1QU9

1.2 A CRYSTAL STRUCTURE OF YJGF GENE PRODUCT 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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1qu9a_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	Conserved 'hypothetical' protein YjgF	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1qu9b_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	Conserved 'hypothetical' protein YjgF	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1qu9c_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	YjgF/L-PSP	Conserved 'hypothetical' protein YjgF	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	YjgF/L-PSP	8023564	4001510	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	YjgF-like	8035944	3001733	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	YjgF-like	8035944	3001733	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YjgF-like	8035944	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	e1qu9A1	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	e1qu9B1	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	e1qu9C1	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)
A	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)
C	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	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	YJGF 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 unfolded protein binding protein binding binding 2-iminopropanoate deaminase activity identical protein binding	oxoacid metabolic process small molecule biosynthetic process cellular biosynthetic process cellular metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process amino acid biosynthetic process biosynthetic process isoleucine biosynthetic process branched-chain amino acid biosynthetic process oxoacid metabolic process small molecule biosynthetic process cellular biosynthetic process cellular metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process amino acid biosynthetic process biosynthetic process isoleucine biosynthetic process branched-chain amino acid biosynthetic process metabolic process small molecule metabolic process cellular process branched-chain amino acid metabolic process isoleucine metabolic process alpha-amino acid biosynthetic process protein-containing complex organization protein trimerization cellular component organization cellular component biogenesis cellular component assembly protein homotrimerization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis response to stimulus response to chemical response to toxic substance	membrane cellular anatomical entity intracellular anatomical structure cytoplasm cytosol protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C	CSP	Parent Component: CYS RESID: AA0034 PSI-MOD : S-phospho-L-cysteine MOD:00043

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.