2CV4 | pdb_00002cv4

Crystal Structure of an Archaeal Peroxiredoxin from the Aerobic Hyperthermophilic Crenarchaeon Aeropyrum pernix K1

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
J	d2cv4j_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	automated matches	(Aeropyrum pernix K1 ) [TaxId: 272557 ],	SCOPe (2.08)
I	d2cv4i_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	automated matches	(Aeropyrum pernix K1 ) [TaxId: 272557 ],	SCOPe (2.08)
H	d2cv4h_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	automated matches	(Aeropyrum pernix K1 ) [TaxId: 272557 ],	SCOPe (2.08)
G	d2cv4g_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	automated matches	(Aeropyrum pernix K1 ) [TaxId: 272557 ],	SCOPe (2.08)
F	d2cv4f_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	automated matches	(Aeropyrum pernix K1 ) [TaxId: 272557 ],	SCOPe (2.08)
E	d2cv4e_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	automated matches	(Aeropyrum pernix K1 ) [TaxId: 272557 ],	SCOPe (2.08)
D	d2cv4d_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	automated matches	(Aeropyrum pernix K1 ) [TaxId: 272557 ],	SCOPe (2.08)
C	d2cv4c_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	automated matches	(Aeropyrum pernix K1 ) [TaxId: 272557 ],	SCOPe (2.08)
B	d2cv4b_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	automated matches	(Aeropyrum pernix K1 ) [TaxId: 272557 ],	SCOPe (2.08)
A	d2cv4a1	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	Peroxiredoxin	(Aeropyrum pernix K1 ) [TaxId: 272557 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	Thioredoxin-like	8057914	3000031	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Thioredoxin-like	8057914	3000031	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Thioredoxin-like	8057914	3000031	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Thioredoxin-like	8057914	3000031	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Thioredoxin-like	8057914	3000031	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Thioredoxin-like	8057914	3000031	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thioredoxin-like	8057914	3000031	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thioredoxin-like	8057914	3000031	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thioredoxin-like	8057914	3000031	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thioredoxin-like	8057914	3000031	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J	e2cv4J1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: PS-DH	F:	ECOD (20:10:01)
I	e2cv4I1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: PS-DH	F:	ECOD (20:10:01)
H	e2cv4H1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: PS-DH	F:	ECOD (20:10:01)
G	e2cv4G2	A: Glutamine synthetase-like	X: Glutamine synthetase/guanido kinase	H: Glutamine synthetase/guanido kinase	T: Thioredoxin	F:	ECOD (20:10:01)
F	e2cv4F1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: PS-DH	F:	ECOD (20:10:01)
E	e2cv4E1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: PS-DH	F:	ECOD (20:10:01)
D	e2cv4D2	A: Glutamine synthetase-like	X: Glutamine synthetase/guanido kinase	H: Glutamine synthetase/guanido kinase	T: Thioredoxin	F:	ECOD (20:10:01)
C	e2cv4C1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: PS-DH	F:	ECOD (20:10:01)
B	e2cv4B1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: PS-DH	F:	ECOD (20:10:01)
A	e2cv4A1	A: jelly-roll	X: Double-stranded beta-helix	H: Double-stranded beta-helix	T: zf-MYND	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
J	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	CATH (4.3.0)
I	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
I	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	CATH (4.3.0)
H	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
H	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	CATH (4.3.0)
G	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
G	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	CATH (4.3.0)
F	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
F	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	CATH (4.3.0)
E	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
E	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	CATH (4.3.0)
D	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
D	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	CATH (4.3.0)
C	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
C	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	CATH (4.3.0)
B	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
B	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	CATH (4.3.0)
A	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
A	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	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	peroxiredoxin	peroxidase activity oxidoreductase activity antioxidant activity oxidoreductase activity, acting on peroxide as acceptor catalytic activity peroxiredoxin activity thioredoxin-dependent peroxiredoxin activity thioredoxin peroxidase activity identical protein binding protein binding binding	catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process metabolic process cellular process hydrogen peroxide catabolic process cellular response to stimulus response to stimulus cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process metabolic process cellular process hydrogen peroxide catabolic process cellular response to stimulus response to stimulus cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to chemical stimulus cellular response to stress response to stress response to chemical cell redox homeostasis cellular homeostasis homeostatic process	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	IPR022915	Peroxiredoxin, TDXH subfamily	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR045020	1-Cys peroxiredoxin	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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	MSE	Parent Component: MET
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	OCS	Parent Component: CYS RESID: AA0556 PSI-MOD : L-cysteic acid (L-cysteine sulfonic acid) MOD:00460