2YBO

The x-ray structure of the SAM-dependent uroporphyrinogen III methyltransferase NirE from Pseudomonas aeruginosa in complex with SAH

Summary for 2YBO

• Entry DOI: 10.2210/pdb2ybo/pdb
• Related: 2YBQ
• Descriptor: METHYLTRANSFERASE, S-ADENOSYL-L-HOMOCYSTEINE (3 entities in total)
• Functional Keywords: sumt, transferase, nire, heme d1 biosynthesis
• Biological source: PSEUDOMONAS AERUGINOSA
• Total number of polymer chains: 1
• Total formula weight: 31786.42

Authors

Storbeck, S.,Saha, S.,Krausze, J.,Klink, B.U.,Heinz, D.W.,Layer, G. (deposition date: 2011-03-08, release date: 2011-06-01, Last modification date: 2025-12-10)

Primary citation

Storbeck, S.,Saha, S.,Krausze, J.,Klink, B.U.,Heinz, D.W.,Layer, G.
Crystal Structure of the Heme D1 Biosynthesis Enzyme Nire in Complex with its Substrate Reveals New Insights Into the Catalytic Mechanism of S-Adenosyl-L-Methionine-Dependent Uroporphyrinogen III Methyltransferases.
J.Biol.Chem., 286:26754-, 2011

PubMed Abstract: During the biosynthesis of heme d(1), the essential cofactor of cytochrome cd(1) nitrite reductase, the NirE protein catalyzes the methylation of uroporphyrinogen III to precorrin-2 using S-adenosyl-L-methionine (SAM) as the methyl group donor. The crystal structure of Pseudomonas aeruginosa NirE in complex with its substrate uroporphyrinogen III and the reaction by-product S-adenosyl-L-homocysteine (SAH) was solved to 2.0 Å resolution. This represents the first enzyme-substrate complex structure for a SAM-dependent uroporphyrinogen III methyltransferase. The large substrate binds on top of the SAH in a "puckered" conformation in which the two pyrrole rings facing each other point into the same direction either upward or downward. Three arginine residues, a histidine, and a methionine are involved in the coordination of uroporphyrinogen III. Through site-directed mutagenesis of the nirE gene and biochemical characterization of the corresponding NirE variants the amino acid residues Arg-111, Glu-114, and Arg-149 were identified to be involved in NirE catalysis. Based on our structural and biochemical findings, we propose a potential catalytic mechanism for NirE in which the methyl transfer reaction is initiated by an arginine catalyzed proton abstraction from the C-20 position of the substrate.

PubMed: 21632530
DOI: 10.1074/JBC.M111.239855

Experimental method

X-RAY DIFFRACTION (2 Å)