title: The crystal structure of siroheme decarboxylase in complex with iron-uroporphyrin III reveals two essential histidine residues.
abstract: The isobacteriochlorin heme d1 serves as an essential cofactor in the cytochrome cd1 nitrite reductase NirS that plays an important role for denitrification. During the biosynthesis of heme d1, the enzyme siroheme decarboxylase catalyzes the conversion of siroheme to 12,18-didecarboxysiroheme. This enzyme was discovered recently (Bali S, Lawrence AD, Lobo SA, Saraiva LM, Golding BT, Palmer DJ et al. Molecular hijacking of siroheme for the synthesis of heme and d1 heme. Proc Natl Acad Sci USA 2011;108:18260-5) and is only scarcely characterized. Here, we present the crystal structure of the siroheme decarboxylase from Hydrogenobacter thermophilus representing the first three-dimensional structure for this type of enzyme. The overall structure strikingly resembles those of transcriptional regulators of the Lrp/AsnC family. Moreover, the structure of the enzyme in complex with a substrate analog reveals first insights into its active-site architecture. Through site-directed mutagenesis and subsequent biochemical characterization of the enzyme variants, two conserved histidine residues within the active site are identified to be involved in substrate binding and catalysis. Based on our results, we propose a potential catalytic mechanism for the enzymatic reaction catalyzed by the siroheme decarboxylase.
authors.affiliation: Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany.
authors.forename: Kristin
authors.initials: K
authors.lastname: Haufschildt
authors.affiliation: Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Schmelz
authors.affiliation: Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany.
authors.forename: Theresa M
authors.initials: TM
authors.lastname: Kriegler
authors.affiliation: Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Neumann
authors.affiliation: Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany.
authors.forename: Judith
authors.initials: J
authors.lastname: Streif
authors.affiliation: Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Arai
authors.affiliation: Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany.
authors.forename: Dirk W
authors.initials: DW
authors.lastname: Heinz
authors.affiliation: Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany. Electronic address: g.layer@tu-braunschweig.de.
authors.forename: Gunhild
authors.initials: G
authors.lastname: Layer
mesh_terms: D000595:Amino Acid Sequence; D001419:Bacteria / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000648:ultrastructure; D001665:Binding Sites; D002262:Carboxy-Lyases / Q000737:chemistry* / Q000648:ultrastructure; D020134:Catalytic Domain; D003653:Decarboxylation; D006418:Heme / Q000031:analogs & derivatives / Q000096:biosynthesis / Q000737:chemistry; D006639:Histidine / Q000737:chemistry*; D007501:Iron / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D011485:Protein Binding; D016415:Sequence Alignment; D014578:Uroporphyrins / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D014578:Uroporphyrins; C022181:uroporphyrin III; D006418:Heme; D006639:Histidine; C009272:siroheme; C029400:heme d1; D007501:Iron; D002262:Carboxy-Lyases
keywords: NirDL; X-ray structure; denitrification; heme d(1); tetrapyrrole biosynthesis