6TCD

Crystal structure of Salmo salar RidA-2

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	d6tcda_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	Atlantic salmon (Salmo salar ) [TaxId: 8030 ],	SCOPe (2.08)
B	d6tcdb1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	Atlantic salmon (Salmo salar ) [TaxId: 8030 ],	SCOPe (2.08)
B	d6tcdb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Atlantic salmon (Salmo salar ) [TaxId: 8030 ],	SCOPe (2.08)
C	d6tcdc1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	Atlantic salmon (Salmo salar ) [TaxId: 8030 ],	SCOPe (2.08)
C	d6tcdc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Atlantic salmon (Salmo salar ) [TaxId: 8030 ],	SCOPe (2.08)
D	d6tcdd1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	Atlantic salmon (Salmo salar ) [TaxId: 8030 ],	SCOPe (2.08)
D	d6tcdd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Atlantic salmon (Salmo salar ) [TaxId: 8030 ],	SCOPe (2.08)
E	d6tcde1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	Atlantic salmon (Salmo salar ) [TaxId: 8030 ],	SCOPe (2.08)
E	d6tcde2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Atlantic salmon (Salmo salar ) [TaxId: 8030 ],	SCOPe (2.08)
F	d6tcdf_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	automated matches	Atlantic salmon (Salmo salar ) [TaxId: 8030 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	YjgF-like	8097354	3001733	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YjgF-like	8097354	3001733	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YjgF-like	8097354	3001733	SCOP2B (2022-06-29)
D	SCOP2 Family	YjgF/L-PSP	8097353	4001510	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	YjgF-like	8097354	3001733	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	YjgF-like	8097354	3001733	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	YjgF-like	8097354	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)
A	Ribonuc_L-PSP	e6tcdA1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
B	Ribonuc_L-PSP	e6tcdB1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
C	Ribonuc_L-PSP	e6tcdC1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
D	Ribonuc_L-PSP	e6tcdD1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
E	Ribonuc_L-PSP	e6tcdE1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
F	Ribonuc_L-PSP	e6tcdF1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	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, C, D, E A, B, C, D, E, F	Ribonuclease UK114	2-iminobutanoate/2-iminopropanoate deaminase hydrolase activity deaminase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR006056	RidA family	Family
A, B, C, D, E A, B, C, D, E, F	IPR035959	RutC-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	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 R01GM157729.