[[Category: Ligase]]
[[Category: Protein-aminoacyladenylate complex class-ii trna synthetase]]

Revision as of 07:57, 14 February 2024

Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus bound to proline sulfamoyl adenylate

1nj5, resolution 2.80Å

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