3E9J

Structure of the charge-transfer intermediate of the transmembrane redox catalyst DsbB

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
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Thioredoxin-like	8035549	3000031	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Thioredoxin-like	8035549	3000031	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	DsbB-like	8033051	3001302	SCOP2B (2022-06-29)
D [auth F]	SCOP2B Superfamily	DsbB-like	8033051	3001302	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 [auth B]	DsbA_DsbA	e3e9jB2	A: alpha arrays	X: Insertion subdomain in DsbA-like	H: Insertion subdomain in DsbA-like (From Topology)	T: Insertion subdomain in DsbA-like	F: DsbA_DsbA	ECOD (1.6)
A [auth B]	Thioredoxin_1	e3e9jB3	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: Thioredoxin_1	ECOD (1.6)
C [auth E]	DsbA_DsbA	e3e9jE2	A: alpha arrays	X: Insertion subdomain in DsbA-like	H: Insertion subdomain in DsbA-like (From Topology)	T: Insertion subdomain in DsbA-like	F: DsbA_DsbA	ECOD (1.6)
C [auth E]	Thioredoxin_1	e3e9jE3	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: Thioredoxin_1	ECOD (1.6)
B [auth C]	DsbB	e3e9jC1	A: alpha bundles	X: Bromodomain-like	H: DsbB-like (From Topology)	T: DsbB-like	F: DsbB	ECOD (1.6)
D [auth F]	DsbB	e3e9jF1	A: alpha bundles	X: Bromodomain-like	H: DsbB-like (From Topology)	T: DsbB-like	F: DsbB	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
C [auth E]	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
B [auth C]	1.20.1550.10	Mainly Alpha	Up-down Bundle	Bromodomain-like	DsbB-like	CATH (4.3.0)
D [auth F]	1.20.1550.10	Mainly Alpha	Up-down Bundle	Bromodomain-like	DsbB-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], C [auth E]	PF01323	DSBA-like thioredoxin domain (DSBA)	DSBA-like thioredoxin domain	This family contains a diverse set of proteins with a thioredoxin-like structure Pfam:PF00085. This family also includes 2-hydroxychromene-2-carboxylate (HCCA) isomerase enzymes catalyse one step in prokaryotic polyaromatic hydrocarbon (PAH) cataboli ...	This family contains a diverse set of proteins with a thioredoxin-like structure Pfam:PF00085. This family also includes 2-hydroxychromene-2-carboxylate (HCCA) isomerase enzymes catalyse one step in prokaryotic polyaromatic hydrocarbon (PAH) catabolic pathways [2,3,4]. This family also contains members with functions other than HCCA isomerisation, such as Kappa family GSTs (e.g. Swiss:P24473), whose similarity to HCCA isomerases was not previously recognised. The sequence Swiss:O07298 has been annotated as a dioxygenase but is almost certainly an HCCA isomerase enzyme. Similarly, the sequence Swiss:Q9ZI67 has been annotated as a dehydrogenase, but is most probably also an HCCA isomerase enzyme. In addition, the Rhizobium leguminosarum Swiss:Q52782 protein has been annotated as a putative glycerol-3-phosphate transfer protein, but is also most likely to be an HCCA isomerase enzyme (see [5]).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], C [auth E]	Thiol/disulfide oxidoreductase DsbA	isomerase activity intramolecular oxidoreductase activity catalytic activity, acting on a protein intramolecular oxidoreductase activity, transposing S-S bonds catalytic activity protein disulfide isomerase activity oxidoreductase activity, acting on a sulfur group of donors disulfide oxidoreductase activity oxidoreductase activity protein-disulfide reductase activity	cellular response to stimulus cellular response to antibiotic cellular response to chemical stimulus response to stimulus response to chemical cellular process response to antibiotic	cellular anatomical structure outer membrane-bounded periplasmic space cell envelope periplasmic space
B [auth C], D [auth F]	Thiol/disulfide oxidoreductase DsbB	binding quinone binding ubiquinone binding small molecule 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 electron transfer activity disulfide oxidoreductase activity catalytic activity, acting on a protein protein-disulfide reductase activity	response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus protein folding biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus protein folding biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], C [auth E]	IPR050824	Bacterial Thiol:disulfide Interchange Protein DsbA	Family
A [auth B], C [auth E]	IPR023205	Thiol:disulphide interchange protein DsbA/DsbL	Family
A [auth B], C [auth E]	IPR001853	DSBA-like thioredoxin domain	Domain
A [auth B], C [auth E]	IPR017937	Thioredoxin, conserved site	Conserved Site
A [auth B], C [auth E]	IPR013766	Thioredoxin domain	Domain
A [auth B], C [auth E]	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
B [auth C], D [auth F]	IPR003752	Disulphide bond formation protein DsbB/BdbC	Family
B [auth C], D [auth F]	IPR022920	Disulphide bond formation protein DsbB	Family
B [auth C], D [auth F]	IPR050183	Disulfide bond formation protein B	Family
B [auth C], D [auth F]	IPR023380	DsbB-like superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth B], B [auth C], C [auth E], D [auth F]	OPM				Disulfide bond oxidoreductase-B (DsbB)

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth B], B [auth C], C [auth E], D [auth F]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth B], B [auth C], C [auth E], D [auth F]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth B], B [auth C], C [auth E], D [auth F]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Oxidoreductases	wtDsbB-DsbA(Cys133A)-Q8 Complex

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.