1ONI | pdb_00001oni

Crystal structure of a human p14.5, a translational inhibitor reveals different mode of ligand binding near the invariant residues of the Yjgf/UK114 protein family

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
I	d1onii_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	14.5 kda translational inhibitor protein, L-PSP	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d1onih_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	14.5 kda translational inhibitor protein, L-PSP	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d1onig_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	14.5 kda translational inhibitor protein, L-PSP	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d1onif_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	14.5 kda translational inhibitor protein, L-PSP	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1onie_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	14.5 kda translational inhibitor protein, L-PSP	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1onid_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	14.5 kda translational inhibitor protein, L-PSP	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1onic_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	14.5 kda translational inhibitor protein, L-PSP	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1onib_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	14.5 kda translational inhibitor protein, L-PSP	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1onia_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	14.5 kda translational inhibitor protein, L-PSP	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I	SCOP2B Superfamily	YjgF-like	8034134	3001733	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	YjgF-like	8034134	3001733	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	YjgF-like	8034134	3001733	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	YjgF-like	8034134	3001733	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	YjgF-like	8034134	3001733	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	YjgF-like	8034134	3001733	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YjgF-like	8034134	3001733	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YjgF-like	8034134	3001733	SCOP2B (2022-06-29)
A	SCOP2 Family	YjgF/L-PSP	8021754	4001510	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	YjgF-like	8034134	3001733	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
I	Ribonuc_L-PSP	e1oniI1	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)
H	Ribonuc_L-PSP	e1oniH1	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)
G	Ribonuc_L-PSP	e1oniG1	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	e1oniF1	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	e1oniE1	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	e1oniD1	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	e1oniC1	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	e1oniB1	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)
A	Ribonuc_L-PSP	e1oniA1	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)

Domain Annotation: CATH CATH Database Homepage

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

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, I	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, G, H, I	14.5 kDa translational inhibitor protein	2-iminobutanoate/2-iminopropanoate deaminase 2-iminobutanoate deaminase activity hydrolase activity deaminase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds RNA binding binding nucleic acid binding mRNA binding 2-iminopropanoate deaminase activity RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism endonuclease activity hydrolase activity, acting on ester bonds 2-iminobutanoate/2-iminopropanoate deaminase 2-iminobutanoate deaminase activity hydrolase activity deaminase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds RNA binding binding nucleic acid binding mRNA binding 2-iminopropanoate deaminase activity RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism endonuclease activity hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process RNA catabolic process mRNA catabolic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process oxoacid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glycine metabolic process glycine biosynthetic process carboxylic acid catabolic process threonine metabolic process small molecule metabolic process amino acid catabolic process L-threonine catabolic process to glycine small molecule biosynthetic process carboxylic acid metabolic process L-amino acid catabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process L-threonine catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process proteinogenic amino acid biosynthetic process serine family amino acid biosynthetic process small molecule catabolic process alpha-amino acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality positive regulation of mRNA metabolic process positive regulation of RNA metabolic process positive regulation of biological process mRNA destabilization regulation of mRNA catabolic process positive regulation of cellular process RNA destabilization regulation of catabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process lipid metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle peroxisome microbody cytosol membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR019897	RidA, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR006175	YjgF/YER057c/UK114 family	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR006056	RidA family	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR035959	RutC-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H, I	Pharos: P52758	acute myeloid leukemia glioblastoma medulloblastoma pancreatic ductal adenocarcinoma primitive neuroectodermal tumor adenoma large cell medulloblastoma nephrosclerosis Pick disease progressive supranuclear palsy atypical teratoid rhabdoid tumor malignant glioma osteosarcoma pilocytic astrocytoma

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.