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.

3a4n

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:19, 24 October 2018

Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase

Structural highlights

3a4n is a 2 chain structure with sequence from Atcc 43067. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	3a4l, 3a4m
Gene:	MJ1538 (ATCC 43067)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PSTK_METJA] Specifically phosphorylates seryl-tRNA(Sec) to O-phosphoseryl-tRNA(Sec), an activated intermediate for selenocysteine biosynthesis.

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

Compared to bacteria, archaea and eukaryotes employ an additional enzyme for the biosynthesis of selenocysteine (Sec), the 21(st) natural amino acid (aa). An essential RNA-dependent kinase, O-phosphoseryl-tRNA(Sec) kinase (PSTK), converts seryl-tRNA(Sec) to O-phosphoseryl-tRNA(Sec), the immediate precursor of selenocysteinyl-tRNA(Sec). The sequence of Methanocaldococcus jannaschii PSTK (MjPSTK) suggests an N-terminal kinase domain (177 aa) followed by a presumed tRNA binding region (75 aa). The structures of MjPSTK complexed with ADP and AMPPNP revealed that this enzyme belongs to the P-loop kinase class, and that the kinase domain is closely related to gluconate kinase and adenylate kinase. ATP is bound by the P-loop domain (residues 11-18). Formed by antiparallel dimerization of two PSTK monomers, the enzyme structure shows a deep groove with positive electrostatic potential. Located in this groove is the enzyme's active site, which biochemical and genetic data suggest is composed of Asp-41, Arg-44, Glu-55, Tyr-82, Tyr-83, Met-86, and Met-132. Based on structural comparison with Escherichia coli adenylate kinase a docking model was generated that assigns these amino acids to the recognition of the terminal A76-Ser moieties of Ser-tRNA(Sec). The geometry and electrostatic environment of the groove in MjPSTK are perfectly complementary to the unusually long acceptor helix of tRNA(Sec).

Structure of a tRNA-dependent kinase essential for selenocysteine decoding.,Araiso Y, Sherrer RL, Ishitani R, Ho JM, Soll D, Nureki O Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16215-20. Epub 2009 Sep 10. PMID:19805283^[1]

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

References

↑ Araiso Y, Sherrer RL, Ishitani R, Ho JM, Soll D, Nureki O. Structure of a tRNA-dependent kinase essential for selenocysteine decoding. Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16215-20. Epub 2009 Sep 10. PMID:19805283

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/3a4n"

@@ Line 1: / Line 1: @@
 ==Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase==
 <StructureSection load='3a4n' size='340' side='right' caption='[[3a4n]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3a4l|3a4l]], [[3a4m|3a4m]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MJ1538 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3a4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a4n OCA], [http://pdbe.org/3a4n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3a4n RCSB], [http://www.ebi.ac.uk/pdbsum/3a4n 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=3a4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a4n OCA], [http://pdbe.org/3a4n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3a4n RCSB], [http://www.ebi.ac.uk/pdbsum/3a4n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3a4n ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a4/3a4n_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a4/3a4n_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

3a4n

From Proteopedia

Revision as of 08:19, 24 October 2018

Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase

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