1O9I

Crystal structure of the Y42F mutant of manganese catalase from Lactobacillus plantarum at 1.33A resolution

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1o9ia_	All alpha proteins	Ferritin-like	Ferritin-like	Manganese catalase (T-catalase)	Manganese catalase (T-catalase)	(Lactiplantibacillus plantarum ) [TaxId: 1590 ],	SCOPe (2.08)
B	d1o9ib_	All alpha proteins	Ferritin-like	Ferritin-like	Manganese catalase (T-catalase)	Manganese catalase (T-catalase)	(Lactiplantibacillus plantarum ) [TaxId: 1590 ],	SCOPe (2.08)
C	d1o9ic_	All alpha proteins	Ferritin-like	Ferritin-like	Manganese catalase (T-catalase)	Manganese catalase (T-catalase)	(Lactiplantibacillus plantarum ) [TaxId: 1590 ],	SCOPe (2.08)
D	d1o9id_	All alpha proteins	Ferritin-like	Ferritin-like	Manganese catalase (T-catalase)	Manganese catalase (T-catalase)	(Lactiplantibacillus plantarum ) [TaxId: 1590 ],	SCOPe (2.08)
E	d1o9ie_	All alpha proteins	Ferritin-like	Ferritin-like	Manganese catalase (T-catalase)	Manganese catalase (T-catalase)	(Lactiplantibacillus plantarum ) [TaxId: 1590 ],	SCOPe (2.08)
F	d1o9if_	All alpha proteins	Ferritin-like	Ferritin-like	Manganese catalase (T-catalase)	Manganese catalase (T-catalase)	(Lactiplantibacillus plantarum ) [TaxId: 1590 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Manganese catalase (T-catalase)	8024967	4000594	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ferritin-like	8037346	3001658	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ferritin-like	8037346	3001658	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ferritin-like	8037346	3001658	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ferritin-like	8037346	3001658	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ferritin-like	8037346	3001658	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ferritin-like	8037346	3001658	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	Mn_catalase	e1o9iA1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Ferritin	F: Mn_catalase	ECOD (1.6)
B	Mn_catalase	e1o9iB1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Ferritin	F: Mn_catalase	ECOD (1.6)
C	Mn_catalase	e1o9iC1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Ferritin	F: Mn_catalase	ECOD (1.6)
D	Mn_catalase	e1o9iD1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Ferritin	F: Mn_catalase	ECOD (1.6)
E	Mn_catalase	e1o9iE1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Ferritin	F: Mn_catalase	ECOD (1.6)
F	Mn_catalase	e1o9iF1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Ferritin	F: Mn_catalase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
A	3.30.1530.10	Alpha Beta	2-Layer Sandwich	manganese catalase, domain 2, chain A	manganese catalase, domain 2, chain A	CATH (4.3.0)
B	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
B	3.30.1530.10	Alpha Beta	2-Layer Sandwich	manganese catalase, domain 2, chain A	manganese catalase, domain 2, chain A	CATH (4.3.0)
C	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
C	3.30.1530.10	Alpha Beta	2-Layer Sandwich	manganese catalase, domain 2, chain A	manganese catalase, domain 2, chain A	CATH (4.3.0)
D	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
D	3.30.1530.10	Alpha Beta	2-Layer Sandwich	manganese catalase, domain 2, chain A	manganese catalase, domain 2, chain A	CATH (4.3.0)
E	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
E	3.30.1530.10	Alpha Beta	2-Layer Sandwich	manganese catalase, domain 2, chain A	manganese catalase, domain 2, chain A	CATH (4.3.0)
F	1.20.1260.10	Mainly Alpha	Up-down Bundle	Ferritin	Ferritin, core subunit, four-helix bundle	CATH (4.3.0)
F	3.30.1530.10	Alpha Beta	2-Layer Sandwich	manganese catalase, domain 2, chain A	manganese catalase, domain 2, chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF05067	Manganese containing catalase (Mn_catalase)	Manganese containing catalase	Catalases are important antioxidant metalloenzymes that catalyse disproportionation of hydrogen peroxide, forming dioxygen and water. Two families of catalases are known, one having a heme cofactor, and this family that is a structurally distinct fam ...	Catalases are important antioxidant metalloenzymes that catalyse disproportionation of hydrogen peroxide, forming dioxygen and water. Two families of catalases are known, one having a heme cofactor, and this family that is a structurally distinct family containing non-heme manganese [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Manganese catalase	peroxidase activity oxidoreductase activity antioxidant activity catalase activity oxidoreductase activity, acting on peroxide as acceptor catalytic activity cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR027407	Manganese catalase, C-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR039377	Manganese catalase, ferritin-like di-iron-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR012347	Ferritin-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR009078	Ferritin-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR007760	Manganese catalase	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	catalase (manganese dependent) M-CSA #572	The catalases are important antioxidant defence enzymes found in a broad range of microorganisms in microaerophilic environments. Manganese catalase, isolated from Lactobacillus plantarum, is a nonheme catalase containing a binuclear manganese cluster, and is responsible for catalysing the disproportionation of hydrogen peroxide into water and dioxygen. The enzyme is a hexamer of identical subunits organised around a catalytic core of close-packed four-helix bundle domains. Manganese catalase catalyses the disproportionation of toxic hydrogen peroxide into dioxygen and water. The overall reaction consists of two distinct half reactions involving alternate reduction and oxidation of the peroxide substrate. An m(1,3)-bridging glutamate anchors the two ions in the binuclear cluster, and each Mn is further coordinated by one histidine and one glutamate bound to opposite sides of the cluster. The Mn core is completed by two solvent derived oxygen bridges, which are structurally distinct.	Defined by 6 residues: GLU:A-35GLU:A-66HIS:A-69GLU:A-148GLU:A-178HIS:A-181 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.11.1.6 (PDB Primary Data) Search M-CSA Motif + EC 1.11.1.6

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.