6VXE | pdb_00006vxe

Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile with substrate trans-4-hydroxy-L-proline bound

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	d6vxea_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	(Clostridioides difficile 70-100-2010 ) [TaxId: 1002369 ],	SCOPe (2.08)
B	d6vxeb_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	(Clostridioides difficile 70-100-2010 ) [TaxId: 1002369 ],	SCOPe (2.08)
C	d6vxec_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	(Clostridioides difficile 70-100-2010 ) [TaxId: 1002369 ],	SCOPe (2.08)
E	d6vxee_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	(Clostridioides difficile 70-100-2010 ) [TaxId: 1002369 ],	SCOPe (2.08)
F	d6vxef_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	(Clostridioides difficile 70-100-2010 ) [TaxId: 1002369 ],	SCOPe (2.08)
G	d6vxeg_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	(Clostridioides difficile 70-100-2010 ) [TaxId: 1002369 ],	SCOPe (2.08)
H	d6vxeh_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	(Clostridioides difficile 70-100-2010 ) [TaxId: 1002369 ],	SCOPe (2.08)
D	d6vxed_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	automated matches	automated matches	(Clostridioides difficile 70-100-2010 ) [TaxId: 1002369 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8096016	3001069	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8096016	3001069	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8096016	3001069	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8096016	3001069	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8096016	3001069	SCOP2B (2022-06-29)
G	SCOP2 Family	PFL-like	8096015	4003576	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	PFL-like glycyl radical enzymes	8096016	3001069	SCOP2 (2022-06-29)
H	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8096016	3001069	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8096016	3001069	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	PFL-like	e6vxeA2	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PFL-like	ECOD (1.6)
A	PFL-like	e6vxeA1	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PFL-like	ECOD (1.6)
B	PFL-like	e6vxeB2	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PFL-like	ECOD (1.6)
B	PFL-like	e6vxeB1	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PFL-like	ECOD (1.6)
C	PFL-like	e6vxeC2	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PFL-like	ECOD (1.6)
C	PFL-like	e6vxeC1	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PFL-like	ECOD (1.6)
E	PFL-like	e6vxeE2	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PFL-like	ECOD (1.6)
E	PFL-like	e6vxeE1	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PFL-like	ECOD (1.6)
F	PFL-like	e6vxeF2	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PFL-like	ECOD (1.6)
F	PFL-like	e6vxeF1	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PFL-like	ECOD (1.6)
G	PFL-like	e6vxeG2	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PFL-like	ECOD (1.6)
G	PFL-like	e6vxeG1	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PFL-like	ECOD (1.6)
H	PFL-like	e6vxeH1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PFL-like	ECOD (1.6)
H	PFL-like	e6vxeH2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PFL-like	ECOD (1.6)
D	PFL-like	e6vxeD1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PFL-like	ECOD (1.6)
D	PFL-like	e6vxeD2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PFL-like	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (utative)
B	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (utative)
C	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (utative)
E	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (utative)
F	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (utative)
G	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (utative)
H	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (utative)
D	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF01228	Glycine radical (Gly_radical)	Glycine radical		Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF02901	Pyruvate formate lyase-like (PFL-like)	Pyruvate formate lyase-like	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Trans-4-hydroxy-L-proline dehydratase	lyase activity catalytic activity carbon-oxygen lyase activity	glutamine family amino acid biosynthetic process oxoacid metabolic process amino acid metabolic process L-proline biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glutamine family amino acid metabolic process metabolic compound salvage proline metabolic process small molecule metabolic process proline salvage small molecule biosynthetic process glutamine family amino acid biosynthetic process oxoacid metabolic process amino acid metabolic process L-proline biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glutamine family amino acid metabolic process metabolic compound salvage proline metabolic process small molecule metabolic process proline salvage small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-amino acid metabolic process amino acid salvage proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR050012	Trans-4-hydroxy-L-proline dehydratase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR051215	Glycyl Radical Enzyme	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR004184	Pyruvate formate lyase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001150	Glycine radical domain	Domain

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.