9qof: Difference between revisions

Latest revision as of 05:50, 14 May 2025

E.coli seryl-tRNA synthetase (Arm deletion mutant) bound to sulphamoyl seryl-adenylate analogue

Structural highlights

9qof is a 2 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.32Å
Ligands:	MG, SO4, SSA
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SYS_ECOLI Catalyzes the attachment of serine to tRNA(Ser) (PubMed:7537870). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).^[1] ^[2] ^[3]

Publication Abstract from PubMed

Escherichia coli seryl-tRNA synthetase (SerRS) a dimeric class II aminoacyl-tRNA synthetase with two structural domains charges specifically the five iso-acceptor tRNA(ser) as well as the tRNA(sec) (selC product) of E. coli. The N-terminal domain is a 60 A long arm-like coiled coil structure built of 2 long antiparallel a-h helices, whereas the C-terminal domain is a alpha-beta structure. A deletion of the N-terminal arm of the enzyme does not affect the amino acid activation step of the reaction, but reduces dramatically amino-acylation activity. The Kcat/Km value for the mutant enzyme is reduced by more than 4 orders of magnitude, with a nearly 30 fold increased Km value for tRNA(ser). An only slightly truncated mutant form (16 amino acids of the tip of the arm replaced by a glycine) has an intermediate aminoacylation activity. Both mutant synthetases have lost their specificity for tRNA(ser) and charge also non-cognate type 1 tRNA(s). Our results support the hypothesis that class II synthetases have evolved from an ancestral catalytic core enzyme by adding non-catalytic N-terminal or C-terminal tRNA binding (specificity) domains which act as determinants for cognate and anti-determinants for non-cognate tRNAs.

Seryl-tRNA synthetase from Escherichia coli: implication of its N-terminal domain in aminoacylation activity and specificity.,Borel F, Vincent C, Leberman R, Hartlein M Nucleic Acids Res. 1994 Aug 11;22(15):2963-9. PMID:8065908^[4]

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

References

↑ Leinfelder W, Zehelein E, Mandrand-Berthelot MA, Böck A. Gene for a novel tRNA species that accepts L-serine and cotranslationally inserts selenocysteine. Nature. 1988 Feb 25;331(6158):723-5. PMID:2963963 doi:10.1038/331723a0
↑ Vincent C, Borel F, Willison JC, Leberman R, Härtlein M. Seryl-tRNA synthetase from Escherichia coli: functional evidence for cross-dimer tRNA binding during aminoacylation. Nucleic Acids Res. 1995 Apr 11;23(7):1113-8. PMID:7537870 doi:10.1093/nar/23.7.1113
↑ Borel F, Vincent C, Leberman R, Härtlein M. Seryl-tRNA synthetase from Escherichia coli: implication of its N-terminal domain in aminoacylation activity and specificity. Nucleic Acids Res. 1994 Aug 11;22(15):2963-9. PMID:8065908 doi:10.1093/nar/22.15.2963
↑ Borel F, Vincent C, Leberman R, Härtlein M. Seryl-tRNA synthetase from Escherichia coli: implication of its N-terminal domain in aminoacylation activity and specificity. Nucleic Acids Res. 1994 Aug 11;22(15):2963-9. PMID:8065908 doi:10.1093/nar/22.15.2963

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Leinfelder W, Zehelein E, Mandrand-Berthelot MA, Böck A. Gene for a novel tRNA species that accepts L-serine and cotranslationally inserts selenocysteine. Nature. 1988 Feb 25;331(6158):723-5. PMID:2963963 doi:10.1038/331723a0

[2] Vincent C, Borel F, Willison JC, Leberman R, Härtlein M. Seryl-tRNA synthetase from Escherichia coli: functional evidence for cross-dimer tRNA binding during aminoacylation. Nucleic Acids Res. 1995 Apr 11;23(7):1113-8. PMID:7537870 doi:10.1093/nar/23.7.1113

[3] Borel F, Vincent C, Leberman R, Härtlein M. Seryl-tRNA synthetase from Escherichia coli: implication of its N-terminal domain in aminoacylation activity and specificity. Nucleic Acids Res. 1994 Aug 11;22(15):2963-9. PMID:8065908 doi:10.1093/nar/22.15.2963

[4] Borel F, Vincent C, Leberman R, Härtlein M. Seryl-tRNA synthetase from Escherichia coli: implication of its N-terminal domain in aminoacylation activity and specificity. Nucleic Acids Res. 1994 Aug 11;22(15):2963-9. PMID:8065908 doi:10.1093/nar/22.15.2963

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9qof is ON HOLD
+==E.coli seryl-tRNA synthetase (Arm deletion mutant) bound to sulphamoyl seryl-adenylate analogue==
+<StructureSection load='9qof' size='340' side='right'caption='[[9qof]], [[Resolution|resolution]] 2.32&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9qof]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9QOF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9QOF 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]] 2.32&#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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</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=9qof FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9qof OCA], [https://pdbe.org/9qof PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9qof RCSB], [https://www.ebi.ac.uk/pdbsum/9qof PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9qof ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYS_ECOLI SYS_ECOLI] Catalyzes the attachment of serine to tRNA(Ser) (PubMed:7537870). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).<ref>PMID:2963963</ref> <ref>PMID:7537870</ref> <ref>PMID:8065908</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Escherichia coli seryl-tRNA synthetase (SerRS) a dimeric class II aminoacyl-tRNA synthetase with two structural domains charges specifically the five iso-acceptor tRNA(ser) as well as the tRNA(sec) (selC product) of E. coli. The N-terminal domain is a 60 A long arm-like coiled coil structure built of 2 long antiparallel a-h helices, whereas the C-terminal domain is a alpha-beta structure. A deletion of the N-terminal arm of the enzyme does not affect the amino acid activation step of the reaction, but reduces dramatically amino-acylation activity. The Kcat/Km value for the mutant enzyme is reduced by more than 4 orders of magnitude, with a nearly 30 fold increased Km value for tRNA(ser). An only slightly truncated mutant form (16 amino acids of the tip of the arm replaced by a glycine) has an intermediate aminoacylation activity. Both mutant synthetases have lost their specificity for tRNA(ser) and charge also non-cognate type 1 tRNA(s). Our results support the hypothesis that class II synthetases have evolved from an ancestral catalytic core enzyme by adding non-catalytic N-terminal or C-terminal tRNA binding (specificity) domains which act as determinants for cognate and anti-determinants for non-cognate tRNAs.
-Authors: Cusack, S., Belrhali, H., Price, S., Leberman, R.
+Seryl-tRNA synthetase from Escherichia coli: implication of its N-terminal domain in aminoacylation activity and specificity.,Borel F, Vincent C, Leberman R, Hartlein M Nucleic Acids Res. 1994 Aug 11;22(15):2963-9. PMID:8065908<ref>PMID:8065908</ref>
-Description: E.coli seryl-tRNA synthetase (Arm deletion mutant) bound to sulphamoyl seryl-adenylate analogue
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Leberman, R]]
+<div class="pdbe-citations 9qof" style="background-color:#fffaf0;"></div>
-[[Category: Cusack, S]]
+== References ==
-[[Category: Belrhali, H]]
+<references/>
-[[Category: Price, S]]
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli K-12]]
+[[Category: Large Structures]]
+[[Category: Belrhali H]]
+[[Category: Cusack S]]
+[[Category: Leberman R]]
+[[Category: Price S]]

9qof: Difference between revisions

Latest revision as of 05:50, 14 May 2025

E.coli seryl-tRNA synthetase (Arm deletion mutant) bound to sulphamoyl seryl-adenylate analogue

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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