Information on EC 3.1.13.5 - ribonuclease D

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY hide
3.1.13.5
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RECOMMENDED NAME
GeneOntology No.
ribonuclease D
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
exonucleolytic cleavage that removes extra residues from the 3'-terminus of tRNA to produce 5'-mononucleotides
show the reaction diagram
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
tRNA processing
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CAS REGISTRY NUMBER
COMMENTARY hide
9073-62-5
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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UniProt
Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
structurally altered tRNA
5'-mononucleotide + ?
show the reaction diagram
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exonuclease activity. RNase D can recognize structurally altered tRNA molecules. The enzyme acts poorly on intact tRNA and is inactive with the synthetic polyribonucleotides, poly(A), poly(U), or double-stranded poly(A)*poly(U). The enzyme acts on diesterase-treated tRNA, but relatively poorly on intact tRNA. RNase D does not attack ribosomal RNA
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-
?
tRNA containing extra residues at the 3'-terminus
5'-mononucleotide + tRNA
show the reaction diagram
tRNA-C-C-A-Cn + H2O
tRNA-C-C-A-Cn-1 + cytosine
show the reaction diagram
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-
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?
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
tRNA containing extra residues at the 3'-terminus
5'-mononucleotide + tRNA
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
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enzyme requires a divalent cation for activity. This requirement can be satisfied by Mg2+, Mn2+ or Co2+
K+
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stimulates
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5,5'-dithiobis(2-nitrobenzoic acid)
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the enzyme is relatively insensitive to sulfhydryl reagents
EDTA
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inhibition can be reversed by Mg2+
HgCl2
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the enzyme is relatively insensitive to sulfhydryl reagents, increased inhibition after addition of dithiothreitol
Na+
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slight
NEM
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the enzyme is relatively insensitive to sulfhydryl reagents
p-hydroxymercuribenzoate
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the enzyme is relatively insensitive to sulfhydryl reagents
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NH4+
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stimulates
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 9
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with diesterase-treated tRNA as substrate
9.1 - 9.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8 - 10.3
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pH 8.0: about 50% of maximal activity, pH 10.3: about 70% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.2
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electrofocusing, pH-range 2-11
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40000
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gel filtration
60000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
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1 * 40000, SDS-PAGE
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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the enzyme is devoid of nucleic acid
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
1.6 A resolution crystal structure. Hanging-drop technique was used for subsequent crystal optimizations. Each drop contains equal volumes of protein and reservoir solution. RNase D protein crystallizes in the presence of 2.02.5 M ammonium sulfate and various buffer conditions. The crystals used here are grown with a reservoir containing 2.22.3 sulfate and 0.1 M HEPES (pH 7.0). Crystals of RNase D usually appeared overnight under these conditions. Crystals grow to full size in 27 days, with a maximum size of over 1 mm in each dimension. Zn2+ -containing crystals are grown with 1 mM ZnSO4 included in the reservoir prior to drop setup. Mercury(II) derivatives are prepared by soaking RNase D crystals (without Zn2+) overnight in the mother liquor containing 5 mM HgSO4
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
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3-4 min, 50% loss of the activity against phosphodiesterase-treated tRNA
additional information
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the enzyme is sensitive to inactivation by elevated temperatures but can be protected by a variety of RNAs
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, 6 months, enzyme retains 90% of its activity
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant GST- and His-tagged TbRND from Escherichia coli by sequential affinity chromatography on glutathione and nickel affinity resins
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ORF Tb09.211.3670, DNA and amino acid sequence determination and analysis, generation of pRND-MHT for tetracycline-regulated expression of TbRND with a C-terminal myc-His6-TAP tag in Trypanosoma brucei, expression of N-terminally GST- and His-tagged TbRND in Escherichia coli
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
the expression of mitochondrial exoribonuclease TbRND is highly up-regulated in the insect proliferative stage of the parasite
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Show AA Sequence (3145 entries)
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