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Information on EC 3.6.4.13 - RNA helicase and Organism(s) Japanese encephalitis virus and UniProt Accession P27395

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IUBMB Comments
RNA helicases utilize the energy from ATP hydrolysis to unwind RNA. Some of them unwind RNA with a 3' to 5' polarity , other show 5' to 3' polarity . Some helicases unwind DNA as well as RNA [7,8]. May be identical with EC 3.6.4.12 (DNA helicase).
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Japanese encephalitis virus
UNIPROT: P27395
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The taxonomic range for the selected organisms is: Japanese encephalitis virus
The enzyme appears in selected viruses and cellular organisms
Synonyms
helicase, rig-i, rna helicase, eif4a, ddx3x, dead-box rna helicase, ns3 helicase, dead-box helicase, ddx21, rna helicase a, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
nonstructural protein 3
ambiguous
SYSTEMATIC NAME
IUBMB Comments
ATP phosphohydrolase (RNA helix unwinding)
RNA helicases utilize the energy from ATP hydrolysis to unwind RNA. Some of them unwind RNA with a 3' to 5' polarity [3], other show 5' to 3' polarity [8]. Some helicases unwind DNA as well as RNA [7,8]. May be identical with EC 3.6.4.12 (DNA helicase).
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + H2O
ADP + phosphate
show the reaction diagram
additional information
?
-
RNA helicases are RNA-binding proteins able to resolve secondary and tertiary RNA structures in an active manner, in some cases coupling this enzymatic activity to the hydrolysis of ATP. Upon enzyme loading, the RNA helicase is able to locally open the RNA duplex facilitating the formation of a single-stranded structure. The proposed model for the catalytic activity of this group of RNA helicases suggests that the hydrolysis of ATP occurs before the strand separation. ATP hydrolysis is essential for the efficient release of the free enzyme from the RNA. The process is performed locally without any displacement of the enzyme along the RNA strands. Some proteins harboring helicase domains are able to recognize specific patterns in RNA molecules, bind to them and act as a skeleton to build ribonucleoprotein complexes without a specific catalytic activity over the RNA secondary structures
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + H2O
ADP + phosphate
show the reaction diagram
-
-
-
?
additional information
?
-
RNA helicases are RNA-binding proteins able to resolve secondary and tertiary RNA structures in an active manner, in some cases coupling this enzymatic activity to the hydrolysis of ATP. Upon enzyme loading, the RNA helicase is able to locally open the RNA duplex facilitating the formation of a single-stranded structure. The proposed model for the catalytic activity of this group of RNA helicases suggests that the hydrolysis of ATP occurs before the strand separation. ATP hydrolysis is essential for the efficient release of the free enzyme from the RNA. The process is performed locally without any displacement of the enzyme along the RNA strands. Some proteins harboring helicase domains are able to recognize specific patterns in RNA molecules, bind to them and act as a skeleton to build ribonucleoprotein complexes without a specific catalytic activity over the RNA secondary structures
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-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
the RNA helicase ubiquitous group of proteins is found in all the kingdoms of life, ranging from viruses to mammals, and it is closely related to DNA helicases. RNA helicases are included in five of the six nucleic acid helicase superfamilies. RNA helicases belonging to superfamilies SF3, SF4, and SF5 are oligomeric proteins (mostly hexamers), being typically encoded by genomes of viruses or bacteria. Superfamilies SF1 and SF2 of RNA helicases are non-oligomeric proteins, containing a conserved bi-lobular core composed by two RecA-like domains as a central structure. Several sub-families of RNA helicases are also defined on the basis of their sequence conservation and biological activity. Human RNA helicases are included in five different sub-families: Upf1-like, DEAD-box, DEAH-RHA, RIG-I like and Ski2-like proteins. The Upf1-like sub-family belongs to the SF1 superfamily, and includes a group of enzymes involved in RNA metabolism centered in processes like splicing or nonsense-mediated decay. The SF2 superfamily includes five different sub-families of RNA helicases: DEAD-box helicases, DEAH-RHA helicases, RIG-I like proteins, Ski2-like proteins and the NS3/NPH-II subfamily. SF1 and SF2 RNA helicases have other variable accessory domains located around their structural cores which frequently contain specific additional functionalities such as DNA-binding, protein-binding or oligomerization. Structure-function relationships of the most widely-studied families of RNA helicases: the DEAD-box, RIG-I-like and viral NS3 classes, overview. Enzyme NS3 falls within NS3/NPH-II subfamily of SF2 helicase superfamily
physiological function
RNA helicases are involved in many biologically relevant processes, not only as RNA chaperones, but also as signal transducers, scaffolds of molecular complexes, and regulatory elements. Cells require either the presence of controlled chemical environments or the assistance of specialized proteins to ensure the stabilization and proper RNA folding. RNA chaperones or RNA helicases help RNA to reach and maintain its functional conformational state. Some of these RNA helicases are chaperone-like proteins that prevent RNA to reach energy minima characterized by an incorrect conformational state during folding. Others are correctors of misfolded RNAs, able to resolve incorrect structural elements and to produce single stranded RNA
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
54000
molecular mass of the helicase/NTPase domain, SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure analysis of helicase core, PDB ID 2Z83
enzymatically active fragment of the JEV NTPase/helicase catalytic domain, recombinant protein, crystal structure determined at 1.8 A resolution, data collection and refinement statistics
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
G199A
mutation in WALKER A motif, PCR-based mutagenesis, ATPase and RNA helicase activity lost
G460A
mutation of residues of the arginine finger within the active sites of ATP hydrolysis, no effect on either ATPase or RNA-unwinding activities
G463A
mutation of residues of the arginine finger within the active sites of ATP hydrolysis, no effect on either ATPase or RNA-unwinding activities
K200A
mutation in WALKER A motif, PCR-based mutagenesis, ATPase and RNA helicase activity lost
K200D
PCR-based mutagenesis, ATPase and RNA helicase activity lost
K200E
PCR-based mutagenesis, ATPase and RNA helicase activity lost
K200H
PCR-based mutagenesis, ATPase and RNA helicase activity lost
K200N
PCR-based mutagenesis, ATPase and RNA helicase activity lost
K200Q
PCR-based mutagenesis, ATPase and RNA helicase activity lost
K200R
PCR-based mutagenesis, ATPase and RNA helicase activity lost
Q457A
mutation of residues of the arginine finger within the active sites of ATP hydrolysis, 80% reduction of ATPase activity, no RNA helicase activity
R458A
mutation of residues of the arginine finger within the active sites of ATP hydrolysis, 90% reduction of ATPase activity, no RNA helicase activity
R459A
mutation of residues of the arginine finger within the active sites of ATP hydrolysis, no effect on either ATPase or RNA-unwinding activities
R461A
mutation of residues of the arginine finger within the active sites of ATP hydrolysis, no ATPase activity, no RNA helicase activity
R464A
mutation of residues of the arginine finger within the active sites of ATP hydrolysis, no ATPase activity, no RNA helicase activity
T201A
mutation in WALKER A motif, PCR-based mutagenesis, ATPase and RNA helicase activity lost
V462A
mutation of residues of the arginine finger within the active sites of ATP hydrolysis, no effect on either ATPase or RNA-unwinding activities
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
gel filtration, recombinant protein
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21 (DE3), recombinant protein, pET21b vector
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pharmacology
conservation of the NTP-binding pocket among viruses of the family Flaviviridae as potential for development of therapeutics
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Yamashita, T.; Unno, H.; Mori, Y.; Tani, H.; Moriishi, K.; Takamizawa, A.; Agoh, M.; Tsukihara, T.; Matsuura, Y.
Crystal structure of the catalytic domain of Japanese encephalitis virus NS3 helicase/nucleoside triphosphatase at a resolution of 1.8 A
Virology
373
426-436
2008
Japanese encephalitis virus (P27395), Japanese encephalitis virus
Manually annotated by BRENDA team
Leitao, A.L.; Costa, M.C.; Enguita, F.J.
Unzippers, resolvers and sensors: a structural and functional biochemistry tale of RNA helicases
Int. J. Mol. Sci.
16
2269-2293
2015
Saccharomyces cerevisiae, Saccharomyces cerevisiae (P21372), Saccharomyces cerevisiae (P47047), Dengue virus, Hepacivirus C, Neurospora crassa, Yellow fever virus, Homo sapiens (O95786), Homo sapiens (Q9UMR2), Murray Valley encephalitis virus (P05769), Kunjin virus (P14335), Japanese encephalitis virus (P27395)
Manually annotated by BRENDA team