2yy8: Difference between revisions

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Revision as of 05:16, 31 March 2008

File:2yy8.jpg

, resolution 2.48Å

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Crystal structure of archaeal tRNA-methylase for position 56 (aTrm56) from Pyrococcus horikoshii, complexed with S-adenosyl-L-methionine

OverviewOverview

The conserved cytidine residue at position 56 of tRNA contributes to the maintenance of the L-shaped tertiary structure. aTrm56 catalyzes the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Based on the amino acid sequence, aTrm56 is the most distant member of the SpoU family. Here, we determined the crystal structure of Pyrococcus horikoshii aTrm56 complexed with S-adenosyl-L-methionine at 2.48 A resolution. aTrm56 consists of the SPOUT domain, which contains the characteristic deep trefoil knot, and a unique C-terminal beta-hairpin. aTrm56 forms a dimer. The S-adenosyl-L-methionine binding and dimerization of aTrm56 were similar to those of the other SpoU members. A structure-based sequence alignment revealed that aTrm56 conserves only motif II, among the four signature motifs. However, an essential Arg16 residue is located at a novel position within motif I. Biochemical assays showed that aTrm56 prefers the L-shaped tRNA to the lambda form as its substrate.

About this StructureAbout this Structure

2YY8 is a Single protein structure of sequence from Pyrococcus horikoshii. Full crystallographic information is available from OCA.

ReferenceReference

Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA., Kuratani M, Bessho Y, Nishimoto M, Grosjean H, Yokoyama S, J Mol Biol. 2008 Jan 25;375(4):1064-75. Epub 2007 Nov 17. PMID:18068186

Page seeded by OCA on Mon Mar 31 05:16:35 2008

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OCA

@@ Line 4: / Line 4: @@
 |PDB= 2yy8 |SIZE=350|CAPTION= <scene name='initialview01'>2yy8</scene>, resolution 2.48&Aring;
 |SITE= <scene name='pdbsite=AC1:Sam+Binding+Site+For+Residue+B+500'>AC1</scene> and <scene name='pdbsite=AC2:Mta+Binding+Site+For+Residue+A+400'>AC2</scene>
-|LIGAND= <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene> and <scene name='pdbligand=MTA:5&#39;-DEOXY-5&#39;-METHYLTHIOADENOSINE'>MTA</scene>
+|LIGAND= <scene name='pdbligand=MTA:5&#39;-DEOXY-5&#39;-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>
 |ACTIVITY=
 |GENE=
+|DOMAIN=
+|RELATEDENTRY=
+|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2yy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yy8 OCA], [http://www.ebi.ac.uk/pdbsum/2yy8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2yy8 RCSB]</span>
 }}
@@ Line 25: / Line 28: @@
 [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
 [[Category: Yokoyama, S.]]
-[[Category: MTA]]
-[[Category: SAM]]
 [[Category: deep trefoil knot]]
 [[Category: national project on protein structural and functional analyse]]
@@ Line 35: / Line 36: @@
 [[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 15:55:47 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:16:35 2008''