2yy8
From Proteopedia
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|PDB= 2yy8 |SIZE=350|CAPTION= <scene name='initialview01'>2yy8</scene>, resolution 2.48Å | |PDB= 2yy8 |SIZE=350|CAPTION= <scene name='initialview01'>2yy8</scene>, resolution 2.48Å | ||
|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> | |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= | + | |LIGAND= <scene name='pdbligand=MTA:5'-DEOXY-5'-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |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> | ||
}} | }} | ||
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]] | [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]] | ||
[[Category: Yokoyama, S.]] | [[Category: Yokoyama, S.]] | ||
| - | [[Category: MTA]] | ||
| - | [[Category: SAM]] | ||
[[Category: deep trefoil knot]] | [[Category: deep trefoil knot]] | ||
[[Category: national project on protein structural and functional analyse]] | [[Category: national project on protein structural and functional analyse]] | ||
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[[Category: transferase]] | [[Category: transferase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:16:35 2008'' |
Revision as of 02:16, 31 March 2008
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| , resolution 2.48Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | and | ||||||
| Ligands: | , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of archaeal tRNA-methylase for position 56 (aTrm56) from Pyrococcus horikoshii, complexed with S-adenosyl-L-methionine
Overview
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 Structure
2YY8 is a Single protein structure of sequence from Pyrococcus horikoshii. Full crystallographic information is available from OCA.
Reference
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
Categories: Pyrococcus horikoshii | Single protein | Kuratani, M. | RSGI, RIKEN Structural Genomics/Proteomics Initiative. | Yokoyama, S. | Deep trefoil knot | National project on protein structural and functional analyse | Nppsfa | Riken structural genomics/proteomics initiative | Rsgi | Structural genomic | Transferase
