2YBQ | pdb_00002ybq

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

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2ybqa_	Alpha and beta proteins (a/b)	Tetrapyrrole methylase	Tetrapyrrole methylase	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Tetrapyrrole methylase	8067843	4000056	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Tetrapyrrole methylase	8067844	3000017	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	TP_methylase_C	e2ybqA1	A: a+b two layers	X: Tetrapyrrole methylase C-terminal domain-like	H: Tetrapyrrole methylase C-terminal domain (From Topology)	T: Tetrapyrrole methylase C-terminal domain	F: TP_methylase_C	ECOD (1.6)
A	TP_methylase_N	e2ybqA2	A: a/b three-layered sandwiches	X: Tetrapyrrole methylase N-terminal domain (From Topology)	H: Tetrapyrrole methylase N-terminal domain (From Topology)	T: Tetrapyrrole methylase N-terminal domain	F: TP_methylase_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1010.10	Alpha Beta	3-Layer(aba) Sandwich	Cobalt-precorrin-4 Transmethylase	domain 1	CATH (4.3.0)
A	3.30.950.10	Alpha Beta	2-Layer Sandwich	Methyltransferase, Cobalt-precorrin-4 Transmethylase	Domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	METHYLTRANSFERASE	oxidoreductase activity catalytic activity lyase activity C-methyltransferase activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity uroporphyrin-III C-methyltransferase activity	heme metabolic process pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process heme biosynthetic process siroheme biosynthetic process pigment biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process cobalamin metabolic process cobalamin biosynthetic process heme metabolic process pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process heme biosynthetic process siroheme biosynthetic process pigment biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process cobalamin metabolic process cobalamin biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process vitamin biosynthetic process vitamin metabolic process small molecule metabolic process methylation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR035996	Tetrapyrrole methylase superfamily	Homologous Superfamily
A	IPR014776	Tetrapyrrole methylase, subdomain 2	Homologous Superfamily
A	IPR006366	Uroporphyrin-III C-methyltransferase	Domain
A	IPR014777	Tetrapyrrole methylase, subdomain 1	Homologous Superfamily
A	IPR003043	Uroporphiryn-III C-methyltransferase, conserved site	Conserved Site
A	IPR000878	Tetrapyrrole methylase	Domain
A	IPR050161	Siroheme/cobalamin biosynthesis enzyme	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.