4IW3

Crystal structure of a Pseudomonas putida prolyl-4-hydroxylase (P4H) in complex with elongation factor Tu (EF-Tu)

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	d4iw3a_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
D [auth J]	d4iw3j_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
B	d4iw3b2	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
B	d4iw3b3	All beta proteins	Elongation factor/aminomethyltransferase common domain	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
B	d4iw3b1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
C [auth K]	d4iw3k2	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
C [auth K]	d4iw3k3	All beta proteins	Elongation factor/aminomethyltransferase common domain	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
C [auth K]	d4iw3k1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8056525	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EF-Tu post-G domain-like	8056528	3002024	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EF-Tu post-G domain-like	8056526	3002024	SCOP2B (2022-06-29)
C [auth K]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056526	3002024	SCOP2B (2022-06-29)
C [auth K]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056528	3002024	SCOP2B (2022-06-29)
C [auth K]	SCOP2B Superfamily	Ras-like P-loop GTPases	8056525	3002022	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	2OG-FeII_Oxy_3	e4iw3A1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: 2OG-FeII_Oxy_3	ECOD (1.6)
D [auth J]	2OG-FeII_Oxy_3	e4iw3J1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: 2OG-FeII_Oxy_3	ECOD (1.6)
B	GTP_EFTU_D2_1	e4iw3B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
B	GTP_EFTU_D3	e4iw3B2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3	ECOD (1.6)
B	MnmE_helical_2nd	e4iw3B3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)
C [auth K]	GTP_EFTU_D2_1	e4iw3K6	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
C [auth K]	GTP_EFTU_D3	e4iw3K4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3	ECOD (1.6)
C [auth K]	MnmE_helical_2nd	e4iw3K5	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
D [auth J]	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
C [auth K]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C [auth K]	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth J]	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
B, C [auth K]	PF00009	Elongation factor Tu GTP binding domain (GTP_EFTU)	Elongation factor Tu GTP binding domain	This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.	Domain
B, C [auth K]	PF03143	Elongation factor Tu C-terminal domain (GTP_EFTU_D3)	Elongation factor Tu C-terminal domain	Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA [1] and binding to EF-Ts Pfam:PF00889 [2].	Domain
B, C [auth K]	PF03144	Elongation factor Tu domain 2 (GTP_EFTU_D2)	Elongation factor Tu domain 2	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ...	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth J]	Putative uncharacterized protein	oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen catalytic activity organic acid binding binding carbohydrate binding vitamin binding ion binding organic cyclic compound binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen catalytic activity organic acid binding binding carbohydrate binding vitamin binding ion binding organic cyclic compound binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding small molecule binding dioxygenase activity cation binding transition metal ion binding iron ion binding metal ion binding	-	-
B, C [auth K]	Elongation factor Tu-A	guanosine tetraphosphate binding guanyl nucleotide binding binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding guanosine tetraphosphate binding guanyl nucleotide binding binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding translation regulator activity translation regulator activity, nucleic acid binding translation elongation factor activity nucleic acid binding translation factor activity, RNA binding GTP binding purine ribonucleoside triphosphate binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	-	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth J]	IPR006620	Prolyl 4-hydroxylase, alpha subunit	Domain
A, D [auth J]	IPR044862	Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain	Domain
A, D [auth J]	IPR051559	Hypoxia-inducible factor prolyl hydroxylases	Family
A, D [auth J]	IPR005123	Oxoglutarate/iron-dependent dioxygenase domain	Domain
B, C [auth K]	IPR005225	Small GTP-binding domain	Domain
B, C [auth K]	IPR000795	Translational (tr)-type GTP-binding domain	Domain
B, C [auth K]	IPR033720	Elongation factor Tu, domain 2	Domain
B, C [auth K]	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
B, C [auth K]	IPR031157	Tr-type G domain, conserved site	Conserved Site
B, C [auth K]	IPR004541	Translation elongation factor EFTu/EF1A, bacterial/organelle	Family
B, C [auth K]	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
B, C [auth K]	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
B, C [auth K]	IPR004160	Translation elongation factor EFTu/EF1A, C-terminal	Domain
B, C [auth K]	IPR050055	Elongation factor Tu GTPase	Family
B, C [auth K]	IPR041709	Elongation factor Tu (EF-Tu), GTP-binding domain	Domain
B, C [auth K]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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.