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.

2.50
HDL Handle:
http://hdl.handle.net/10033/215524
Title:
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.
Authors:
Storbeck, Sonja; Saha, Sayantan; Krausze, Joern; Klink, Björn U; Heinz, Dirk W; Layer, Gunhild
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.
Affiliation:
Institute of Microbiology, Technische Universität Braunschweig, 38106 Braunschweig, Germany.
Citation:
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. 2011, 286 (30):26754-67 J. Biol. Chem.
Journal:
The Journal of biological chemistry
Issue Date:
29-Jul-2011
URI:
http://hdl.handle.net/10033/215524
DOI:
10.1074/jbc.M111.239855
PubMed ID:
21632530
Type:
Article
Language:
en
ISSN:
1083-351X
Appears in Collections:
Publications from Division of Molekulare Struktur Biologie (MOSB)

Full metadata record

DC FieldValueLanguage
dc.contributor.authorStorbeck, Sonjaen_GB
dc.contributor.authorSaha, Sayantanen_GB
dc.contributor.authorKrausze, Joernen_GB
dc.contributor.authorKlink, Björn Uen_GB
dc.contributor.authorHeinz, Dirk Wen_GB
dc.contributor.authorLayer, Gunhilden_GB
dc.date.accessioned2012-03-13T13:12:18Z-
dc.date.available2012-03-13T13:12:18Z-
dc.date.issued2011-07-29-
dc.identifier.citationCrystal 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. 2011, 286 (30):26754-67 J. Biol. Chem.en_GB
dc.identifier.issn1083-351X-
dc.identifier.pmid21632530-
dc.identifier.doi10.1074/jbc.M111.239855-
dc.identifier.urihttp://hdl.handle.net/10033/215524-
dc.description.abstractDuring 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.en_GB
dc.language.isoenen
dc.rightsArchived with thanks to The Journal of biological chemistryen_GB
dc.subject.meshBacterial Proteinsen_GB
dc.subject.meshCatalysisen_GB
dc.subject.meshCrystallography, X-Rayen_GB
dc.subject.meshHemeen_GB
dc.subject.meshMethyltransferasesen_GB
dc.subject.meshMutagenesis, Site-Directeden_GB
dc.subject.meshMutation, Missenseen_GB
dc.subject.meshProtein Structure, Tertiaryen_GB
dc.subject.meshPseudomonas aeruginosaen_GB
dc.subject.meshUroporphyrinogensen_GB
dc.titleCrystal 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.en
dc.typeArticleen
dc.contributor.departmentInstitute of Microbiology, Technische Universität Braunschweig, 38106 Braunschweig, Germany.en_GB
dc.identifier.journalThe Journal of biological chemistryen_GB

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