6VXC

Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile

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	d6vxca_	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	d6vxcb_	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	d6vxcc_	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	d6vxcd_	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	d6vxce_	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	d6vxcf_	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	d6vxcg_	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	d6vxch_	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	8099194	3001069	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8099194	3001069	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8099194	3001069	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8099194	3001069	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8099194	3001069	SCOP2B (2022-06-29)
F	SCOP2 Family	PFL-like	8099193	4003576	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	PFL-like glycyl radical enzymes	8099194	3001069	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8099194	3001069	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8099194	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	PF02901	e6vxcA2	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: PF02901	ECOD (1.6)
A	PF01228	e6vxcA1	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	ECOD (1.6)
B	PF02901	e6vxcB2	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: PF02901	ECOD (1.6)
B	PF01228	e6vxcB1	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	ECOD (1.6)
C	PF02901	e6vxcC1	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: PF02901	ECOD (1.6)
C	PF01228	e6vxcC2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	ECOD (1.6)
D	PF02901	e6vxcD2	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: PF02901	ECOD (1.6)
D	PF01228	e6vxcD1	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	ECOD (1.6)
E	PF02901	e6vxcE1	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: PF02901	ECOD (1.6)
E	PF01228	e6vxcE2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	ECOD (1.6)
F	PF02901	e6vxcF2	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: PF02901	ECOD (1.6)
F	PF01228	e6vxcF1	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	ECOD (1.6)
G	PF02901	e6vxcG1	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: PF02901	ECOD (1.6)
G	PF01228	e6vxcG2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	ECOD (1.6)
H	PF02901	e6vxcH1	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: PF02901	ECOD (1.6)
H	PF01228	e6vxcH2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PF01228	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)
D	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)

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 acetyltransferase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity C-acyltransferase activity C-acetyltransferase activity formate C-acetyltransferase activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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 R01GM133198.