2HI7

Crystal structure of DsbA-DsbB-ubiquinone complex

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
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2hi7a1	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	DsbA-like	Disulfide-bond formation facilitator (DsbA)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2hi7b1	All alpha proteins	Bromodomain-like	DsbB-like	DsbB-like	Disulfide bond formation protein DsbB	(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	Thioredoxin-like	8035549	3000031	SCOP2B (2022-06-29)
B	SCOP2 Family	DsbB-like	8020671	4001329	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	DsbB-like	8033051	3001302	SCOP2 (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	PF01323	e2hi7A2	A: alpha arrays	X: Insertion subdomain in DsbA-like	H: Insertion subdomain in DsbA-like (From Topology)	T: Insertion subdomain in DsbA-like	F: PF01323	ECOD (1.6)
A	PF01323	e2hi7A3	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: PF01323	ECOD (1.6)
B	PF02600	e2hi7B1	A: alpha bundles	X: Bromodomain-like	H: DsbB-like (From Topology)	T: DsbB-like	F: PF02600	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
B	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	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
B	PF02600	Disulfide bond formation protein DsbB (DsbB)	Disulfide bond formation protein DsbB	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Thiol:disulfide interchange protein 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	outer membrane-bounded periplasmic space cell envelope periplasmic space cellular anatomical entity
B	Disulfide bond formation protein B	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 organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein folding response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein folding biosynthetic process organic substance biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process	cell periphery plasma membrane membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR023205	Thiol:disulphide interchange protein DsbA/DsbL	Family
A	IPR001853	DSBA-like thioredoxin domain	Domain
A	IPR017937	Thioredoxin, conserved site	Conserved Site
A	IPR013766	Thioredoxin domain	Domain
A	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
B	IPR003752	Disulphide bond formation protein DsbB/BdbC	Family
B	IPR022920	Disulphide bond formation protein DsbB	Family
B	IPR023380	DsbB-like superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM				Disulfide bond oxidoreductase-B (DsbB)

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Oxidoreductases	DsbB-DsbA Periplasmic Oxidase Complex

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
B	protein disulfide oxidoreductase M-CSA #734	DsbB isolated from Escherichia coli is able to create disulfide bonds de novo. It forms a complex with DsbA and overall there is a net formation of a disulfide bridge in DsbA and a quinone cofactor is reduced in DsbB. The quinone can either be ubiquinone (under aerobic conditions) or menaquinone (under anaerobic conditions). DsbA is a periplasmic dithiol oxidase and it is the primary disulfide bond donor in the periplasm. The disulfide bond to be produced in DsbA is between Cys30 and Cys33. Two disulfide bonds exist in DsbB in the resting state, Cys41-Cys44 and Cys104-Cys130; they are involved in the catalytic pathway.	Defined by 5 residues: CYS:B-41CYS:B-44ARG:B-48CYS:B-104SER:B-130 Some residues are not modelled and lack atomic coordinates. Visualization is not available. Some residues are not modelled and lack atomic coordinates. Structure Motif searching is not available. EC: 1.8.5 (PDB Primary Data)

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.