2D0P

Structure of diol dehydratase-reactivating factor in nucleotide free form

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	d2d0pa1	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	Swiveling domain of dehydratase reactivase alpha subunit	Swiveling domain of dehydratase reactivase alpha subunit	Diol dehydratase-reactivating factor large subunit DdrA	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
A	d2d0pa2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	ATPase domain of dehydratase reactivase alpha subunit	Diol dehydratase-reactivating factor large subunit DdrA	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
C	d2d0pc1	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	Swiveling domain of dehydratase reactivase alpha subunit	Swiveling domain of dehydratase reactivase alpha subunit	Diol dehydratase-reactivating factor large subunit DdrA	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
C	d2d0pc2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	ATPase domain of dehydratase reactivase alpha subunit	Diol dehydratase-reactivating factor large subunit DdrA	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
B	d2d0pb_	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	B12-dependent dehydatase associated subunit	Dehydratase-reactivating factor beta subunit	automated matches	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
D	d2d0pd_	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	B12-dependent dehydatase associated subunit	Dehydratase-reactivating factor beta subunit	automated matches	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Swiveling domain of dehydratase reactivase alpha subunit	8039452	3001885	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Actin-like ATPases	8039454	3000092	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Actin-like ATPases	8039455	3000092	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Actin-like ATPases	8039455	3000092	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Swiveling domain of dehydratase reactivase alpha subunit	8039452	3001885	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Actin-like ATPases	8039454	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	B12-dependent dehydatase associated subunit	8039456	3000491	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	B12-dependent dehydatase associated subunit	8039456	3000491	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	reactive_PduG	e2d0pA3	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: reactive_PduG	ECOD (1.6)
A	DDR_C	e2d0pA2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DDR_C	ECOD (1.6)
A	DDR_N	e2d0pA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DDR_N	ECOD (1.6)
C	reactive_PduG	e2d0pC3	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: reactive_PduG	ECOD (1.6)
C	DDR_C	e2d0pC2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DDR_C	ECOD (1.6)
C	DDR_N	e2d0pC1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DDR_N	ECOD (1.6)
B	Dehydratase_MU	e2d0pB1	A: a/b three-layered sandwiches	X: B12-dependent dehydratase associated subunit (From Topology)	H: B12-dependent dehydratase associated subunit (From Topology)	T: B12-dependent dehydratase associated subunit	F: Dehydratase_MU	ECOD (1.6)
D	Dehydratase_MU	e2d0pD1	A: a/b three-layered sandwiches	X: B12-dependent dehydratase associated subunit (From Topology)	H: B12-dependent dehydratase associated subunit (From Topology)	T: B12-dependent dehydratase associated subunit	F: Dehydratase_MU	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.90.470.30	Alpha Beta	Alpha-Beta Complex	Ribosomal Protein L22	Chain A	CATH (4.3.0)
A	3.50.30.70	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
C	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	3.90.470.30	Alpha Beta	Alpha-Beta Complex	Ribosomal Protein L22	Chain A	CATH (4.3.0)
C	3.50.30.70	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
C	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	3.40.50.10150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	B12-dependent dehydatase associated subunit	CATH (4.3.0)
D	3.40.50.10150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	B12-dependent dehydatase associated subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF08841	Diol dehydratase reactivase ATPase-like domain (DDR)	Diol dehydratase reactivase ATPase-like domain	-	Family
A, C	PF18427	DD-reactivating factor swiveling domain (DDR_swiveling)	DD-reactivating factor swiveling domain	AdoCbl-dependent diol dehydratase (DD) (EC 4.2.1.28) is one of the enzymes that catalyzes the conversion of 1,2-propanediol, 1,2-ethanediol, and glycerol to the corresponding aldehydes. A DD-reactivating factor (DDR) is responsible for the rapid reac ...	AdoCbl-dependent diol dehydratase (DD) (EC 4.2.1.28) is one of the enzymes that catalyzes the conversion of 1,2-propanediol, 1,2-ethanediol, and glycerol to the corresponding aldehydes. A DD-reactivating factor (DDR) is responsible for the rapid reactivation of the inactivated holoDD in the presence of AdoCbl, ATP, and Mg2+. DDR exists as a dimer of heterodimer (alpha-beta)2. The alpha subunit has four domains: ATPase domain, swiveling domain, linker domain, and insert domain. The beta subunit, composed of a single domain, has a similar fold to the beta subunit of diol dehydratase (DD). This entry describes the swiveling domain of DDR, which structurally connects the beta subunit and the ATPase domain of the other alpha subunit. Furthermore, the beta subunit moves with the swiveling domain while the linker domain acts as a flat spring or a hinge for the domain movement of the swiveling domain [1].	Domain
B, D	PF02288	Dehydratase medium subunit (Dehydratase_MU)	Dehydratase medium subunit	This family contains the medium subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	diol dehydratase-reactivating factor large subunit	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding hydrolase activity catalytic activity cation binding metal ion binding	-	-
B, D	diol dehydratase-reactivating factor small subunit	hydrolase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR028975	Diol dehydratase-reactivating factor, alpha subunit, swiveling domain superfamily	Homologous Superfamily
A, C	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, C	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A, C	IPR009191	Diol dehydratase-reactivating factor large subunit	Family
A, C	IPR030994	Diol dehydratase reactivase ATPase-like domain	Domain
A, C	IPR040916	DD-reactivating factor swiveling domain	Domain
B, D	IPR009192	Diol/glycerol dehydratase reactivating factor, small subunit	Family
B, D	IPR003208	Diol/glycerol dehydratase/dehydratase reactivating factor	Family
B, D	IPR010254	B12-dependent dehydratases, beta subunit	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.