1YF1

Structural and biochemical analysis of the link between enzymatic activity and oligomerization in AhpC, a bacterial peroxiredoxin.

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	d1yf1a1	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	Alkyl hydroperoxide reductase AhpC	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
B	d1yf1b_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	Alkyl hydroperoxide reductase AhpC	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
D	d1yf1d_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	Alkyl hydroperoxide reductase AhpC	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
E	d1yf1e_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	Alkyl hydroperoxide reductase AhpC	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
F	d1yf1f_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	Alkyl hydroperoxide reductase AhpC	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
G	d1yf1g_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	Alkyl hydroperoxide reductase AhpC	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
I	d1yf1i_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	Alkyl hydroperoxide reductase AhpC	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
J	d1yf1j_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	Alkyl hydroperoxide reductase AhpC	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
C	d1yf1c_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	Alkyl hydroperoxide reductase AhpC	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
H	d1yf1h_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	Alkyl hydroperoxide reductase AhpC	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Thioredoxin-like	8057925	3000031	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thioredoxin-like	8057925	3000031	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thioredoxin-like	8057925	3000031	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Thioredoxin-like	8057925	3000031	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Thioredoxin-like	8057925	3000031	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Thioredoxin-like	8057925	3000031	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Thioredoxin-like	8057925	3000031	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Thioredoxin-like	8057925	3000031	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thioredoxin-like	8057925	3000031	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Thioredoxin-like	8057925	3000031	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	AhpC-TSA_1	e1yf1A1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)
B	AhpC-TSA_1	e1yf1B1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)
D	AhpC-TSA_1	e1yf1D1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)
E	AhpC-TSA_1	e1yf1E1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)
F	AhpC-TSA_1	e1yf1F1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)
G	AhpC-TSA_1	e1yf1G1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)
I	AhpC-TSA_1	e1yf1I1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)
J	AhpC-TSA_1	e1yf1J1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)
C	AhpC-TSA_1	e1yf1C1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)
H	AhpC-TSA_1	e1yf1H1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
B	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
D	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
E	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
F	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
G	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
I	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
J	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
C	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
H	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	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, G, H, I, J	PF00578	AhpC/TSA family (AhpC-TSA)	AhpC/TSA family	This family contains proteins related to alkyl hydroperoxide reductase (AhpC) and thiol specific antioxidant (TSA).	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	PF10417	C-terminal domain of 1-Cys peroxiredoxin (1-cysPrx_C)	C-terminal domain of 1-Cys peroxiredoxin	This is the C-terminal domain of 1-Cys peroxiredoxin (1-cysPrx), a member of the peroxiredoxin superfamily which protect cells against membrane oxidation through glutathione (GSH)-dependent reduction of phospholipid hydroperoxides to corresponding al ...	This is the C-terminal domain of 1-Cys peroxiredoxin (1-cysPrx), a member of the peroxiredoxin superfamily which protect cells against membrane oxidation through glutathione (GSH)-dependent reduction of phospholipid hydroperoxides to corresponding alcohols [1]. The C-terminal domain is crucial for providing the extra cysteine necessary for dimerisation of the whole molecule. Loss of the enzyme's peroxidase activity is associated with oxidation of the catalytic cysteine, upstream of this domain; and glutathionylation, presumably through its disruption of protein structure, facilitates access for GSH, resulting in spontaneous reduction of the mixed disulfide to the sulfhydryl and consequent activation of the enzyme [2]. The domain is associated with family AhpC-TSA, Pfam:PF00578, which carries the catalytic cysteine.	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, G, H, I, J	Alkyl hydroperoxide reductase subunit C	peroxidase activity oxidoreductase activity thioredoxin-dependent peroxiredoxin activity antioxidant activity oxidoreductase activity, acting on peroxide as acceptor thioredoxin peroxidase activity catalytic activity peroxiredoxin activity NADH-dependent peroxiredoxin activity	cellular response to stimulus cellular response to stress response to stimulus response to stress cellular process catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process metabolic process hydrogen peroxide catabolic process cell redox homeostasis cellular homeostasis homeostatic process response to oxidative stress	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR019479	Peroxiredoxin, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR024706	Peroxiredoxin, AhpC-type	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR050217	Thiol-specific antioxidant peroxiredoxin	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR013766	Thioredoxin domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR017559	Alkyl hydroperoxide reductase subunit C	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR000866	Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant	Domain

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.