RNase A-like superfamily

SCOP classification

Root:	SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:	Alpha and beta proteins (a+b) [ 53931] (376)
Fold:	RNase A-like [ 54075]
Superfamily:	RNase A-like [ 54076]
Families:	Ribonuclease A-like [ 54077] (8)

Superfamily statistics

	Genomes (54)	Uniprot 2013_05	PDB chains (SCOP 1.75)
Domains	568	1,004	61
Proteins	568	1,002	61

Functional annotation

General category	Information
Detailed category	RNA processing

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)

	GO term	FDR (singleton)	FDR (all)	SDFO level	Annotation (direct or inherited)
Biological Process (BP)	cellular aromatic compound metabolic process	7.634e-10	1.143e-07	Least Informative	Direct
Biological Process (BP)	nitrogen compound metabolic process	1.198e-07	2.933e-06	Least Informative	Direct
Biological Process (BP)	biosynthetic process	0.0002782	0.0002012	Least Informative	Direct
Biological Process (BP)	cellular macromolecule metabolic process	3.493e-08	0.0001077	Least Informative	Direct
Biological Process (BP)	heterocycle metabolic process	5.729e-10	7.002e-08	Least Informative	Direct
Biological Process (BP)	organic cyclic compound metabolic process	5.508e-09	4.382e-07	Least Informative	Direct
Biological Process (BP)	regulation of cellular process	0.1017	0.3195	Least Informative	Inherited
Biological Process (BP)	single-organism metabolic process	0.01557	0.001305	Least Informative	Inherited
Biological Process (BP)	regulation of metabolic process	4.985e-05	0.01149	Least Informative	Inherited
Biological Process (BP)	cellular component organization or biogenesis	3.2e-05	0.02084	Least Informative	Inherited
Biological Process (BP)	single-organism cellular process	0.03286	0.8148	Least Informative	Inherited
Biological Process (BP)	response to stimulus	1.127e-06	0.002125	Least Informative	Inherited
Biological Process (BP)	developmental process	8.064e-09	0.003126	Least Informative	Inherited
Biological Process (BP)	multicellular organismal process	3.636e-08	0.005567	Least Informative	Inherited
Biological Process (BP)	organelle organization	1.446e-09	6.332e-06	Moderately Informative	Direct
Biological Process (BP)	lipid biosynthetic process	1.195e-14	9.754e-15	Moderately Informative	Direct
Biological Process (BP)	response to abiotic stimulus	3.256e-07	6.633e-07	Moderately Informative	Direct
Biological Process (BP)	anatomical structure morphogenesis	5.052e-07	1.5e-05	Moderately Informative	Direct
Biological Process (BP)	gene expression	7.976e-08	8.536e-07	Moderately Informative	Direct
Biological Process (BP)	RNA metabolic process	0	4.008e-15	Moderately Informative	Direct
Biological Process (BP)	heterocycle biosynthetic process	3e-07	2.789e-07	Moderately Informative	Direct
Biological Process (BP)	aromatic compound biosynthetic process	2.6e-08	2.457e-07	Moderately Informative	Direct
Biological Process (BP)	regulation of localization	8.345e-12	2.675e-10	Moderately Informative	Direct
Biological Process (BP)	cellular macromolecule biosynthetic process	1.024e-08	2.005e-07	Moderately Informative	Direct
Biological Process (BP)	macromolecular complex subunit organization	3.939e-13	1.794e-10	Moderately Informative	Direct
Biological Process (BP)	cellular component biogenesis	5.415e-11	2.802e-08	Moderately Informative	Direct
Biological Process (BP)	cellular lipid metabolic process	1.217e-10	9.584e-12	Moderately Informative	Direct
Biological Process (BP)	cellular nitrogen compound biosynthetic process	3.946e-07	3.878e-07	Moderately Informative	Direct
Biological Process (BP)	single-organism developmental process	8.343e-11	0.000129	Moderately Informative	Direct
Biological Process (BP)	positive regulation of cellular process	8.764e-10	5.674e-05	Moderately Informative	Direct
Biological Process (BP)	negative regulation of cellular process	1.344e-07	8.148e-05	Moderately Informative	Direct
Biological Process (BP)	regulation of molecular function	6.812e-11	3.247e-09	Moderately Informative	Direct
Biological Process (BP)	organic cyclic compound biosynthetic process	7.599e-07	1.527e-06	Moderately Informative	Direct
Biological Process (BP)	multi-organism process	0.01266	0.05013	Moderately Informative	Inherited
Biological Process (BP)	transcription, DNA-dependent	9.05e-15	1.088e-11	Informative	Direct
Biological Process (BP)	cytoskeleton organization	0	8.064e-12	Informative	Direct
Biological Process (BP)	actin filament-based process	0	2.076e-15	Informative	Direct
Biological Process (BP)	regulation of protein localization	0	0	Informative	Direct
Biological Process (BP)	cellular macromolecular complex assembly	0	0	Informative	Direct
Biological Process (BP)	regulation of cell proliferation	0	1.7e-12	Informative	Direct
Biological Process (BP)	positive regulation of catalytic activity	0	1.5e-13	Informative	Direct
Biological Process (BP)	glycerolipid metabolic process	0	0	Informative	Direct
Biological Process (BP)	anatomical structure formation involved in morphogenesis	0	1.711e-13	Informative	Direct
Biological Process (BP)	regulation of secretion	0	0	Informative	Direct
Biological Process (BP)	positive regulation of transport	1.598e-15	0	Informative	Direct
Biological Process (BP)	regulation of hydrolase activity	0	4.008e-15	Informative	Direct
Biological Process (BP)	cardiovascular system development	0	0	Informative	Direct
Biological Process (BP)	response to other organism	0.05779	0.06016	Informative	Inherited
Biological Process (BP)	angiogenesis	0	0	Highly Informative	Direct
Biological Process (BP)	response to hypoxia	0	0	Highly Informative	Direct
Biological Process (BP)	acylglycerol metabolic process	0	0	Highly Informative	Direct
Biological Process (BP)	actin filament organization	0	0	Highly Informative	Direct
Biological Process (BP)	negative regulation of cell proliferation	1.34e-14	7.835e-15	Highly Informative	Direct
Biological Process (BP)	regulation of phospholipase activity	0	0	Highly Informative	Direct
Biological Process (BP)	regulation of smooth muscle cell proliferation	0	0	Highly Informative	Direct
Biological Process (BP)	positive regulation of epithelial cell proliferation	2.081e-11	4.96e-11	Highly Informative	Direct
Biological Process (BP)	regulation of protein secretion	0	0	Highly Informative	Direct
Biological Process (BP)	positive regulation of secretion	0	0	Highly Informative	Direct
Biological Process (BP)	positive regulation of protein transport	0	0	Highly Informative	Direct
Biological Process (BP)	protein polymerization	0	0	Highly Informative	Direct
Molecular Function (MF)	hydrolase activity	0	0	Least Informative	Direct
Molecular Function (MF)	binding	0.03119	0.8823	Least Informative	Inherited
Molecular Function (MF)	hydrolase activity, acting on ester bonds	0	0	Moderately Informative	Direct
Molecular Function (MF)	anion binding	8.872e-13	1.128e-11	Moderately Informative	Direct
Molecular Function (MF)	cation binding	2.159e-12	8.09e-13	Moderately Informative	Direct
Molecular Function (MF)	protein binding	0.03163	0.1538	Moderately Informative	Inherited
Molecular Function (MF)	nuclease activity	0	0	Informative	Direct
Molecular Function (MF)	receptor binding	0	1.325e-14	Informative	Direct
Molecular Function (MF)	cytoskeletal protein binding	0	0	Informative	Direct
Molecular Function (MF)	transition metal ion binding	0	0	Informative	Direct
Molecular Function (MF)	copper ion binding	0	0	Highly Informative	Direct
Molecular Function (MF)	glycosaminoglycan binding	0	0	Highly Informative	Direct
Molecular Function (MF)	sulfur compound binding	0	0	Highly Informative	Direct
Cellular Component (CC)	intracellular non-membrane-bounded organelle	5.223e-08	0.000137	Least Informative	Direct
Cellular Component (CC)	protein complex	3.12e-07	0.0001834	Least Informative	Direct
Cellular Component (CC)	intracellular organelle part	0.0001319	0.02285	Least Informative	Inherited
Cellular Component (CC)	intracellular membrane-bounded organelle	0.04304	0.6045	Least Informative	Inherited
Cellular Component (CC)	extracellular region	0	0	Moderately Informative	Direct
Cellular Component (CC)	nuclear part	3.477e-11	5.515e-06	Moderately Informative	Direct
Cellular Component (CC)	intracellular organelle lumen	1.989e-11	2.342e-06	Moderately Informative	Direct
Cellular Component (CC)	extracellular space	0	0	Informative	Direct
Cellular Component (CC)	extracellular matrix	0	0	Informative	Direct
Cellular Component (CC)	proteinaceous extracellular matrix	0	6.137e-10	Highly Informative	Direct
Cellular Component (CC)	extracellular matrix part	0	0	Highly Informative	Direct

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)

	GO term	FDR (all)	SDFO level	Annotation (direct or inherited)
Biological Process (BP)	cellular aromatic compound metabolic process	1.143e-07	Least Informative	Direct
Biological Process (BP)	nitrogen compound metabolic process	2.933e-06	Least Informative	Direct
Biological Process (BP)	biosynthetic process	0.0002012	Least Informative	Direct
Biological Process (BP)	cellular macromolecule metabolic process	0.0001077	Least Informative	Direct
Biological Process (BP)	heterocycle metabolic process	7.002e-08	Least Informative	Direct
Biological Process (BP)	organic cyclic compound metabolic process	4.382e-07	Least Informative	Direct
Biological Process (BP)	regulation of cellular process	0.3195	Least Informative	Inherited
Biological Process (BP)	single-organism metabolic process	0.001305	Least Informative	Inherited
Biological Process (BP)	regulation of metabolic process	0.01149	Least Informative	Inherited
Biological Process (BP)	cellular component organization or biogenesis	0.02084	Least Informative	Inherited
Biological Process (BP)	single-organism cellular process	0.8148	Least Informative	Inherited
Biological Process (BP)	response to stimulus	0.002125	Least Informative	Inherited
Biological Process (BP)	developmental process	0.003126	Least Informative	Inherited
Biological Process (BP)	multicellular organismal process	0.005567	Least Informative	Inherited
Biological Process (BP)	organelle organization	6.332e-06	Moderately Informative	Direct
Biological Process (BP)	lipid biosynthetic process	9.754e-15	Moderately Informative	Direct
Biological Process (BP)	response to abiotic stimulus	6.633e-07	Moderately Informative	Direct
Biological Process (BP)	anatomical structure morphogenesis	1.5e-05	Moderately Informative	Direct
Biological Process (BP)	gene expression	8.536e-07	Moderately Informative	Direct
Biological Process (BP)	RNA metabolic process	4.008e-15	Moderately Informative	Direct
Biological Process (BP)	heterocycle biosynthetic process	2.789e-07	Moderately Informative	Direct
Biological Process (BP)	aromatic compound biosynthetic process	2.457e-07	Moderately Informative	Direct
Biological Process (BP)	regulation of localization	2.675e-10	Moderately Informative	Direct
Biological Process (BP)	cellular macromolecule biosynthetic process	2.005e-07	Moderately Informative	Direct
Biological Process (BP)	macromolecular complex subunit organization	1.794e-10	Moderately Informative	Direct
Biological Process (BP)	cellular component biogenesis	2.802e-08	Moderately Informative	Direct
Biological Process (BP)	cellular lipid metabolic process	9.584e-12	Moderately Informative	Direct
Biological Process (BP)	cellular nitrogen compound biosynthetic process	3.878e-07	Moderately Informative	Direct
Biological Process (BP)	single-organism developmental process	0.000129	Moderately Informative	Direct
Biological Process (BP)	positive regulation of cellular process	5.674e-05	Moderately Informative	Direct
Biological Process (BP)	negative regulation of cellular process	8.148e-05	Moderately Informative	Direct
Biological Process (BP)	regulation of molecular function	3.247e-09	Moderately Informative	Direct
Biological Process (BP)	organic cyclic compound biosynthetic process	1.527e-06	Moderately Informative	Direct
Biological Process (BP)	multi-organism process	0.05013	Moderately Informative	Inherited
Biological Process (BP)	transcription, DNA-dependent	1.088e-11	Informative	Direct
Biological Process (BP)	cytoskeleton organization	8.064e-12	Informative	Direct
Biological Process (BP)	actin filament-based process	2.076e-15	Informative	Direct
Biological Process (BP)	regulation of protein localization	0	Informative	Direct
Biological Process (BP)	cellular macromolecular complex assembly	0	Informative	Direct
Biological Process (BP)	regulation of cell proliferation	1.7e-12	Informative	Direct
Biological Process (BP)	positive regulation of catalytic activity	1.5e-13	Informative	Direct
Biological Process (BP)	glycerolipid metabolic process	0	Informative	Direct
Biological Process (BP)	anatomical structure formation involved in morphogenesis	1.711e-13	Informative	Direct
Biological Process (BP)	regulation of secretion	0	Informative	Direct
Biological Process (BP)	positive regulation of transport	0	Informative	Direct
Biological Process (BP)	regulation of hydrolase activity	4.008e-15	Informative	Direct
Biological Process (BP)	cardiovascular system development	0	Informative	Direct
Biological Process (BP)	response to other organism	0.06016	Informative	Inherited
Biological Process (BP)	angiogenesis	0	Highly Informative	Direct
Biological Process (BP)	response to hypoxia	0	Highly Informative	Direct
Biological Process (BP)	acylglycerol metabolic process	0	Highly Informative	Direct
Biological Process (BP)	actin filament organization	0	Highly Informative	Direct
Biological Process (BP)	negative regulation of cell proliferation	7.835e-15	Highly Informative	Direct
Biological Process (BP)	regulation of phospholipase activity	0	Highly Informative	Direct
Biological Process (BP)	regulation of smooth muscle cell proliferation	0	Highly Informative	Direct
Biological Process (BP)	positive regulation of epithelial cell proliferation	4.96e-11	Highly Informative	Direct
Biological Process (BP)	regulation of protein secretion	0	Highly Informative	Direct
Biological Process (BP)	positive regulation of secretion	0	Highly Informative	Direct
Biological Process (BP)	positive regulation of protein transport	0	Highly Informative	Direct
Biological Process (BP)	protein polymerization	0	Highly Informative	Direct
Molecular Function (MF)	hydrolase activity	0	Least Informative	Direct
Molecular Function (MF)	binding	0.8823	Least Informative	Inherited
Molecular Function (MF)	hydrolase activity, acting on ester bonds	0	Moderately Informative	Direct
Molecular Function (MF)	anion binding	1.128e-11	Moderately Informative	Direct
Molecular Function (MF)	cation binding	8.09e-13	Moderately Informative	Direct
Molecular Function (MF)	protein binding	0.1538	Moderately Informative	Inherited
Molecular Function (MF)	nuclease activity	0	Informative	Direct
Molecular Function (MF)	receptor binding	1.325e-14	Informative	Direct
Molecular Function (MF)	cytoskeletal protein binding	0	Informative	Direct
Molecular Function (MF)	transition metal ion binding	0	Informative	Direct
Molecular Function (MF)	copper ion binding	0	Highly Informative	Direct
Molecular Function (MF)	glycosaminoglycan binding	0	Highly Informative	Direct
Molecular Function (MF)	sulfur compound binding	0	Highly Informative	Direct
Cellular Component (CC)	intracellular non-membrane-bounded organelle	0.000137	Least Informative	Direct
Cellular Component (CC)	protein complex	0.0001834	Least Informative	Direct
Cellular Component (CC)	intracellular organelle part	0.02285	Least Informative	Inherited
Cellular Component (CC)	intracellular membrane-bounded organelle	0.6045	Least Informative	Inherited
Cellular Component (CC)	extracellular region	0	Moderately Informative	Direct
Cellular Component (CC)	nuclear part	5.515e-06	Moderately Informative	Direct
Cellular Component (CC)	intracellular organelle lumen	2.342e-06	Moderately Informative	Direct
Cellular Component (CC)	extracellular space	0	Informative	Direct
Cellular Component (CC)	extracellular matrix	0	Informative	Direct
Cellular Component (CC)	proteinaceous extracellular matrix	6.137e-10	Highly Informative	Direct
Cellular Component (CC)	extracellular matrix part	0	Highly Informative	Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Acting on ester bonds	0	Least Informative	Direct
Enzyme Commission (EC)	Endoribonucleases producing other than 5'-phosphom	0	Highly Informative	Direct

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Hydrolases	0	Least Informative	Direct
Enzyme Commission (EC)	Endoribonucleases producing other than 5'-phosphomonoesters	0	Highly Informative	Direct

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)

	DB term	FDR (all)	SDDB level	Annotation (direct or inherited)
Drugbank ATC_code (DB)	digestives, incl. enzymes	0	Moderately Informative	Direct
Drugbank ATC_code (DB)	citric acid	0	Informative	Direct

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)

	KW term	FDR (all)	SDKW level	Annotation (direct or inherited)
Biological process	Differentiation	0	Moderately Informative	Direct
Biological process	Angiogenesis	0	Informative	Direct
Biological process	Stress response	2.877e-11	Informative	Direct
Cellular component	Secreted	0	Moderately Informative	Direct
Cellular component	Lysosome	0	Informative	Direct
Cellular component	Extracellular matrix	5.111e-05	Informative	Direct
Cellular component	Basement membrane	0	Highly Informative	Direct
Coding sequence diversity	Polymorphism	0.0007858	Moderately Informative	Direct
Domain	Signal	0	Least Informative	Direct
Post-translational modification	Hydrolase	0	Least Informative	Direct
Post-translational modification	Nuclease	0	Moderately Informative	Direct
Post-translational modification	Developmental protein	1.472e-12	Moderately Informative	Direct
Post-translational modification	Endonuclease	0	Informative	Direct
Post-translational modification	Glycoprotein	0	Least Informative	Direct
Post-translational modification	Disulfide bond	0	Least Informative	Direct
Post-translational modification	Pyrrolidone carboxylic acid	0	Informative	Direct
Post-translational modification	Nitration	0	Highly Informative	Direct

Document: KW annotation of SCOP domains

InterPro annotation

Cross references IPR001427 SSF54076 Protein matches

Abstract Pancreatic ribonucleases (RNAse) are pyrimidine-specific endonucleases found in high quantity in the pancreas of certain mammals and of some reptiles [ PubMed 3940901]. Specifically, the enzymes are involved in endonucleolytic cleavage of 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates. Ribonuclease can unwind the DNA helix by complexing with single-stranded DNA; the complex arises by an extended multi-site cation-anion interaction between lysine and arginine residues of the enzyme and phosphate groups of the nucleotides. Other proteins belonging to the pancreatic RNAse family include: bovine seminal vesicle and brain ribonucleases; kidney non-secretory ribonucleases [ PubMed 2734298]; liver-type ribonucleases [ PubMed 2611266]; angiogenin, which induces vascularisation of normal and malignant tissues; eosinophil cationic protein [ PubMed 2473157], a cytotoxin and helminthotoxin with ribonuclease activity; and frog liver ribonuclease and frog sialic acid-binding lectin. The sequence of pancreatic RNases contains four conserved disulphide bonds and three amino acid residues involved in the catalytic activity.

InterPro database

PDBeMotif information about ligands, sequence and structure motifs

Cross references

PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.

Alignments of sequences to 16 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.

Browse and view proteins in genomes which have different domain combinations including a RNase A-like domain.

Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.

Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 16 hidden Markov models representing the RNase A-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.

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RNase A-like superfamily