5YSH

Diol dehydratase - alpha/T172A mutant complexed with AdoCbl, aerobically-prepared crystal

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	d5ysha_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Cobalamin (vitamin B12)-dependent enzymes	Diol dehydratase, alpha subunit	Diol dehydratase, alpha subunit	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
D	d5yshd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Cobalamin (vitamin B12)-dependent enzymes	Diol dehydratase, alpha subunit	Diol dehydratase, alpha subunit	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
G	d5yshg_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Cobalamin (vitamin B12)-dependent enzymes	Diol dehydratase, alpha subunit	Diol dehydratase, alpha subunit	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
J	d5yshj_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Cobalamin (vitamin B12)-dependent enzymes	Diol dehydratase, alpha subunit	Diol dehydratase, alpha subunit	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
H	d5yshh1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	B12-dependent dehydatase associated subunit	Diol dehydratase, beta subunit	Diol dehydratase, beta subunit	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
H	d5yshh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
K	d5yshk_	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	B12-dependent dehydatase associated subunit	Diol dehydratase, beta subunit	Diol dehydratase, beta subunit	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
B	d5yshb_	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	B12-dependent dehydatase associated subunit	Diol dehydratase, beta subunit	Diol dehydratase, beta subunit	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
E	d5yshe_	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	B12-dependent dehydatase associated subunit	Diol dehydratase, beta subunit	Diol dehydratase, beta subunit	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
C	d5yshc_	All alpha proteins	Open three-helical up-and-down bundle	Diol dehydratase, gamma subunit	Diol dehydratase, gamma subunit	automated matches	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
F	d5yshf_	All alpha proteins	Open three-helical up-and-down bundle	Diol dehydratase, gamma subunit	Diol dehydratase, gamma subunit	automated matches	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
I	d5yshi_	All alpha proteins	Open three-helical up-and-down bundle	Diol dehydratase, gamma subunit	Diol dehydratase, gamma subunit	automated matches	(Klebsiella oxytoca ) [TaxId: 571 ],	SCOPe (2.08)
L	d5yshl_	All alpha proteins	Open three-helical up-and-down bundle	Diol dehydratase, gamma subunit	Diol dehydratase, gamma 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	Cobalamin (vitamin B12)-dependent enzymes	8043858	3000609	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8043858	3000609	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8043858	3000609	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8043858	3000609	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	B12-dependent dehydatase associated subunit	8044419	3000491	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	B12-dependent dehydatase associated subunit	8044419	3000491	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	B12-dependent dehydatase associated subunit	8044419	3000491	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	B12-dependent dehydatase associated subunit	8044419	3000491	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Diol dehydratase gamma subunit	8036835	3001460	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Diol dehydratase gamma subunit	8036835	3001460	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Diol dehydratase gamma subunit	8036835	3001460	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Diol dehydratase gamma subunit	8036835	3001460	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	PF02286	e5yshA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF02286	ECOD (1.6)
D	PF02286	e5yshD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF02286	ECOD (1.6)
G	PF02286	e5yshG1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF02286	ECOD (1.6)
J	PF02286	e5yshJ1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF02286	ECOD (1.6)
H	PF02288	e5yshH1	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: PF02288	ECOD (1.6)
K	PF02288	e5yshK1	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: PF02288	ECOD (1.6)
B	PF02288	e5yshB1	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: PF02288	ECOD (1.6)
E	PF02288	e5yshE1	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: PF02288	ECOD (1.6)
C	PF02287	e5yshC1	A: alpha bundles	X: Diol dehydratase, gamma subunit (From Topology)	H: Diol dehydratase, gamma subunit (From Topology)	T: Diol dehydratase, gamma subunit	F: PF02287	ECOD (1.6)
F	PF02287	e5yshF1	A: alpha bundles	X: Diol dehydratase, gamma subunit (From Topology)	H: Diol dehydratase, gamma subunit (From Topology)	T: Diol dehydratase, gamma subunit	F: PF02287	ECOD (1.6)
I	PF02287	e5yshI1	A: alpha bundles	X: Diol dehydratase, gamma subunit (From Topology)	H: Diol dehydratase, gamma subunit (From Topology)	T: Diol dehydratase, gamma subunit	F: PF02287	ECOD (1.6)
L	PF02287	e5yshL1	A: alpha bundles	X: Diol dehydratase, gamma subunit (From Topology)	H: Diol dehydratase, gamma subunit (From Topology)	T: Diol dehydratase, gamma subunit	F: PF02287	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.350	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Diol/glycerol dehydratase, large subunit	CATH (4.3.0)
D	3.20.20.350	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Diol/glycerol dehydratase, large subunit	CATH (4.3.0)
G	3.20.20.350	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Diol/glycerol dehydratase, large subunit	CATH (4.3.0)
J	3.20.20.350	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Diol/glycerol dehydratase, large subunit	CATH (4.3.0)
H	3.40.50.10150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	B12-dependent dehydatase associated subunit	CATH (4.3.0)
K	3.40.50.10150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	B12-dependent dehydatase associated subunit	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)
E	3.40.50.10150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	B12-dependent dehydatase associated subunit	CATH (4.3.0)
C	1.10.1510.20	Mainly Alpha	Orthogonal Bundle	Hypothetical Protein Yqey	Chain: A	CATH (4.3.0)
F	1.10.1510.20	Mainly Alpha	Orthogonal Bundle	Hypothetical Protein Yqey	Chain: A	CATH (4.3.0)
I	1.10.1510.20	Mainly Alpha	Orthogonal Bundle	Hypothetical Protein Yqey	Chain: A	CATH (4.3.0)
L	1.10.1510.20	Mainly Alpha	Orthogonal Bundle	Hypothetical Protein Yqey	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G, J	PF02286	Dehydratase large subunit (Dehydratase_LU)	Dehydratase large subunit	This family contains the large subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.	Domain
B, E, H, K	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
C, F, I, L	PF02287	Dehydratase small subunit (Dehydratase_SU)	Dehydratase small subunit	This family contains the small 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, D, G, J	Diol dehydrase alpha subunit	vitamin binding binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding small molecule binding hydro-lyase activity lyase activity propanediol dehydratase activity catalytic activity carbon-oxygen lyase activity cation binding ion binding vitamin binding binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding small molecule binding hydro-lyase activity lyase activity propanediol dehydratase activity catalytic activity carbon-oxygen lyase activity cation binding ion binding metal ion binding	-	-
B, E, H, K	Diol dehydrase beta subunit	hydro-lyase activity lyase activity propanediol dehydratase activity catalytic activity carbon-oxygen lyase activity	-	-
C, F, I, L	Diol dehydrase gamma subunit	hydro-lyase activity lyase activity propanediol dehydratase activity catalytic activity carbon-oxygen lyase activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G, J	IPR003206	Diol/glycerol dehydratase, large subunit	Domain
A, D, G, J	IPR036999	Diol/glycerol dehydratase, large subunit superfamily	Homologous Superfamily
A, D, G, J	IPR016176	Cobalamin (vitamin B12)-dependent enzyme, catalytic	Homologous Superfamily
B, E, H, K	IPR025541	Propanediol/glycerol dehydratase, medium subunit	Family
B, E, H, K	IPR003208	Diol/glycerol dehydratase/dehydratase reactivating factor	Family
B, E, H, K	IPR010254	B12-dependent dehydratases, beta subunit	Homologous Superfamily
C, F, I, L	IPR036091	Propanediol/glycerol dehydratase, small subunit superfamily	Homologous Superfamily
C, F, I, L	IPR003207	Propanediol/glycerol dehydratase, small subunit	Family

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.