1p9p

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spinqualitylabelsall models PDB ID 1p9p Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
, resolution 2.5Å
Ligands:
Gene:	TRMD OR B2607 OR C3128 OR Z3901 OR ECS3470 OR SF2667 (Escherichia coli, Escherichia coli O6, Escherichia coli O157:H7, and Shigella flexneri)
Activity:	tRNA (guanine-N(1)-)-methyltransferase, with EC number 2.1.1.31
Resources:	FirstGlance, OCA, PDBsum, RCSB
Coordinates:	save as pdb, mmCIF, xml

The Crystal Structure of a M1G37 tRNA Methyltransferase, TrmD

Overview

The crystal structure of Escherichia coli tRNA (guanosine-1) methyltransferase (TrmD) complexed with S-adenosyl homocysteine (AdoHcy) has been determined at 2.5A resolution. TrmD, which methylates G37 of tRNAs containing the sequence G36pG37, is a homo-dimer. Each monomer consists of a C-terminal domain connected by a flexible linker to an N-terminal AdoMet-binding domain. The two bound AdoHcy moieties are buried at the bottom of deep clefts. The dimer structure appears integral to the formation of the catalytic center of the enzyme and this arrangement strongly suggests that the anticodon loop of tRNA fits into one of these clefts for methyl transfer to occur. In addition, adjacent hydrophobic sites in the cleft delineate a defined pocket, which may accommodate the GpG sequence during catalysis. The dimer contains two deep trefoil peptide knots and a peptide loop extending from each knot embraces the AdoHcy adenine ring. Mutational analyses demonstrate that the knot is important for AdoMet binding and catalytic activity, and that the C-terminal domain is not only required for tRNA binding but plays a functional role in catalytic activity.

About this Structure

1P9P is a Single protein structure of sequence from Escherichia coli, escherichia coli o6, escherichia coli o157:h7, and shigella flexneri. Full crystallographic information is available from OCA.

Reference

Insights into catalysis by a knotted TrmD tRNA methyltransferase., Elkins PA, Watts JM, Zalacain M, van Thiel A, Vitazka PR, Redlak M, Andraos-Selim C, Rastinejad F, Holmes WM, J Mol Biol. 2003 Nov 7;333(5):931-49. PMID:14583191

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