4J25 | pdb_00004j25

Crystal structure of a Pseudomonas putida prolyl-4-hydroxylase (P4H)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
H	d4j25h_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
G	d4j25g_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
F	d4j25f_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
E	d4j25e_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
D	d4j25d1	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
D	d4j25d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
C	d4j25c1	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
C	d4j25c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
B	d4j25b1	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
B	d4j25b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
A	d4j25a1	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
A	d4j25a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	Ribosomal_L3	e4j25H1	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Ribosomal_L3	ECOD (develop294)
G	Ribosomal_L3	e4j25G1	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Ribosomal_L3	ECOD (develop294)
F	Ribosomal_L3	e4j25F1	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Ribosomal_L3	ECOD (develop294)
E	Ribosomal_L3	e4j25E1	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Ribosomal_L3	ECOD (develop294)
D	Ribosomal_L3	e4j25D1	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Ribosomal_L3	ECOD (develop294)
C	DNA_pack_C	e4j25C1	A: alpha bundles	X: alpha/beta-Hydrolases	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: DNA_pack_C	ECOD (develop294)
B	DNA_pack_C	e4j25B1	A: alpha bundles	X: alpha/beta-Hydrolases	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: DNA_pack_C	ECOD (develop294)
A	DNA_pack_C	e4j25A1	A: alpha bundles	X: alpha/beta-Hydrolases	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: DNA_pack_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
G	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
F	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
E	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
D	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
C	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
B	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
A	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)

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	PF13640	2OG-Fe(II) oxygenase superfamily (2OG-FeII_Oxy_3)	2OG-Fe(II) oxygenase superfamily	This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1].	Domain

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	Putative uncharacterized protein	oxidoreductase activity catalytic activity, acting on a protein oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen peptidyl-proline dioxygenase activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity dioxygenase activity organic acid binding binding carbohydrate binding vitamin binding ion binding anion binding monosaccharide binding oxidoreductase activity catalytic activity, acting on a protein oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen peptidyl-proline dioxygenase activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity dioxygenase activity organic acid binding binding carbohydrate binding vitamin binding ion binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding small molecule binding cation binding transition metal ion binding iron ion binding ferrous iron binding metal ion binding	response to decreased oxygen levels cellular response to stimulus response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006620	Prolyl 4-hydroxylase, alpha subunit	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR044862	Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR051559	Hypoxia-inducible factor prolyl hydroxylases	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR005123	Oxoglutarate/iron-dependent dioxygenase 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.