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1h4s

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Prolyl-tRNA synthetase from Thermus thermophilus complexed with tRNApro(CGG) and a prolyl-adenylate analogue

Structural highlights

1h4s is a 3 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.85Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SYP_THET8 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.^[1] ^[2]

Evolutionary Conservation

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

Publication Abstract from PubMed

We describe the recognition by Thermus thermophilus prolyl-tRNA synthetase (ProRSTT) of proline, ATP and prolyl-adenylate and the sequential conformational changes occurring when the substrates bind and the activated intermediate is formed. Proline and ATP binding cause respectively conformational changes in the proline binding loop and motif 2 loop. However formation of the activated intermediate is necessary for the final conformational ordering of a ten residue peptide ("ordering loop") close to the active site which would appear to be essential for functional tRNA 3' end binding. These induced fit conformational changes ensure that the enzyme is highly specific for proline activation and aminoacylation. We also present new structures of apo and AMP bound histidyl-tRNA synthetase (HisRS) from T. thermophilus which we compare to our previous structures of the histidine and histidyl-adenylate bound enzyme. Qualitatively, similar results to those observed with T. thermophilus prolyl-tRNA synthetase are found. However histidine binding is sufficient to induce the co-operative ordering of the topologically equivalent histidine binding loop and ordering loop. These two examples contrast with most other class II aminoacyl-tRNA synthetases whose pocket for the cognate amino acid side-chain is largely preformed. T. thermophilus prolyl-tRNA synthetase appears to be the second class II aminoacyl-tRNA synthetase, after HisRS, to use a positively charged amino acid instead of a divalent cation to catalyse the amino acid activation reaction.

A succession of substrate induced conformational changes ensures the amino acid specificity of Thermus thermophilus prolyl-tRNA synthetase: comparison with histidyl-tRNA synthetase.,Yaremchuk A, Tukalo M, Grotli M, Cusack S J Mol Biol. 2001 Jun 15;309(4):989-1002. PMID:11399074^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Feng L, Stathopoulos C, Ahel I, Mitra A, Tumbula-Hansen D, Hartsch T, Söll D. Aminoacyl-tRNA formation in the extreme thermophile Thermus thermophilus. Extremophiles. 2002 Apr;6(2):167-74. PMID:12013438 doi:10.1007/s007920100245
↑ Ahel I, Stathopoulos C, Ambrogelly A, Sauerwald A, Toogood H, Hartsch T, Söll D. Cysteine activation is an inherent in vitro property of prolyl-tRNA synthetases. J Biol Chem. 2002 Sep 20;277(38):34743-8. PMID:12130657 doi:10.1074/jbc.M206928200
↑ Yaremchuk A, Tukalo M, Grotli M, Cusack S. A succession of substrate induced conformational changes ensures the amino acid specificity of Thermus thermophilus prolyl-tRNA synthetase: comparison with histidyl-tRNA synthetase. J Mol Biol. 2001 Jun 15;309(4):989-1002. PMID:11399074 doi:10.1006/jmbi.2001.4712

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1h4s"

Categories: Large Structures | Thermus thermophilus | Cusack S | Tukalo M | Yaremchuk A

@@ Line 1: / Line 1: @@
 ==Prolyl-tRNA synthetase from Thermus thermophilus complexed with tRNApro(CGG) and a prolyl-adenylate analogue==
-<StructureSection load='1h4s' size='340' side='right' caption='[[1h4s]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
+<StructureSection load='1h4s' size='340' side='right'caption='[[1h4s]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1h4s]] is a 3 chain structure with sequence 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=1H4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1H4S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1h4s]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H4S FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PSD:5-O-[N-(PROLYL)-SULFAMOYL]ADENOSINE'>PSD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.85&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=PSD:5-O-[N-(PROLYL)-SULFAMOYL]ADENOSINE'>PSD</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1h4q|1h4q]], [[1h4t|1h4t]], [[1hc7|1hc7]]</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=1h4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h4s OCA], [https://pdbe.org/1h4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h4s RCSB], [https://www.ebi.ac.uk/pdbsum/1h4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h4s 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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1h4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h4s OCA], [http://pdbe.org/1h4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1h4s RCSB], [http://www.ebi.ac.uk/pdbsum/1h4s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1h4s ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYP_THET8 SYP_THET8] 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.<ref>PMID:12013438</ref> <ref>PMID:12130657</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/h4/1h4s_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h4/1h4s_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]]
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-*[[TRNA|TRNA]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Proline--tRNA ligase]]
+[[Category: Large Structures]]
 [[Category: Thermus thermophilus]]
-[[Category: Cusack, S]]
+[[Category: Cusack S]]
-[[Category: Tukalo, M]]
+[[Category: Tukalo M]]
-[[Category: Yaremchuk, A]]
+[[Category: Yaremchuk A]]
-[[Category: Aminoacyl-trna synthetase]]
-[[Category: Class ii aminoacyl-trna synthetase]]

1h4s

From Proteopedia

Current revision

Prolyl-tRNA synthetase from Thermus thermophilus complexed with tRNApro(CGG) and a prolyl-adenylate analogue

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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