This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1nzj

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:57, 21 April 2021

Crystal Structure and Activity Studies of Escherichia Coli Yadb ORF

Structural highlights

1nzj is a 1 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[GLUQ_ECOLI] Catalyzes the tRNA-independent activation of glutamate in presence of ATP and the subsequent transfer of glutamate onto tRNA(Asp). Glutamate is transferred on the 2-amino-5-(4,5-dihydroxy-2-cyclopenten-1-yl) moiety of the queuosine in position 34 of the tRNA(Asp), the wobble position of the QUC anticodon. Does not transfer glutamate to either tRNA(Glu) or tRNA(Gln). The incapacity of the glutamylated tRNA(Asp) to bind elongation factor Tu suggests that it is not involved in ribosomal protein biosynthesis.^[1] ^[2] ^[3]

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

In the course of a structural genomics program aiming at solving the structures of Escherichia coli open reading frame products of unknown function, we have determined the structure of YadB at 1.5A using molecular replacement. The YadB protein is 298 amino acid residues long and displays 34% sequence identity with E.coli glutamyl-tRNA synthetase (GluRS). It is much shorter than GluRS, which contains 468 residues, and lacks the complete domain interacting with the tRNA anticodon loop. As E.coli GluRS, YadB possesses a Zn2+ located in the putative tRNA acceptor stem-binding domain. The YadB cluster uses cysteine residues as the first three zinc ligands, but has a weaker tyrosine ligand at the fourth position. It shares with canonical amino acid RNA synthetases a major functional feature, namely activation of the amino acid (here glutamate). It differs, however, from GluRSs by the fact that the activation step is tRNA-independent and that it does not catalyze attachment of the activated glutamate to E.coli tRNAGlu, but to another, as yet unknown tRNA. These results suggest thus a novel function, distinct from that of GluRSs, for the yadB gene family.

The Escherichia coli YadB gene product reveals a novel aminoacyl-tRNA synthetase like activity.,Campanacci V, Dubois DY, Becker HD, Kern D, Spinelli S, Valencia C, Pagot F, Salomoni A, Grisel S, Vincentelli R, Bignon C, Lapointe J, Giege R, Cambillau C J Mol Biol. 2004 Mar 19;337(2):273-83. PMID:15003446^[4]

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

References

↑ Dubois DY, Blaise M, Becker HD, Campanacci V, Keith G, Giege R, Cambillau C, Lapointe J, Kern D. An aminoacyl-tRNA synthetase-like protein encoded by the Escherichia coli yadB gene glutamylates specifically tRNAAsp. Proc Natl Acad Sci U S A. 2004 May 18;101(20):7530-5. Epub 2004 Apr 19. PMID:15096594 doi:http://dx.doi.org/10.1073/pnas.0401634101
↑ Salazar JC, Ambrogelly A, Crain PF, McCloskey JA, Soll D. A truncated aminoacyl-tRNA synthetase modifies RNA. Proc Natl Acad Sci U S A. 2004 May 18;101(20):7536-41. Epub 2004 Apr 19. PMID:15096612 doi:http://dx.doi.org/10.1073/pnas.0401982101
↑ Blaise M, Becker HD, Keith G, Cambillau C, Lapointe J, Giege R, Kern D. A minimalist glutamyl-tRNA synthetase dedicated to aminoacylation of the tRNAAsp QUC anticodon. Nucleic Acids Res. 2004 May 18;32(9):2768-75. Print 2004. PMID:15150343 doi:http://dx.doi.org/10.1093/nar/gkh608
↑ Campanacci V, Dubois DY, Becker HD, Kern D, Spinelli S, Valencia C, Pagot F, Salomoni A, Grisel S, Vincentelli R, Bignon C, Lapointe J, Giege R, Cambillau C. The Escherichia coli YadB gene product reveals a novel aminoacyl-tRNA synthetase like activity. J Mol Biol. 2004 Mar 19;337(2):273-83. PMID:15003446 doi:10.1016/j.jmb.2004.01.027

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 3: / Line 3: @@
 <StructureSection load='1nzj' size='340' side='right'caption='[[1nzj]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1nzj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NZJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1nzj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NZJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nzj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzj OCA], [http://pdbe.org/1nzj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nzj RCSB], [http://www.ebi.ac.uk/pdbsum/1nzj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nzj ProSAT]</span></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=1nzj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzj OCA], [https://pdbe.org/1nzj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nzj RCSB], [https://www.ebi.ac.uk/pdbsum/1nzj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nzj ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GLUQ_ECOLI GLUQ_ECOLI]] Catalyzes the tRNA-independent activation of glutamate in presence of ATP and the subsequent transfer of glutamate onto tRNA(Asp). Glutamate is transferred on the 2-amino-5-(4,5-dihydroxy-2-cyclopenten-1-yl) moiety of the queuosine in position 34 of the tRNA(Asp), the wobble position of the QUC anticodon. Does not transfer glutamate to either tRNA(Glu) or tRNA(Gln). The incapacity of the glutamylated tRNA(Asp) to bind elongation factor Tu suggests that it is not involved in ribosomal protein biosynthesis.<ref>PMID:15096594</ref> <ref>PMID:15096612</ref> <ref>PMID:15150343</ref>
+[[https://www.uniprot.org/uniprot/GLUQ_ECOLI GLUQ_ECOLI]] Catalyzes the tRNA-independent activation of glutamate in presence of ATP and the subsequent transfer of glutamate onto tRNA(Asp). Glutamate is transferred on the 2-amino-5-(4,5-dihydroxy-2-cyclopenten-1-yl) moiety of the queuosine in position 34 of the tRNA(Asp), the wobble position of the QUC anticodon. Does not transfer glutamate to either tRNA(Glu) or tRNA(Gln). The incapacity of the glutamylated tRNA(Asp) to bind elongation factor Tu suggests that it is not involved in ribosomal protein biosynthesis.<ref>PMID:15096594</ref> <ref>PMID:15096612</ref> <ref>PMID:15150343</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

1nzj

From Proteopedia

Revision as of 08:57, 21 April 2021

Crystal Structure and Activity Studies of Escherichia Coli Yadb ORF

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox