5OVQ | pdb_00005ovq

Crystal Structure of the peroxiredoxin (AhpC2) from the Hyperthermophilic bacteria Aquifex aeolicus VF

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
G	d5ovqg_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
H	d5ovqh_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
I	d5ovqi_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
L	d5ovql_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
J	d5ovqj_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
F	d5ovqf_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
D	d5ovqd_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
B	d5ovqb1	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
B	d5ovqb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
K	d5ovqk1	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
K	d5ovqk2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
E	d5ovqe1	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
E	d5ovqe2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
C	d5ovqc1	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
C	d5ovqc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
A	d5ovqa1	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
A	d5ovqa2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
G	Chlorophyllase2	e5ovqG1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
H	Chlorophyllase2	e5ovqH1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
I	Chlorophyllase2	e5ovqI1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
L	Chlorophyllase2	e5ovqL1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
J	Chlorophyllase2	e5ovqJ1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
F	Chlorophyllase2	e5ovqF1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
D	Chlorophyllase2	e5ovqD1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
B	PIN	e5ovqB1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: PIN	ECOD (v294.1)
K	Chlorophyllase2	e5ovqK1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
E	Chlorophyllase2	e5ovqE1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
C	Chlorophyllase2	e5ovqC1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
A	Chlorophyllase2	e5ovqA1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
H	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
I	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
L	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
J	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
F	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
D	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
B	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
K	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
E	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
C	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
A	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, F, G, H, I D, F, G, H, I, J, L	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
D, F, G, H, I D, F, G, H, I, J, L	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
A, B, C, E, K	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, E, K	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
D, F, G, H, I D, F, G, H, I, J, L	Peroxiredoxin	peroxidase activity oxidoreductase activity thioredoxin-dependent peroxiredoxin activity antioxidant activity oxidoreductase activity, acting on peroxide as acceptor catalytic activity peroxiredoxin activity	cell redox homeostasis cellular homeostasis homeostatic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
A, B, C, E, K	Peroxiredoxin	peroxidase activity oxidoreductase activity thioredoxin-dependent peroxiredoxin activity antioxidant activity oxidoreductase activity, acting on peroxide as acceptor catalytic activity peroxiredoxin activity	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
D, F, G, H, I D, F, G, H, I, J, L	IPR019479	Peroxiredoxin, C-terminal	Domain
D, F, G, H, I D, F, G, H, I, J, L	IPR024706	Peroxiredoxin, AhpC-type	Family
D, F, G, H, I D, F, G, H, I, J, L	IPR050217	Thiol-specific antioxidant peroxiredoxin	Family
D, F, G, H, I D, F, G, H, I, J, L	IPR013766	Thioredoxin domain	Domain
D, F, G, H, I D, F, G, H, I, J, L	IPR045020	1-Cys peroxiredoxin	Family
D, F, G, H, I D, F, G, H, I, J, L	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
D, F, G, H, I D, F, G, H, I, J, L	IPR000866	Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant	Domain
D, F, G, H, I D, F, G, H, I, J, L	IPR022915	Peroxiredoxin, TDXH subfamily	Family
A, B, C, E, K	IPR019479	Peroxiredoxin, C-terminal	Domain
A, B, C, E, K	IPR024706	Peroxiredoxin, AhpC-type	Family
A, B, C, E, K	IPR050217	Thiol-specific antioxidant peroxiredoxin	Family
A, B, C, E, K	IPR013766	Thioredoxin domain	Domain
A, B, C, E, K	IPR045020	1-Cys peroxiredoxin	Family
A, B, C, E, K	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
A, B, C, E, K	IPR000866	Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant	Domain
A, B, C, E, K	IPR022915	Peroxiredoxin, TDXH subfamily	Family

Protein Modification Annotation

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

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.