2JI3

X-ray structure of the iron-peroxide intermediate of superoxide reductase (E114A mutant) from Desulfoarculus baarsii

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	d2ji3a1	All beta proteins	Immunoglobulin-like beta-sandwich	Superoxide reductase-like	Superoxide reductase-like	automated matches	(Desulfarculus baarsii ) [TaxId: 453230 ],	SCOPe (2.08)
A	d2ji3a2	Small proteins	Rubredoxin-like	Rubredoxin-like	automated matches	automated matches	(Desulfarculus baarsii ) [TaxId: 453230 ],	SCOPe (2.08)
B	d2ji3b1	All beta proteins	Immunoglobulin-like beta-sandwich	Superoxide reductase-like	Superoxide reductase-like	automated matches	(Desulfarculus baarsii ) [TaxId: 453230 ],	SCOPe (2.08)
B	d2ji3b2	Small proteins	Rubredoxin-like	Rubredoxin-like	automated matches	automated matches	(Desulfarculus baarsii ) [TaxId: 453230 ],	SCOPe (2.08)
C	d2ji3c1	All beta proteins	Immunoglobulin-like beta-sandwich	Superoxide reductase-like	Superoxide reductase-like	automated matches	(Desulfarculus baarsii ) [TaxId: 453230 ],	SCOPe (2.08)
C	d2ji3c2	Small proteins	Rubredoxin-like	Rubredoxin-like	automated matches	automated matches	(Desulfarculus baarsii ) [TaxId: 453230 ],	SCOPe (2.08)
D	d2ji3d1	All beta proteins	Immunoglobulin-like beta-sandwich	Superoxide reductase-like	Superoxide reductase-like	automated matches	(Desulfarculus baarsii ) [TaxId: 453230 ],	SCOPe (2.08)
D	d2ji3d2	Small proteins	Rubredoxin-like	Rubredoxin-like	automated matches	automated matches	(Desulfarculus baarsii ) [TaxId: 453230 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Superoxide reductase-like	8055351	3002044	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Rubredoxin-like	8041582	3001257	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Superoxide reductase-like	8055351	3002044	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Rubredoxin-like	8041582	3001257	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Rubredoxin-like	8041582	3001257	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Superoxide reductase-like	8055351	3002044	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Rubredoxin-like	8041582	3001257	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Superoxide reductase-like	8055351	3002044	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	Desulfoferrodox	e2ji3A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Desulfoferrodox	ECOD (1.6)
A	Desulfoferrod_N	e2ji3A2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Desulforedoxin	F: Desulfoferrod_N	ECOD (1.6)
B	Desulfoferrodox	e2ji3B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Desulfoferrodox	ECOD (1.6)
B	Desulfoferrod_N	e2ji3B2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Desulforedoxin	F: Desulfoferrod_N	ECOD (1.6)
C	Desulfoferrodox	e2ji3C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Desulfoferrodox	ECOD (1.6)
C	Desulfoferrod_N	e2ji3C2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Desulforedoxin	F: Desulfoferrod_N	ECOD (1.6)
D	Desulfoferrodox	e2ji3D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Desulfoferrodox	ECOD (1.6)
D	Desulfoferrod_N	e2ji3D2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Desulforedoxin	F: Desulfoferrod_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.20.28.100	Mainly Beta	Single Sheet	Rubrerythrin, domain 2	Desulphoferrodoxin, N-terminal domain	CATH (4.3.0)
A	2.60.40.730	Mainly Beta	Sandwich	Immunoglobulin-like	SOR catalytic domain	CATH (4.3.0)
B	2.20.28.100	Mainly Beta	Single Sheet	Rubrerythrin, domain 2	Desulphoferrodoxin, N-terminal domain	CATH (4.3.0)
B	2.60.40.730	Mainly Beta	Sandwich	Immunoglobulin-like	SOR catalytic domain	CATH (4.3.0)
C	2.20.28.100	Mainly Beta	Single Sheet	Rubrerythrin, domain 2	Desulphoferrodoxin, N-terminal domain	CATH (4.3.0)
C	2.60.40.730	Mainly Beta	Sandwich	Immunoglobulin-like	SOR catalytic domain	CATH (4.3.0)
D	2.20.28.100	Mainly Beta	Single Sheet	Rubrerythrin, domain 2	Desulphoferrodoxin, N-terminal domain	CATH (4.3.0)
D	2.60.40.730	Mainly Beta	Sandwich	Immunoglobulin-like	SOR catalytic domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF06397	Desulfoferrodoxin, N-terminal domain (Desulfoferrod_N)	Desulfoferrodoxin, N-terminal domain	Most members of this family are small (approximately 36 amino acids) proteins that from homodimeric complexes. Each subunit contains a high-spin iron atom tetrahedrally bound to four cysteinyl sulphur atoms This family has a similar fold to the rubre ...	Most members of this family are small (approximately 36 amino acids) proteins that from homodimeric complexes. Each subunit contains a high-spin iron atom tetrahedrally bound to four cysteinyl sulphur atoms This family has a similar fold to the rubredoxin metal binding domain [1]. It is also found as the N-terminal domain of desulfoferrodoxin, see (Pfam:PF01880).	Domain
A, B, C, D	PF01880	Desulfoferrodoxin (Desulfoferrodox)	Desulfoferrodoxin	Desulfoferrodoxins contains two types of iron: an Fe-S4 site very similar to that found in desulforedoxin from Desulfovibrio gigas and an octahedral coordinated high-spin ferrous site most probably with nitrogen/oxygen-containing ligands. Due to this ...	Desulfoferrodoxins contains two types of iron: an Fe-S4 site very similar to that found in desulforedoxin from Desulfovibrio gigas and an octahedral coordinated high-spin ferrous site most probably with nitrogen/oxygen-containing ligands. Due to this rather unusual combination of active centres, this novel protein is named desulfoferrodoxin [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Desulfoferrodoxin	oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase activity antioxidant activity superoxide reductase activity catalytic activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding	cellular response to stimulus response to stimulus cellular response to oxidative stress detoxification reactive oxygen species metabolic process cellular response to chemical stress response to superoxide cellular oxidant detoxification cellular response to oxygen radical cellular response to reactive oxygen species cellular response to stress response to stress cellular detoxification cellular metabolic process cellular response to stimulus response to stimulus cellular response to oxidative stress detoxification reactive oxygen species metabolic process cellular response to chemical stress response to superoxide cellular oxidant detoxification cellular response to oxygen radical cellular response to reactive oxygen species cellular response to stress response to stress cellular detoxification cellular metabolic process response to oxygen-containing compound cellular response to oxygen-containing compound response to reactive oxygen species response to toxic substance removal of superoxide radicals superoxide metabolic process response to oxidative stress cellular response to chemical stimulus response to chemical cellular response to superoxide metabolic process cellular process cellular response to toxic substance response to oxygen radical	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR051233	Desulfoferrodoxin superoxide reductase	Family
A, B, C, D	IPR004462	Desulfoferrodoxin, N-terminal domain	Domain
A, B, C, D	IPR036073	Desulfoferrodoxin, ferrous iron-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR038094	Desulfoferrodoxin, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR002742	Desulfoferrodoxin, ferrous iron-binding domain	Domain
A, B, C, D	IPR004793	Desulfoferrodoxin	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.