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.

1dbu

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:22, 6 December 2017

Crystal structure of cysteinyl-tRNA(Pro) deacylase protein from H. influenzae (HI1434)

Structural highlights

1dbu is a 1 chain structure with sequence from "bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	1dbx
Gene:	YbaK ("Bacterium influenzae" Lehmann and Neumann 1896)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[YBAK_HAEIN] Functions in trans to edit the amino acid from incorrectly charged Cys-tRNA(Pro) via a Cys-tRNA(Pro) deacylase activity. Probably compensates for the lack of Cys-tRNA(Pro) editing by ProRS. Is also able to deacylate Cys-tRNA(Cys), and displays weak deacylase activity in vitro against Gly-tRNA(Gly), as well as, at higher concentrations, some other correctly charged tRNAs. Does not cleave Pro-tRNA(Pro).^[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

Structural genomics of proteins of unknown function most straightforwardly assists with assignment of biochemical activity when the new structure resembles that of proteins whose functions are known. When a new fold is revealed, the universe of known folds is enriched, and once the function is determined by other means, novel structure-function relationships are established. The previously unannotated protein HI1434 from H. influenzae provides a hybrid example of these two paradigms. It is a member of a microbial protein family, labeled in SwissProt as YbaK and ebsC. The crystal structure at 1.8 A resolution reported here reveals a fold that is only remotely related to the C-lectin fold, in particular to endostatin, and thus is not sufficiently similar to imply that YbaK proteins are saccharide binding proteins. However, a crevice that may accommodate a small ligand is evident. The putative binding site contains only one invariant residue, Lys46, which carries a functional group that could play a role in catalysis, indicating that YbaK is probably not an enzyme. Detailed sequence analysis, including a number of newly sequenced microbial organisms, highlights sequence homology to an insertion domain in prolyl-tRNA synthetases (proRS) from prokaryote, a domain whose function is unknown. A HI1434-based model of the insertion domain shows that it should also contain the putative binding site. Being part of a tRNA synthetases, the insertion domain is likely to be involved in oligonucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA. By analogy, YbaK may also play a role in nucleotide or oligonucleotide binding, the nature of which is yet to be determined.

Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications.,Zhang H, Huang K, Li Z, Banerjei L, Fisher KE, Grishin NV, Eisenstein E, Herzberg O Proteins. 2000 Jul 1;40(1):86-97. PMID:10813833^[4]

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

References

↑ An S, Musier-Forsyth K. Trans-editing of Cys-tRNAPro by Haemophilus influenzae YbaK protein. J Biol Chem. 2004 Oct 8;279(41):42359-62. Epub 2004 Aug 20. PMID:15322138 doi:http://dx.doi.org/10.1074/jbc.C400304200
↑ Ruan B, Soll D. The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNA Cys deacylase. J Biol Chem. 2005 Jul 8;280(27):25887-91. Epub 2005 May 10. PMID:15886196 doi:http://dx.doi.org/10.1074/jbc.M502174200
↑ So BR, An S, Kumar S, Das M, Turner DA, Hadad CM, Musier-Forsyth K. Substrate-mediated fidelity mechanism ensures accurate decoding of proline codons. J Biol Chem. 2011 Sep 9;286(36):31810-20. doi: 10.1074/jbc.M111.232611. Epub 2011, Jul 18. PMID:21768119 doi:http://dx.doi.org/10.1074/jbc.M111.232611
↑ Zhang H, Huang K, Li Z, Banerjei L, Fisher KE, Grishin NV, Eisenstein E, Herzberg O. Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications. Proteins. 2000 Jul 1;40(1):86-97. PMID:10813833

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/1dbu"

@@ Line 1: / Line 1: @@
 ==Crystal structure of cysteinyl-tRNA(Pro) deacylase protein from H. influenzae (HI1434)==
 <StructureSection load='1dbu' size='340' side='right' caption='[[1dbu]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
@@ Line 7: / Line 8: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dbx|1dbx]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YbaK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</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=1dbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dbu OCA], [http://pdbe.org/1dbu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dbu RCSB], [http://www.ebi.ac.uk/pdbsum/1dbu PDBsum]</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=1dbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dbu OCA], [http://pdbe.org/1dbu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dbu RCSB], [http://www.ebi.ac.uk/pdbsum/1dbu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dbu ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 15: / Line 16: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/db/1dbu_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/db/1dbu_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1dbu

From Proteopedia

Revision as of 08:22, 6 December 2017

Crystal structure of cysteinyl-tRNA(Pro) deacylase protein from H. influenzae (HI1434)

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