5I8T

Structure of Mouse Acireductone dioxygenase with Ni2+ ion and D-lactic acid in the active site

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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	d5i8ta_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	Acireductone dioxygenase	Acireductone dioxygenase	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RmlC-like cupins	8032687	3001825	SCOP2B (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	ARD	e5i8tA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: ARD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03079	ARD/ARD' family (ARD)	ARD/ARD' family	The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence Swiss:Q9ZFE7, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be ...	The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence Swiss:Q9ZFE7, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions [1,2]. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalysed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels [1,2]. This family also contains other members, whose functions are not well characterised.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase	oxidoreductase activity catalytic activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen acireductone dioxygenase (Ni2+-requiring) activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen dioxygenase activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding iron ion binding oxidoreductase activity catalytic activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen acireductone dioxygenase (Ni2+-requiring) activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen dioxygenase activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding iron ion binding acireductone dioxygenase [iron(II)-requiring] activity	oxoacid metabolic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process metabolic compound salvage small molecule metabolic process sulfur compound metabolic process L-methionine biosynthetic process methionine biosynthetic process oxoacid metabolic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process metabolic compound salvage small molecule metabolic process sulfur compound metabolic process L-methionine biosynthetic process methionine biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process methionine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid salvage amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process L-methionine salvage from methylthioadenosine proteinogenic amino acid biosynthetic process metabolic process cellular process L-methionine salvage sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR014710	RmlC-like jelly roll fold	Homologous Superfamily
A	IPR011051	RmlC-like cupin domain superfamily	Homologous Superfamily
A	IPR027496	Acireductone dioxygenase, eukaryotes	Family
A	IPR004313	Acireductone dioxygenase ARD family	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.