1P80 | pdb_00001p80

Crystal structure of the D181Q variant of catalase HPII from E. coli

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	d1p80a1	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Catalase, C-terminal domain	Catalase, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1p80a2	Multi-domain proteins (alpha and beta)	Heme-dependent catalase-like	Heme-dependent catalase-like	Heme-dependent catalases	Catalase II	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1p80b1	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Catalase, C-terminal domain	Catalase, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1p80b2	Multi-domain proteins (alpha and beta)	Heme-dependent catalase-like	Heme-dependent catalase-like	Heme-dependent catalases	Catalase II	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1p80c1	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Catalase, C-terminal domain	Catalase, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1p80c2	Multi-domain proteins (alpha and beta)	Heme-dependent catalase-like	Heme-dependent catalase-like	Heme-dependent catalases	Catalase II	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1p80d1	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Catalase, C-terminal domain	Catalase, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1p80d2	Multi-domain proteins (alpha and beta)	Heme-dependent catalase-like	Heme-dependent catalase-like	Heme-dependent catalases	Catalase II	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Catalase, C-terminal domain	8026014	4003754	SCOP2 (2022-06-29)
A	SCOP2 Family	Heme-dependent catalases	8026017	4002736	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Class I glutamine amidotransferase-like	8038393	3001405	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Heme-dependent catalase-like	8038396	3001681	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8038393	3001405	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Heme-dependent catalase-like	8038396	3001681	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8038393	3001405	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Heme-dependent catalase-like	8038396	3001681	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Heme-dependent catalase-like	8038396	3001681	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8038393	3001405	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	Catalase	e1p80A1	A: beta barrels	X: Barrel domain in heme-dependent catalases	H: Barrel domain in heme-dependent catalases	T: Barrel domain in heme-dependent catalases	F: Catalase	ECOD (develop294)
A	Catalase	e1p80A2	A: alpha bundles	X: First alpha-helical domain in heme-dependent catalases	H: First alpha-helical domain in heme-dependent catalases	T: First alpha-helical domain in heme-dependent catalases	F: Catalase	ECOD (develop294)
A	Catalase-rel	e1p80A3	A: alpha bundles	X: Second alpha-helical domain in heme-dependent catalases	H: Second alpha-helical domain in heme-dependent catalases	T: Second alpha-helical domain in heme-dependent catalases	F: Catalase-rel	ECOD (develop294)
A	DJ-1_PfpI	e1p80A4	A: alpha bundles	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: DJ-1_PfpI	ECOD (develop294)
B	Catalase	e1p80B1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Catalase	ECOD (develop294)
B	ACOX	e1p80B2	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: ACOX	ECOD (develop294)
B	B12-binding	e1p80B4	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (develop294)
C	Catalase	e1p80C1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Catalase	ECOD (develop294)
C	ACOX	e1p80C2	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: ACOX	ECOD (develop294)
C	B12-binding	e1p80C4	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (develop294)
D	Catalase	e1p80D1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Catalase	ECOD (develop294)
D	ACOX	e1p80D2	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: ACOX	ECOD (develop294)
D	B12-binding	e1p80D4	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.180.10	Mainly Beta	Beta Barrel	Catalase HpII, Chain A, domain 1	Catalase core domain	CATH (4.3.0)
A	1.20.1370.20	Mainly Alpha	Up-down Bundle	Hemocyanin, N-terminal domain	Catalase, four-helical domain	CATH (4.3.0)
A	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
B	2.40.180.10	Mainly Beta	Beta Barrel	Catalase HpII, Chain A, domain 1	Catalase core domain	CATH (4.3.0)
B	1.20.1370.20	Mainly Alpha	Up-down Bundle	Hemocyanin, N-terminal domain	Catalase, four-helical domain	CATH (4.3.0)
B	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
C	2.40.180.10	Mainly Beta	Beta Barrel	Catalase HpII, Chain A, domain 1	Catalase core domain	CATH (4.3.0)
C	1.20.1370.20	Mainly Alpha	Up-down Bundle	Hemocyanin, N-terminal domain	Catalase, four-helical domain	CATH (4.3.0)
C	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
D	2.40.180.10	Mainly Beta	Beta Barrel	Catalase HpII, Chain A, domain 1	Catalase core domain	CATH (4.3.0)
D	1.20.1370.20	Mainly Alpha	Up-down Bundle	Hemocyanin, N-terminal domain	Catalase, four-helical domain	CATH (4.3.0)
D	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF18011	C-terminal domain found in long catalases (Catalase_C)	C-terminal domain found in long catalases	This domain is found at the C-terminus of a variety of large catalase enzymes from bacteria. Structurally it is related to class I glutamine amidotransferase domains. The precise molecular function of this domain is uncertain.	Domain
A, B, C, D	PF06628	Catalase-related immune-responsive (Catalase-rel)	Catalase-related immune-responsive	-	Family
A, B, C, D	PF00199	Catalase (Catalase)	Catalase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Catalase HPII	peroxidase activity oxidoreductase activity antioxidant activity catalase activity oxidoreductase activity, acting on peroxide as acceptor catalytic activity binding tetrapyrrole binding heme binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding peroxidase activity oxidoreductase activity antioxidant activity catalase activity oxidoreductase activity, acting on peroxide as acceptor catalytic activity binding tetrapyrrole binding heme binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding identical protein binding protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process metabolic process hydrogen peroxide catabolic process response to oxidative stress response to osmotic stress hyperosmotic response cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process metabolic process hydrogen peroxide catabolic process response to oxidative stress response to osmotic stress hyperosmotic response response to abiotic stimulus	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029062	Class I glutamine amidotransferase-like	Homologous Superfamily
A, B, C, D	IPR024708	Catalase active site	Active Site
A, B, C, D	IPR041399	Large catalase, C-terminal domain	Domain
A, B, C, D	IPR010582	Catalase immune-responsive domain	Domain
A, B, C, D	IPR043156	Catalase, mono-functional, haem-containing, clade 2, helical domain	Homologous Superfamily
A, B, C, D	IPR002226	Catalase haem-binding site	Binding Site
A, B, C, D	IPR020835	Catalase superfamily	Homologous Superfamily
A, B, C, D	IPR024712	Catalase, mono-functional, haem-containing, clade 2	Family
A, B, C, D	IPR011614	Catalase core domain	Domain
A, B, C, D	IPR018028	Catalase, mono-functional, haem-containing	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.