1wk8: Difference between revisions

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Revision as of 00:37, 31 March 2008

File:1wk8.gif

, resolution 1.70Å

Ligands:

Gene:

ILES (Thermus thermophilus)

Activity:

Isoleucine--tRNA ligase, with EC number 6.1.1.5

Resources:

FirstGlance, OCA, PDBsum, RCSB

Coordinates:

save as pdb, mmCIF, xml

Isoleucyl-tRNA synthetase editing domain complexed with the pre-transfer editing substrate analogue, Val-AMS

OverviewOverview

In isoleucyl-tRNA synthetase (IleRS), the "editing" domain contributes to accurate aminoacylation by hydrolyzing the mis-synthesized intermediate, valyl-adenylate, in the "pre-transfer" editing mode and the incorrect final product, valyl-tRNA(Ile), in the "post-transfer" editing mode. In the present study, we determined the crystal structures of the Thermus thermophilus IleRS editing domain complexed with the substrate analogues in the pre and post-transfer modes, both at 1.7 A resolution. The active site accommodates the two analogues differently, with the valine side-chain rotated by about 120 degrees and the adenosine moiety oriented upside down. The substrate-binding pocket adjusts to the adenosine-monophosphate and adenosine moieties in the pre and post-transfer modes, respectively, by flipping the Trp227 side-chain by about 180 degrees . The substrate recognition mechanisms of IleRS are characterized by the active-site rearrangement between the two editing modes, and therefore differ from those of the homologous valyl and leucyl-tRNA synthetases from T.thermophilus, in which the post-transfer mode is predominant. Both modes of editing activities were reduced by replacements of Trp227 with Ala, Val, Leu, and His, but not by those with Phe and Tyr, indicating that the aromatic ring of Trp227 is important for the substrate recognition. In both editing modes, Thr233 and His319 recognize the substrate valine side-chain, regardless of the valine side-chain rotation, and reject the isoleucine side-chain. The T233A and H319A mutants have detectable editing activities against the cognate isoleucine.

About this StructureAbout this Structure

1WK8 is a Single protein structure of sequence from Thermus thermophilus. Full crystallographic information is available from OCA.

ReferenceReference

Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase., Fukunaga R, Yokoyama S, J Mol Biol. 2006 Jun 16;359(4):901-12. Epub 2006 Apr 25. PMID:16697013

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OCA

@@ Line 5: / Line 5: @@
 |SITE=
 |LIGAND= <scene name='pdbligand=VMS:5&#39;O-[N-(L-VALYL)SULPHAMOYL]ADENOSINE'>VMS</scene>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Isoleucine--tRNA_ligase Isoleucine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.5 6.1.1.5]
+|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Isoleucine--tRNA_ligase Isoleucine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.5 6.1.1.5] </span>
 |GENE= ILES ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])
+|DOMAIN=
+|RELATEDENTRY=
+|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wk8 OCA], [http://www.ebi.ac.uk/pdbsum/1wk8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1wk8 RCSB]</span>
 }}
@@ Line 26: / Line 29: @@
 [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
 [[Category: Yokoyama, S.]]
-[[Category: VMS]]
 [[Category: amino acid]]
 [[Category: cp1]]
@@ Line 40: / Line 42: @@
 [[Category: translation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 14:07:06 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:37:20 2008''