3V4D

Crystal structure of RutC protein a member of the YjgF family from E.coli

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)
C [auth F]	d3v4df1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
C [auth F]	d3v4df2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
D [auth B]	d3v4db1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
D [auth B]	d3v4db2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
E [auth D]	d3v4dd1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
E [auth D]	d3v4dd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
A	d3v4da_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
B [auth C]	d3v4dc1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
B [auth C]	d3v4dc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
F [auth E]	d3v4de1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)
F [auth E]	d3v4de2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli O6 ) [TaxId: 217992 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth F]	SCOP2B Superfamily	YjgF-like	8059841	3001733	SCOP2B (2022-06-29)
D [auth B]	SCOP2 Family	YjgF/L-PSP	8059840	4001510	SCOP2 (2022-06-29)
D [auth B]	SCOP2 Superfamily	YjgF-like	8059841	3001733	SCOP2 (2022-06-29)
E [auth D]	SCOP2B Superfamily	YjgF-like	8059841	3001733	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	YjgF-like	8059841	3001733	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	YjgF-like	8059841	3001733	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	YjgF-like	8059841	3001733	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)
C [auth F]	PF01042	e3v4dF1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: PF01042	ECOD (1.6)
D [auth B]	PF01042	e3v4dB1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: PF01042	ECOD (1.6)
E [auth D]	PF01042	e3v4dD1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: PF01042	ECOD (1.6)
A	PF01042	e3v4dA1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: PF01042	ECOD (1.6)
B [auth C]	PF01042	e3v4dC1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: PF01042	ECOD (1.6)
F [auth E]	PF01042	e3v4dE1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: PF01042	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth F]	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
D [auth B]	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
E [auth D]	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
A	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
B [auth C]	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
F [auth E]	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth F], D [auth B], E [auth D], A, B [auth C], C [auth F], D [auth B], E [auth D], F [auth E]	PF01042	Endoribonuclease L-PSP (Ribonuc_L-PSP)	Endoribonuclease L-PSP	Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA [1]. Previously thought to inhibit protein synthesis initiation [2]. This protein may also be involved in the regulation of purine biosynthesis [3]. Yjg ...	Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA [1]. Previously thought to inhibit protein synthesis initiation [2]. This protein may also be involved in the regulation of purine biosynthesis [3]. YjgF (renamed RidA) family members are enamine/imine deaminases. They hydrolyze reactive intermediates released by PLP-dependent enzymes, including threonine dehydratase [5]. YjgF also prevents inhibition of transaminase B (IlvE) in Salmonella [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C], C [auth F], D [auth B], E [auth D], A, B [auth C], C [auth F], D [auth B], E [auth D], F [auth E]	Aminoacrylate peracid reductase RutC	hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	response to nutrient levels cellular homeostasis chemical homeostasis response to stimulus homeostatic process intracellular nitrogen homeostasis nitrogen utilization intracellular chemical homeostasis organonitrogen compound catabolic process organonitrogen compound metabolic process pyrimidine-containing compound metabolic process catabolic process pyrimidine-containing compound catabolic process uracil metabolic process response to nutrient levels cellular homeostasis chemical homeostasis response to stimulus homeostatic process intracellular nitrogen homeostasis nitrogen utilization intracellular chemical homeostasis organonitrogen compound catabolic process organonitrogen compound metabolic process pyrimidine-containing compound metabolic process catabolic process pyrimidine-containing compound catabolic process uracil metabolic process primary metabolic process organic cyclic compound catabolic process pyrimidine nucleobase catabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process organic cyclic compound metabolic process organic substance metabolic process uracil catabolic process nucleobase-containing small molecule metabolic process nucleobase catabolic process nucleobase metabolic process small molecule metabolic process metabolic process organic substance catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth F], D [auth B], E [auth D], A, B [auth C], C [auth F], D [auth B], E [auth D], F [auth E]	IPR019897	RidA, conserved site	Conserved Site
A, B [auth C], C [auth F], D [auth B], E [auth D], A, B [auth C], C [auth F], D [auth B], E [auth D], F [auth E]	IPR019898	3-aminoacrylate deaminase RutC	Family
A, B [auth C], C [auth F], D [auth B], E [auth D], A, B [auth C], C [auth F], D [auth B], E [auth D], F [auth E]	IPR035959	RutC-like superfamily	Homologous Superfamily
A, B [auth C], C [auth F], D [auth B], E [auth D], A, B [auth C], C [auth F], D [auth B], E [auth D], F [auth E]	IPR006175	YjgF/YER057c/UK114 family	Family

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.