4UWQ | pdb_00004uwq

Crystal structure of the disulfide-linked complex of the thiosulfodyrolase SoxB with the carrier-protein SoxYZ from Thermus thermophilus

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	E set domains	8091812	3000070	SCOP2B (2022-06-29)
E	SCOP2 Family	SoxY-like	8048827	4006232	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	E set domains	8091812	3000070	SCOP2 (2022-06-29)
H	SCOP2B Superfamily	E set domains	8091812	3000070	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	E set domains	8091812	3000070	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	E set domains	8086228	3000070	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	E set domains	8086228	3000070	SCOP2B (2022-06-29)
I	SCOP2 Family	SoxZ-like	8086227	4007568	SCOP2 (2022-06-29)
I	SCOP2 Superfamily	E set domains	8086228	3000070	SCOP2 (2022-06-29)
L	SCOP2B Superfamily	E set domains	8086228	3000070	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	Metallophos_2_1	e4uwqA3	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2_1	ECOD (1.6)
A	5_nucleotid_C	e4uwqA2	A: a+b complex topology	X: 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain (From Topology)	H: 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain (From Topology)	T: 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain	F: 5_nucleotid_C	ECOD (1.6)
D	Metallophos_2_1	e4uwqD3	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2_1	ECOD (1.6)
D	5_nucleotid_C	e4uwqD2	A: a+b complex topology	X: 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain (From Topology)	H: 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain (From Topology)	T: 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain	F: 5_nucleotid_C	ECOD (1.6)
G	Metallophos_2_1	e4uwqG2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2_1	ECOD (1.6)
G	5_nucleotid_C	e4uwqG1	A: a+b complex topology	X: 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain (From Topology)	H: 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain (From Topology)	T: 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain	F: 5_nucleotid_C	ECOD (1.6)
J	Metallophos_2_1	e4uwqJ3	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2_1	ECOD (1.6)
J	5_nucleotid_C	e4uwqJ2	A: a+b complex topology	X: 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain (From Topology)	H: 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain (From Topology)	T: 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain	F: 5_nucleotid_C	ECOD (1.6)
B	SoxY	e4uwqB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SoxY	ECOD (1.6)
E	SoxY	e4uwqE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SoxY	ECOD (1.6)
H	SoxY	e4uwqH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SoxY	ECOD (1.6)
K	SoxY	e4uwqK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SoxY	ECOD (1.6)
C	SoxZ	e4uwqC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SoxZ	ECOD (1.6)
F	SoxZ	e4uwqF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SoxZ	ECOD (1.6)
I	SoxZ	e4uwqI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SoxZ	ECOD (1.6)
L	SoxZ	e4uwqL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SoxZ	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
A	6.10.140.570	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
A	3.90.780.10	Alpha Beta	Alpha-Beta Complex	5'-nucleotidase	domain 2	CATH (4.3.0)
D	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
D	6.10.140.570	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
D	3.90.780.10	Alpha Beta	Alpha-Beta Complex	5'-nucleotidase	domain 2	CATH (4.3.0)
G	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
G	6.10.140.570	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
G	3.90.780.10	Alpha Beta	Alpha-Beta Complex	5'-nucleotidase	domain 2	CATH (4.3.0)
J	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
J	6.10.140.570	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
J	3.90.780.10	Alpha Beta	Alpha-Beta Complex	5'-nucleotidase	domain 2	CATH (4.3.0)
B	2.60.40.2470	Mainly Beta	Sandwich	Immunoglobulin-like	SoxY domain	CATH (4.3.0)
E	2.60.40.2470	Mainly Beta	Sandwich	Immunoglobulin-like	SoxY domain	CATH (4.3.0)
H	2.60.40.2470	Mainly Beta	Sandwich	Immunoglobulin-like	SoxY domain	CATH (4.3.0)
K	2.60.40.2470	Mainly Beta	Sandwich	Immunoglobulin-like	SoxY domain	CATH (4.3.0)
L	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G, J	PF02872	5'-nucleotidase, C-terminal domain (5_nucleotid_C)	5'-nucleotidase, C-terminal domain		Domain
B, E, H, K	PF13501	Sulfur oxidation protein SoxY (SoxY)	Sulfur oxidation protein SoxY	This domain is found in the sulfur oxidation protein SoxY. It is closely related to the Desulfoferrodoxin family Pfam:PF01880. Dissimilatory oxidation of thiosulfate is carried out by the ubiquitous sulfur-oxidizing (Sox) multi-enzyme system. In this ...	This domain is found in the sulfur oxidation protein SoxY. It is closely related to the Desulfoferrodoxin family Pfam:PF01880. Dissimilatory oxidation of thiosulfate is carried out by the ubiquitous sulfur-oxidizing (Sox) multi-enzyme system. In this system, SoxY plays a key role, functioning as the sulfur substrate-binding protein that offers its sulfur substrate, which is covalently bound to a conserved C-terminal cysteine, to another oxidizing Sox enzyme [1]. The structure of this domain shows an Ig-like fold [1].	Domain
C, F, I, L	PF08770	Sulphur oxidation protein SoxZ (SoxZ)	Sulphur oxidation protein SoxZ	SoxZ forms an anti parallel beta structure and forms a complex with SoxY. Sulphur oxidation occurs at the thiol of a conserved cysteine residue of the SoxY subunit [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, G, J	SULFUR OXIDATION PROTEIN SOXB	hydrolase activity catalytic activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	nucleoside phosphate metabolic process catabolic process organophosphate catabolic process primary metabolic process nucleoside phosphate catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process nucleoside phosphate metabolic process catabolic process organophosphate catabolic process primary metabolic process nucleoside phosphate catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process nucleotide catabolic process	cellular anatomical structure outer membrane-bounded periplasmic space cell envelope periplasmic space
B, E, H, K	SOXY PROTEIN	cation binding ion binding binding metal ion binding small molecule binding	-	-
C, F, I, L	SOXZ	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G, J	IPR008334	5'-Nucleotidase, C-terminal	Domain
A, D, G, J	IPR041829	SoxB, N-terminal metallophosphatase domain	Domain
A, D, G, J	IPR030998	Thiosulfohydrolase SoxB	Family
A, D, G, J	IPR036907	5'-Nucleotidase, C-terminal domain superfamily	Homologous Superfamily
A, D, G, J	IPR006179	5'-Nucleotidase/apyrase	Family
A, D, G, J	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
B, E, H, K	IPR016568	Sulphur oxidation, SoxY	Family
B, E, H, K	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
B, E, H, K	IPR038162	Ig-like SoxY domain superfamily	Homologous Superfamily
B, E, H, K	IPR032711	Ig-like SoxY domain	Domain
B, E, H, K	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site
C, F, I, L	IPR030995	Thiosulfate oxidation carrier complex protein SoxZ	Family
C, F, I, L	IPR014880	Sulphur oxidation protein SoxZ	Domain
C, F, I, L	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, F, I, L	IPR014756	Immunoglobulin E-set	Homologous Superfamily

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.