1XDY | pdb_00001xdy

Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase, W-containing cofactor

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	d1xdya_	Alpha and beta proteins (a+b)	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Bacterial sulfite oxidase YedY	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1xdyb_	Alpha and beta proteins (a+b)	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Bacterial sulfite oxidase YedY	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1xdyc_	Alpha and beta proteins (a+b)	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Bacterial sulfite oxidase YedY	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1xdyd_	Alpha and beta proteins (a+b)	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Bacterial sulfite oxidase YedY	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1xdye_	Alpha and beta proteins (a+b)	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Bacterial sulfite oxidase YedY	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1xdyf_	Alpha and beta proteins (a+b)	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Bacterial sulfite oxidase YedY	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d1xdyg_	Alpha and beta proteins (a+b)	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Bacterial sulfite oxidase YedY	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d1xdyh_	Alpha and beta proteins (a+b)	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Bacterial sulfite oxidase YedY	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I	d1xdyi_	Alpha and beta proteins (a+b)	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Bacterial sulfite oxidase YedY	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J	d1xdyj_	Alpha and beta proteins (a+b)	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Oxidoreductase molybdopterin-binding domain	Bacterial sulfite oxidase YedY	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Oxidoreductase molybdopterin-binding domain	8043844	3001433	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Oxidoreductase molybdopterin-binding domain	8043844	3001433	SCOP2B (2022-06-29)
C	SCOP2 Family	Oxidoreductase molybdopterin-binding domain	8031466	4002574	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Oxidoreductase molybdopterin-binding domain	8043844	3001433	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Oxidoreductase molybdopterin-binding domain	8043844	3001433	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Oxidoreductase molybdopterin-binding domain	8043844	3001433	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Oxidoreductase molybdopterin-binding domain	8043844	3001433	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Oxidoreductase molybdopterin-binding domain	8043844	3001433	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Oxidoreductase molybdopterin-binding domain	8043844	3001433	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Oxidoreductase molybdopterin-binding domain	8043844	3001433	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Oxidoreductase molybdopterin-binding domain	8043844	3001433	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	Oxidored_molyb	e1xdyA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Sulfite oxidase, middle catalytic domain	F: Oxidored_molyb	ECOD (1.6)
B	Oxidored_molyb	e1xdyB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Sulfite oxidase, middle catalytic domain	F: Oxidored_molyb	ECOD (1.6)
C	Oxidored_molyb	e1xdyC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Sulfite oxidase, middle catalytic domain	F: Oxidored_molyb	ECOD (1.6)
D	Oxidored_molyb	e1xdyD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Sulfite oxidase, middle catalytic domain	F: Oxidored_molyb	ECOD (1.6)
E	Oxidored_molyb	e1xdyE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Sulfite oxidase, middle catalytic domain	F: Oxidored_molyb	ECOD (1.6)
F	Oxidored_molyb	e1xdyF1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Sulfite oxidase, middle catalytic domain	F: Oxidored_molyb	ECOD (1.6)
G	Oxidored_molyb	e1xdyG1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Sulfite oxidase, middle catalytic domain	F: Oxidored_molyb	ECOD (1.6)
H	Oxidored_molyb	e1xdyH1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Sulfite oxidase, middle catalytic domain	F: Oxidored_molyb	ECOD (1.6)
I	Oxidored_molyb	e1xdyI1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Sulfite oxidase, middle catalytic domain	F: Oxidored_molyb	ECOD (1.6)
J	Oxidored_molyb	e1xdyJ1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Sulfite oxidase, middle catalytic domain	F: Oxidored_molyb	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.420.10	Alpha Beta	Alpha-Beta Complex	Sulfite Oxidase	Chain A, domain 2	CATH (4.3.0)
B	3.90.420.10	Alpha Beta	Alpha-Beta Complex	Sulfite Oxidase	Chain A, domain 2	CATH (4.3.0)
C	3.90.420.10	Alpha Beta	Alpha-Beta Complex	Sulfite Oxidase	Chain A, domain 2	CATH (4.3.0)
D	3.90.420.10	Alpha Beta	Alpha-Beta Complex	Sulfite Oxidase	Chain A, domain 2	CATH (4.3.0)
E	3.90.420.10	Alpha Beta	Alpha-Beta Complex	Sulfite Oxidase	Chain A, domain 2	CATH (4.3.0)
F	3.90.420.10	Alpha Beta	Alpha-Beta Complex	Sulfite Oxidase	Chain A, domain 2	CATH (4.3.0)
G	3.90.420.10	Alpha Beta	Alpha-Beta Complex	Sulfite Oxidase	Chain A, domain 2	CATH (4.3.0)
H	3.90.420.10	Alpha Beta	Alpha-Beta Complex	Sulfite Oxidase	Chain A, domain 2	CATH (4.3.0)
I	3.90.420.10	Alpha Beta	Alpha-Beta Complex	Sulfite Oxidase	Chain A, domain 2	CATH (4.3.0)
J	3.90.420.10	Alpha Beta	Alpha-Beta Complex	Sulfite Oxidase	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	PF00174	Oxidoreductase molybdopterin binding domain (Oxidored_molyb)	Oxidoreductase molybdopterin binding domain	This domain is found in a variety of oxidoreductases. This domain binds to a molybdopterin cofactor. Xanthine dehydrogenases, that also bind molybdopterin, have essentially no similarity.	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	Bacterial Sulfite Oxidase	binding molybdopterin cofactor binding oxidoreductase activity, acting on a sulfur group of donors oxidoreductase activity catalytic activity oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor oxidoreductase activity, acting on a heme group of donors cation binding ion binding metal ion binding small molecule binding	response to oxidative stress response to stimulus response to hypochlorite response to stress response to chemical response to oxygen-containing compound response to reactive oxygen species protein repair metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure outer membrane-bounded periplasmic space cell envelope periplasmic space

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	IPR000572	Oxidoreductase, molybdopterin-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR036374	Oxidoreductase, molybdopterin-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR022867	Protein-methionine-sulfoxide reductase subunit MsrP	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.