Literature summary for 4.6.1.18 extracted from

Gagne, D.; Doucet, N.
Structural and functional importance of local and global conformational fluctuations in the RNase A superfamily (2013), FEBS J., 280, 5596-5607.

Crystallization (Commentary)

Crystallization (Comment)	Organism
crystal structure analysis, PDB ID 1RRA	Rattus norvegicus
crystal structure analysis, PDB ID 2VQ9	Danio rerio
crystal structure analysis, PDB ID 3DJX	Bos taurus
crystal structure analysis, PDB ID 3PHN	Lithobates pipiens
crystal structure analysis, PDB IDs 1GQV, 1QMT, 1RNF, and 1ANG	Homo sapiens

Protein Variants

Protein Variants	Comment	Organism
additional information	construction of a chimeric hybrid RNase AECP variant, in which the short and rigid six-residue loop 1 from human isozyme RNase 3 replaces the 12-residue flexible loop 1 in RNase A, the mutation perturbs the flexibility of the hinge/loop 1 environment and causes a 10fold decrease in the product release rate constant koff and a 4fold decrease in ligand affinity relative to the parent enzyme	Homo sapiens

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
additional information	Gallus gallus	the enzyme degrades single-stranded and/or double-stranded RNA	?	-	?
additional information	Homo sapiens	the enzyme degrades single-stranded and/or double-stranded RNA	?	-	?
additional information	Danio rerio	the enzyme degrades single-stranded and/or double-stranded RNA	?	-	?
additional information	Bos taurus	the enzyme degrades single-stranded and/or double-stranded RNA	?	-	?
additional information	Lithobates pipiens	the enzyme degrades single-stranded and/or double-stranded RNA	?	-	?
additional information	Rattus norvegicus	the enzyme degrades single-stranded and/or double-stranded RNA	?	-	?

Organism

Organism	UniProt	Comment	Textmining
Bos taurus	P00669	isozymes RNase A and BS-RNase	-
Danio rerio	A5HAK0	-	-
Gallus gallus	-	-	-
Homo sapiens	-	-	-
Homo sapiens	-	isozymes RNases 1, 2, 3, 4, and 5	-
Lithobates pipiens	P22069	i.e. Pantherana pipiens	-
Rattus norvegicus	P00684	-	-

Reaction

Reaction	Comment	Organism	Reaction ID
an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]	RNase A catalyzes a well-characterized acid-base mechanism involving two histidines (His12 and His119) and a transition state stabilizing positive charge (Lys41). The transphosphorylation of a single-stranded RNA molecule by the enzyme yields a 2',3'-cyclic phosphomonoester intermediate, which can be expelled from the active site or hydrolyzed in a microscopic reverse reaction involving the same two histidines	Gallus gallus	a
an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]	RNase A catalyzes a well-characterized acid-base mechanism involving two histidines (His12 and His119) and a transition state stabilizing positive charge (Lys41). The transphosphorylation of a single-stranded RNA molecule by the enzyme yields a 2',3'-cyclic phosphomonoester intermediate, which can be expelled from the active site or hydrolyzed in a microscopic reverse reaction involving the same two histidines	Homo sapiens	a
an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]	RNase A catalyzes a well-characterized acid-base mechanism involving two histidines (His12 and His119) and a transition state stabilizing positive charge (Lys41). The transphosphorylation of a single-stranded RNA molecule by the enzyme yields a 2',3'-cyclic phosphomonoester intermediate, which can be expelled from the active site or hydrolyzed in a microscopic reverse reaction involving the same two histidines	Danio rerio	a
an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]	RNase A catalyzes a well-characterized acid-base mechanism involving two histidines (His12 and His119) and a transition state stabilizing positive charge (Lys41). The transphosphorylation of a single-stranded RNA molecule by the enzyme yields a 2',3'-cyclic phosphomonoester intermediate, which can be expelled from the active site or hydrolyzed in a microscopic reverse reaction involving the same two histidines	Bos taurus	a
an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]	RNase A catalyzes a well-characterized acid-base mechanism involving two histidines (His12 and His119) and a transition state stabilizing positive charge (Lys41). The transphosphorylation of a single-stranded RNA molecule by the enzyme yields a 2',3'-cyclic phosphomonoester intermediate, which can be expelled from the active site or hydrolyzed in a microscopic reverse reaction involving the same two histidines	Lithobates pipiens	a
an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]	RNase A catalyzes a well-characterized acid-base mechanism involving two histidines (His12 and His119) and a transition state stabilizing positive charge (Lys41). The transphosphorylation of a single-stranded RNA molecule by the enzyme yields a 2',3'-cyclic phosphomonoester intermediate, which can be expelled from the active site or hydrolyzed in a microscopic reverse reaction involving the same two histidines	Rattus norvegicus	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
additional information	the enzyme degrades single-stranded and/or double-stranded RNA	Gallus gallus	?	-	?
additional information	the enzyme degrades single-stranded and/or double-stranded RNA	Homo sapiens	?	-	?
additional information	the enzyme degrades single-stranded and/or double-stranded RNA	Danio rerio	?	-	?
additional information	the enzyme degrades single-stranded and/or double-stranded RNA	Bos taurus	?	-	?
additional information	the enzyme degrades single-stranded and/or double-stranded RNA	Lithobates pipiens	?	-	?
additional information	the enzyme degrades single-stranded and/or double-stranded RNA	Rattus norvegicus	?	-	?

Synonyms

Synonyms	Comment	Organism
BS-RNase	-	Bos taurus
Ecp	-	Homo sapiens
eosinophil cationic protein	-	Homo sapiens
onconase	-	Lithobates pipiens
ranpirnase	-	Lithobates pipiens
RNase 1	-	Homo sapiens
RNase 1	-	Rattus norvegicus
RNase 2	-	Homo sapiens
RNase 3	-	Homo sapiens
RNase 3	-	Danio rerio
RNase 4	-	Homo sapiens
RNase 5	-	Homo sapiens
RNase A	-	Gallus gallus
RNase A	-	Homo sapiens
RNase A	-	Danio rerio
RNase A	-	Bos taurus
RNase A	-	Lithobates pipiens
RNase A	-	Rattus norvegicus
RNase A2	-	Gallus gallus
RNase ZF-3e	-	Danio rerio

General Information

General Information	Comment	Organism
evolution	the enzyme belongs to the vertebrate pancreatic-like RNase A superfamily, sequence comparisons and phylogenetic analysis, overview	Gallus gallus
evolution	the enzyme belongs to the vertebrate pancreatic-like RNase A superfamily, sequence comparisons and phylogenetic analysis, overview	Homo sapiens
evolution	the enzyme belongs to the vertebrate pancreatic-like RNase A superfamily, sequence comparisons and phylogenetic analysis, overview	Danio rerio
evolution	the enzyme belongs to the vertebrate pancreatic-like RNase A superfamily, sequence comparisons and phylogenetic analysis, overview	Bos taurus
evolution	the enzyme belongs to the vertebrate pancreatic-like RNase A superfamily, sequence comparisons and phylogenetic analysis, overview	Lithobates pipiens
evolution	the enzyme belongs to the vertebrate pancreatic-like RNase A superfamily, sequence comparisons and phylogenetic analysis, overview	Rattus norvegicus
additional information	RNA subsites and reaction mechanism catalyzed by RNase A, molecular interactions between the RNA substrate and residues of the catalytic groove. The following residues are known to interact with each subsite: Lys66 (P0), Thr45 and Asp83 (B1), Gln11, His12, Lys41, His119, and Asp121 (P1), Asn71 and Glu111 (B2), and Lys7 and Arg10 (P2). Structure-function relationship, overview	Homo sapiens
additional information	RNA subsites and reaction mechanism catalyzed by RNase A, molecular interactions between the RNA substrate and residues of the catalytic groove. The following residues are known to interact with each subsite: Lys66 (P0), Thr45 and Asp83 (B1), Gln11, His12, Lys41, His119, and Asp121 (P1), Asn71 and Glu111 (B2), and Lys7 and Arg10 (P2). Structure-function relationship, overview. Potential role for catalytic base His119 in ligand discrimination and/or stabilization in addition to its critical role in catalysis, molecular dynamic simulations show that His119 adopts both rotameric positions in solution, most likely experiencing conformational exchange over the course of a catalytic reaction. Functional importance of long-range conformational rearrangements in RNase A	Gallus gallus
additional information	RNA subsites and reaction mechanism catalyzed by RNase A, molecular interactions between the RNA substrate and residues of the catalytic groove. The following residues are known to interact with each subsite: Lys66 (P0), Thr45 and Asp83 (B1), Gln11, His12, Lys41, His119, and Asp121 (P1), Asn71 and Glu111 (B2), and Lys7 and Arg10 (P2). Structure-function relationship, overview. Potential role for catalytic base His119 in ligand discrimination and/or stabilization in addition to its critical role in catalysis, molecular dynamic simulations show that His119 adopts both rotameric positions in solution, most likely experiencing conformational exchange over the course of a catalytic reaction. Functional importance of long-range conformational rearrangements in RNase A	Homo sapiens
additional information	RNA subsites and reaction mechanism catalyzed by RNase A, molecular interactions between the RNA substrate and residues of the catalytic groove. The following residues are known to interact with each subsite: Lys66 (P0), Thr45 and Asp83 (B1), Gln11, His12, Lys41, His119, and Asp121 (P1), Asn71 and Glu111 (B2), and Lys7 and Arg10 (P2). Structure-function relationship, overview. Potential role for catalytic base His119 in ligand discrimination and/or stabilization in addition to its critical role in catalysis, molecular dynamic simulations show that His119 adopts both rotameric positions in solution, most likely experiencing conformational exchange over the course of a catalytic reaction. Functional importance of long-range conformational rearrangements in RNase A	Danio rerio
additional information	RNA subsites and reaction mechanism catalyzed by RNase A, molecular interactions between the RNA substrate and residues of the catalytic groove. The following residues are known to interact with each subsite: Lys66 (P0), Thr45 and Asp83 (B1), Gln11, His12, Lys41, His119, and Asp121 (P1), Asn71 and Glu111 (B2), and Lys7 and Arg10 (P2). Structure-function relationship, overview. Potential role for catalytic base His119 in ligand discrimination and/or stabilization in addition to its critical role in catalysis, molecular dynamic simulations show that His119 adopts both rotameric positions in solution, most likely experiencing conformational exchange over the course of a catalytic reaction. Functional importance of long-range conformational rearrangements in RNase A	Bos taurus
additional information	RNA subsites and reaction mechanism catalyzed by RNase A, molecular interactions between the RNA substrate and residues of the catalytic groove. The following residues are known to interact with each subsite: Lys66 (P0), Thr45 and Asp83 (B1), Gln11, His12, Lys41, His119, and Asp121 (P1), Asn71 and Glu111 (B2), and Lys7 and Arg10 (P2). Structure-function relationship, overview. Potential role for catalytic base His119 in ligand discrimination and/or stabilization in addition to its critical role in catalysis, molecular dynamic simulations show that His119 adopts both rotameric positions in solution, most likely experiencing conformational exchange over the course of a catalytic reaction. Functional importance of long-range conformational rearrangements in RNase A	Lithobates pipiens
additional information	RNA subsites and reaction mechanism catalyzed by RNase A, molecular interactions between the RNA substrate and residues of the catalytic groove. The following residues are known to interact with each subsite: Lys66 (P0), Thr45 and Asp83 (B1), Gln11, His12, Lys41, His119, and Asp121 (P1), Asn71 and Glu111 (B2), and Lys7 and Arg10 (P2). Structure-function relationship, overview. Potential role for catalytic base His119 in ligand discrimination and/or stabilization in addition to its critical role in catalysis, molecular dynamic simulations show that His119 adopts both rotameric positions in solution, most likely experiencing conformational exchange over the course of a catalytic reaction. Functional importance of long-range conformational rearrangements in RNase A	Rattus norvegicus
physiological function	the human isozymes have evolved additional biological activities, often linked to innate host defense, neurotoxicity, angiogenesis, and immunosuppressive and/or antibacterial/antiviral activities	Homo sapiens