3MQW

Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica with higher solvent content and an ordered N-terminal tag

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	d3mqwa1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
A	d3mqwa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
B	d3mqwb1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
B	d3mqwb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
C	d3mqwc1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
C	d3mqwc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
D	d3mqwd1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
D	d3mqwd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
E	d3mqwe1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
E	d3mqwe2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
F	d3mqwf1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
F	d3mqwf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Entamoeba histolytica ) [TaxId: 5759 ],	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	8059836	4001510	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	YjgF-like	8059837	3001733	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	YjgF-like	8059837	3001733	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YjgF-like	8059837	3001733	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	YjgF-like	8059837	3001733	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	YjgF-like	8059837	3001733	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	YjgF-like	8059837	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	e3mqwA1	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	e3mqwB1	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	e3mqwC1	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	e3mqwD1	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	e3mqwE1	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	e3mqwF1	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)
D	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)
F	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	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	putative Endoribonuclease L-PSP	hydrolase activity deaminase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	organonitrogen compound catabolic process organonitrogen compound metabolic process organic substance metabolic process catabolic process metabolic process organic substance catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity 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 National Science Foundation (DBI-1832184), 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.