1NV8

N5-glutamine methyltransferase, HemK

Summary for 1NV8

• Entry DOI: 10.2210/pdb1nv8/pdb
• Related: 1NV9
• Descriptor: hemK protein, S-ADENOSYLMETHIONINE, N5-METHYLGLUTAMINE, ... (4 entities in total)
• Functional Keywords: class i adomet-dependent methyltransferase, transferase
• Biological source: Thermotoga maritima
• Total number of polymer chains: 2
• Total formula weight: 64680.29

Authors

Schubert, H.L.,Phillips, J.D.,Hill, C.P. (deposition date: 2003-02-02, release date: 2003-05-27, Last modification date: 2024-02-14)

Primary citation

Schubert, H.L.,Phillips, J.D.,Hill, C.P.
Structures along the Catalytic Pathway of PrmC/HemK, an N(5)-Glutamine AdoMet-Dependent Methyltransferase
Biochemistry, 42:5592-5599, 2003

PubMed Abstract: Posttranslational methylation of release factors on the glutamine residue of a conserved GGQ motif is required for efficient termination of protein synthesis. This methylation is performed by an N(5)-glutamine methyltransferase called PrmC/HemK, whose crystal structure we report here at 2.2 A resolution. The electron density at the active site appears to contain a mixture of the substrates, S-adenosyl-L-methionine (AdoMet) and glutamine, and the products, S-adenosyl-L-homocysteine (AdoHcy) and N(5)-methylglutamine. The C-terminal domain of PrmC adopts the canonical AdoMet-dependent methyltransferase fold and shares structural similarity with the nucleotide N-methyltransferases in the active site, including use of a conserved (D/N)PPY motif to select and position the glutamine substrate. Residues of the PrmC (197)NPPY(200) motif form hydrogen bonds that position the planar Gln side chain such that the lone-pair electrons on the nitrogen nucleophile are oriented toward the methyl group of AdoMet. In the product complex, the methyl group remains pointing toward the sulfur, consistent with either an sp(3)-hybridized, positively charged Gln nitrogen, or a neutral sp(2)-hybridized nitrogen in a strained conformation. Due to steric overlap within the active site, proton loss and formation of the neutral planar methylamide product are likely to occur during or after product release. These structures, therefore, represent intermediates along the catalytic pathway of PrmC and show how the (D/N)PPY motif can be used to select a wide variety substrates.

PubMed: 12741815
DOI: 10.1021/bi034026p

Experimental method

X-RAY DIFFRACTION (2.2 Å)