1QI9
X-RAY SIRAS STRUCTURE DETERMINATION OF A VANADIUM-DEPENDENT HALOPEROXIDASE FROM ASCOPHYLLUM NODOSUM AT 2.0 A RESOLUTION
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d1qi9a_ | All alpha proteins | Acid phosphatase/Vanadium-dependent haloperoxidase | Acid phosphatase/Vanadium-dependent haloperoxidase | Haloperoxidase (bromoperoxidase) | Haloperoxidase (bromoperoxidase) | (Ascophyllum nodosum ) [TaxId: 52969 ], | SCOPe (2.08) |
B | d1qi9b_ | All alpha proteins | Acid phosphatase/Vanadium-dependent haloperoxidase | Acid phosphatase/Vanadium-dependent haloperoxidase | Haloperoxidase (bromoperoxidase) | Haloperoxidase (bromoperoxidase) | (Ascophyllum nodosum ) [TaxId: 52969 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2 Family | Haloperoxidase (bromoperoxidase) | 8026113 | 4001228 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Acid phosphatase/Vanadium-dependent haloperoxidase | 8038492 | 3001110 | SCOP2 (2022-06-29) |
B | SCOP2B Superfamily | Acid phosphatase/Vanadium-dependent haloperoxidase | 8038492 | 3001110 | 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 | PAP2 | e1qi9A1 | A: alpha bundles | X: Acid phosphatase/Vanadium-dependent haloperoxidase (From Topology) | H: Acid phosphatase/Vanadium-dependent haloperoxidase (From Topology) | T: Acid phosphatase/Vanadium-dependent haloperoxidase | F: PAP2 | ECOD (1.6) |
B | PAP2 | e1qi9B1 | A: alpha bundles | X: Acid phosphatase/Vanadium-dependent haloperoxidase (From Topology) | H: Acid phosphatase/Vanadium-dependent haloperoxidase (From Topology) | T: Acid phosphatase/Vanadium-dependent haloperoxidase | F: PAP2 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 1.10.606.10 | Mainly Alpha | Orthogonal Bundle | Vanadium-containing Chloroperoxidase | domain 2 | CATH (4.3.0) |
B | 1.10.606.10 | Mainly Alpha | Orthogonal Bundle | Vanadium-containing Chloroperoxidase | domain 2 | CATH (4.3.0) |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR036938 | Phosphatidic acid phosphatase type 2/haloperoxidase superfamily | Homologous Superfamily | |
IPR016119 | Bromoperoxidase/chloroperoxidase C-terminal | Homologous Superfamily | |
IPR052559 | Vanadium-dependent haloperoxidase | Family | |
IPR036938 | Phosphatidic acid phosphatase type 2/haloperoxidase superfamily | Homologous Superfamily | |
IPR016119 | Bromoperoxidase/chloroperoxidase C-terminal | Homologous Superfamily | |
IPR052559 | Vanadium-dependent haloperoxidase | Family |
Protein Modification Annotation
Modified Residue(s) | ||
---|---|---|
Chain | Residue(s) | Description |
IYR | Parent Component: TYR :  AA0509 :  3'-iodo-L-tyrosine MOD:01612 | |
PCA | Parent Component: GLN :  AA0509 , AA0031 :  3'-iodo-L-tyrosine MOD:01612 , 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420 | |
TYI | Parent Component: TYR :  AA0509 , AA0031 , AA0510 :  3'-iodo-L-tyrosine MOD:01612 , 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420 , 3',5'-diiodo-L-tyrosine MOD:01613 | |
PCA | Parent Component: GLN :  AA0509 , AA0031 , AA0510 , AA0031 :  3'-iodo-L-tyrosine MOD:01612 , 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420 , 3',5'-diiodo-L-tyrosine MOD:01613 , 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420 | |
TYI | Parent Component: TYR :  AA0509 , AA0031 , AA0510 , AA0031 , AA0510 :  3'-iodo-L-tyrosine MOD:01612 , 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420 , 3',5'-diiodo-L-tyrosine MOD:01613 , 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420 , 3',5'-diiodo-L-tyrosine MOD:01613 |
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
Vanadium-dependent bromoperoxidase (organic sulfide oxidation) M-CSA #373 | V-BPO, isolated from Ascophyllum nodosum, is a vanadium-dependent haloperoxidase. It catalyses the oxidation of halides by hydrogen peroxide to form hypohalides, which can go on to react with organic substrates in halogenation reactions. In this entry, we show one of the side reactions of the vanadium-dependent haloperoxidases: the oxidation or organic sulfides. V-BPO has the ability to oxidise bromide and, to a lesser extent, chloride and iodide as well as chlorinate organic hydrocarbons. V-BPO contains a vanadium(V) ion with a trigonal bipyramidal coordination sphere. It is coordinated to His486 and a hydroxide in the axial positions, and two oxygen atoms and a hydroxide in the equatorial positions. | Defined by 9 residues: LYS:A-341ARG:A-349HIS:A-411SER:A-416GLY:A-417HIS:A-418ARG:A-480HIS:A-486ASP:A-490 | EC: 1.11.1.18 (PDB Primary Data) | |
Vanadium-dependent bromoperoxidase (organic molecule bromination) M-CSA #374 | V-BPO, isolated from Ascophyllum nodosum, is a vanadium-dependent haloperoxidase. | Defined by 9 residues: LYS:A-341ARG:A-349HIS:A-411SER:A-416GLY:A-417HIS:A-418ARG:A-480HIS:A-486ASP:A-490 | EC: 1.11.1.18 (PDB Primary Data) | |
Vanadium-dependent bromoperoxidase (HOBr Formation) M-CSA #386 | V-BPO, isolated from Ascophyllum nodosum, is a vanadium-dependent haloperoxidase. It catalyses the oxidation of halides by hydrogen peroxide to form hypohalides, which can go on to react with organic substrates in halogenation reactions. In this entry, we show the primary biological reaction of V-BPO: the formation of HOBr. V-BPO has the ability to oxidise bromide and, to a lesser extent, chloride and iodide as well as chlorinate organic hydrocarbons and oxidise organic sulfides. V-BPO contains a vanadium(V) ion with a trigonal bipyramidal coordination sphere. It is coordinated to His486 and a hydroxide in the axial positions, and two oxygen atoms and a hydroxide in the equatorial positions. | Defined by 9 residues: LYS:A-341ARG:A-349HIS:A-411SER:A-416GLY:A-417HIS:A-418ARG:A-480HIS:A-486ASP:A-490 | EC: 1.11.1.18 (PDB Primary Data) |