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Information on EC 3.6.4.13 - RNA helicase and Organism(s) Saccharomyces cerevisiae and UniProt Accession P06634
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3.6.4.13 RNA helicaseIUBMB 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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Word Map
- 3.6.4.13
-
single-stranded
- strand
- viruses
- duplex
- fork
-
retinoic
- nucleic
- chromatin
-
acid-inducible
- mda5
- dsrnas
- ssdna
-
rna-binding
-
stall
-
werner
-
nonstructural
-
bloom
- polyproteins
-
dna-dependent
- primase
-
exonuclease
- replisome
-
spliceosome
-
hexameric
-
minichromosome
-
differentiation-associated
- dengue
-
g-quadruplexes
- eif4g
-
single-molecule
-
unwound
-
replicase
-
restart
-
ifn-stimulated
-
nonsense-mediated
- rpa
- rad51
-
holliday
-
polyi:c
- flavivirus
- tfiih
- exoribonuclease
-
ifn-beta
-
d-loops
- pigmentosum
-
cap-dependent
- xeroderma
-
positive-stranded
- pre-rrnas
-
overhang
- pharmacology
- medicine
- drug development
The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
Synonyms
helicase, rig-i, rna helicase, eif4a, ddx3x, dead-box rna helicase, ns3 helicase, dead-box helicase, ddx21, rna helicase a, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
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)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
dATP + H2O
dADP + phosphate
ATP and dATP are the preferred nucleotide substrates. In the presence of ATP or dATP Mtr4p unwinds the duplex region of a partial duplex RNA substrate in the 3' to 5' direction. Mtr4p displays a marked preference for binding to poly(A) RNA relative to an oligoribonucleotide of the same length and a random sequence
-
-
?
ATP + H2O
ADP + phosphate
the DEAD-box protein DED1 has the ability to balance RNA unwinding with a profound strand annealing activity in a highly dynamic fashion
-
-
?
ATP + H2O
ADP + phosphate
promotes RNA unwinding. The enzyme also catalyzes strand annealing. The balance between unwinding and annealing activities of DED1 depends on the RNA substrate. ADP also modulates the balance between RNA unwinding and strand annealing
-
-
?
ATP + H2O
ADP + phosphate
the Q motif regulates ATP binding and hydrolysis, the affinity of the protein for RNA substrates and the helicase activity. At least three different protein conformations that are associated with free, ADP-bound and ATP-bound forms of the protein
-
-
?
ATP + H2O
ADP + phosphate
Mtr4p can unwind duplex RNA in the presence of ATP and a single-stranded RNA tail in the 3' to 5' direction
-
-
?
ATP + H2O
ADP + phosphate
ATP and dATP are the preferred nucleotide substrates. In the presence of ATP or dATP Mtr4p unwinds the duplex region of a partial duplex RNA substrate in the 3' to 5' direction. Mtr4p displays a marked preference for binding to poly(A) RNA relative to an oligoribonucleotide of the same length and a random sequence
-
-
?
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
-
-
?
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
-
-
?
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
-
-
?
additional information
?
-
Brr2 participates in a transient opening of the catalytic core between the 2 steps of splicing, which is characterized by the intermittent disruption of U6-5SS and U2-U6 interactions
-
-
-
additional information
?
-
-
Brr2 participates in a transient opening of the catalytic core between the 2 steps of splicing, which is characterized by the intermittent disruption of U6-5SS and U2-U6 interactions
-
-
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + H2O
ADP + phosphate
the DEAD-box protein DED1 has the ability to balance RNA unwinding with a profound strand annealing activity in a highly dynamic fashion
-
-
?
ATP + H2O
ADP + phosphate
Mtr4p can unwind duplex RNA in the presence of ATP and a single-stranded RNA tail in the 3' to 5' direction
-
-
?
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
-
-
?
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
-
-
?
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
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
a 20-bp duplex RNA is ineffective in stimulating the (d)ATPase activity of Mtr4p
-
additional information
-
a 20-bp duplex RNA is ineffective in stimulating the (d)ATPase activity of Mtr4p
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
C-terminal mutants of DED1 are defective in downregulating transxadlation following TORC1 inhibition using rapamycin. EIF4G1 normally dissociates from translation complexes and is degraded, and this process is attenuated in mutant cells. The repressive function of overexpressed Ded1 is partially dependent on the Ded1 C-terminal domain, which is a predicted low-complexity sequence that lies outside of the core helicase domains. Deletion of this domain (amino acids 536-604) substantially rescues growth inhibition on overexpression. Deletion of the Ded1 C-terminus confers resistance against small molecule growth inhibitor rapamycin, a specific inhibitor of TORC1
metabolism
Ded1 activity plays an important role in promoting translation repression and adaptation to stress conditions. Ded1 activity is essential for translaxadtion initiation, but above a certain threshold Ded1 becomes inhibitory toward translation
physiological function
Ded1 is a DEAD-box RNA helicase with essential roles in translation initiation. It binds to the eukaryotic initiation factor 4F (eIF4F) complex and promotes 48S preinitiation complex assembly and start-site scanning of 5' untranslated regions of mRNAs. Role of the enzyme in the translational response during target of rapamycin (TOR)C1 inhibition and function of Ded1 as a translation repressor, overview. Both the rapamycin resistance and impaired survivability following nutrient starvation suggest an important role for the Ded1 C-terminus in the cellular changes that occur during long-term nutrient stress and inhibition of TORC1. Ded1 enzymatic activity and interaction with eIF4G1 are required, while homooligomerization may be dispensable, mapping of the functional requirements for Ded1 in the translaxadtional response. Ded1 stalls translation and specifically removes eIF4G1 from translation preinitiation complexes, thus removing eIF4G1 from the translating mRNA pool and leading to the codegradation of both proteins. The enzyme's role is conserved and may be implicated in pathologies such as oncogenesis
evolution
metabolism
the enzyme is involved in the pre-mRNA splicing cycle by the spliceosome, reaction steps in processing, detailed overview. The most dramatic rearrangements occur during spliceosome activation, where the Prp28 helicase aids in the displacement of U1 snRNA from the 5SS,8,23,24 followed by Brr2 unwinding the U4 and U6 snRNAs and leading to displacement of U4 snRNA and U4/U6-bound proteins. Brr2 requires tight regulation
physiological function
additional information
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. 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, detailed overview
evolution
SF2 helicases can be grouped into 5 families, 3 of which are represented among the spliceosomal remodeling enzymes: 3 DEAD box proteins (Prp5, Sup2/UAP56, Prp28) act during initial spliceosome assembly and activation, a single Ski2-like helicase (Brr2) is involved in spliceosome activation and 4 DEAH/RHA enzymes (Prp2, Prp16, Prp22, Prp43) are required during spliceosome activation, catalysis and disassembly
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
physiological function
functions and regulation of the Brr2 RNA helicase during splicing, structure-function analysis, overview. Brr2 is transported to the nucleus independent of other U5 snRNP components and its helicase activity may have to be shut off during this phase to avoid detrimental off-target effects. Once assembled in the nucleus, mature U5 snRNP joins the U4/U6 di-snRNP to form the U4/U6-U5 trisnRNP, in which Brr2 already encounters its U4/U6 di-snRNA substrate before incorporation into the spliceosome. Brr2 requires tight regulation. Isolated Brr2 is a comparatively weak helicase and its U4/U6 di-snRNA substrate is stabilized by extensive base pairing and bound proteins, suggesting that the helicase may also depend on specific activation to efficiently unwind the U4/U6 duplex at the right time. Implications for Brr2-dependent proofreading and regulation of alternative splicing, model for putative Brr2-mediated enhancement of splicing fidelity and regulation of alternative splicing. Brr2 may be more or less prone to disrupt the tri-snRNP in a non-productive fashion, thus differentially channeling the different substrates along the splicing or discard pathways. Similarly, depending on the level of Brr2 inhibition in competing alternative splicing scenarios, the helicase may elicit spliceosome activation slowly or quickly, kinetically controlling the levels of protein isoforms produced
additional information
the C-terminal domain of Ded1 (amino acids 536-604) is a low complexity sequence that is necessary for the interaction with eIF4G1 and for self-association and the formation of Ded1 oligomers
additional information
-
molecular mechanism of dsRNA unwinding by yeast Mss116p helicase, overview
additional information
molecular mechanism of dsRNA unwinding by yeast Mss116p helicase, overview
additional information
molecular mechanism of dsRNA unwinding by yeast Mss116p helicase, overview
additional information
the structure of Brr2 differs decisively from that of other spliceosomal helicases, enzyme structure analysis, detailed overview. Comparison of human and yeast enzymes, comparative modeling. Analysis of the mechanism of spliceosome activation using multi-wavelength single-molecule co-localization spectroscopy demonstrates that after tri-snRNP binding, the spliceosome can either proceed to activation or release U4 and U5 snRNAs. The ATP-dependent loss of U4 and U5 snRNAs is suggested to represent Prp28-mediated displacement of the tri-snRNP
additional information
-
the structure of Brr2 differs decisively from that of other spliceosomal helicases, enzyme structure analysis, detailed overview. Comparison of human and yeast enzymes, comparative modeling. Analysis of the mechanism of spliceosome activation using multi-wavelength single-molecule co-localization spectroscopy demonstrates that after tri-snRNP binding, the spliceosome can either proceed to activation or release U4 and U5 snRNAs. The ATP-dependent loss of U4 and U5 snRNAs is suggested to represent Prp28-mediated displacement of the tri-snRNP
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
Ded1 domain structure, the C-terminal domain lies outside of the helicase core domain. It contains TORC1-dependent phosphoserines, and two conserved tryptophans at the C-terminal tail
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E909K
site-directed mutagenesis, the temperature-sensitive mutant, encoded by the slt22-1 allele, is synthetically lethal with mutations in U2 or U6 snRNAs that affect the stability or conformation of U2/U6 helix II. The ATPase activity of this variant is no longer stimulated by a U2/ U6 duplex, it is proposed that Brr2 might proofread U2/U6 interactions. The E909K exchange in Brr2 blocks splicing in extracts at or before the first catalytic step and leads to the appearance of an off-pathway spliceosomal particle following B complex formation, which lacks U4 and U5 snRNAs
G858R
site-directed mutagenesis, the mutant shows differing cross-linking profiles compared to wild-type Brr2, the mutation is in the NC 5'HP/separator loop with U6 snRNA
K177A
mutant enzyme shows no stimulation of ATPase activity by single-stranded RNA
R681C
site-directed mutagenesis, a brr2 mutation linked to the RP33 form of autosomal dominant retinitis pigmentosa, it maps to the linker between the RecA domains of the NC, the mutation leads to altered Brr2 ATPase activity and aberrant partitioning of spliceosomes along activation and discard pathways
R681H
site-directed mutagenesis, a brr2 mutation linked to the RP33 form of autosomal dominant retinitis pigmentosa, it maps to the linker between the RecA domains of the NC, the mutation leads to altered Brr2 ATPase activity and aberrant partitioning of spliceosomes along activation and discard pathways
V683L
site-directed mutagenesis, a brr2 mutation linked to the RP33 form of autosomal dominant retinitis pigmentosa, it maps to the linker between the RecA domains of the NC, the mutation leads to altered Brr2 ATPase activity and aberrant partitioning of spliceosomes along activation and discard pathways
Y689C
site-directed mutagenesis, a brr2 mutation linked to the RP33 form of autosomal dominant retinitis pigmentosa, it maps to the beginning of the RecA2 domain
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Yang, Q.; Jankowsky, E.
ATP- and ADP-dependent modulation of RNA unwinding and strand annealing activities by the DEAD-box protein DED1
Biochemistry
44
13591-13601
2005
Saccharomyces cerevisiae (P06634), Saccharomyces cerevisiae
Cordin, O.; Tanner, N.K.; Doere, M.; Linder, P.; Banroques, J.
The newly discovered Q motif of DEAD-box RNA helicases regulates RNA-binding and helicase activity
EMBO J.
23
2478-2487
2004
Saccharomyces cerevisiae (P06634), Saccharomyces cerevisiae
Bernstein, J.; Patterson, D.N.; Wilson, G.M.; Toth, E.A.
Characterization of the essential activities of Saccharomyces cerevisiae Mtr4p, a 3'->5' helicase partner of the nuclear exosome
J. Biol. Chem.
283
4930-4942
2008
Saccharomyces cerevisiae (P47047), Saccharomyces cerevisiae
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)
Absmeier, E.; Santos, K.F.; Wahl, M.C.
Functions and regulation of the Brr2 RNA helicase during splicing
Cell Cycle
15
3362-3377
2016
Homo sapiens (O75643), Homo sapiens, Saccharomyces cerevisiae (P32639), Saccharomyces cerevisiae, Saccharomyces cerevisiae ATCC 204508 (P32639)
Aryanpur, P.P.; Renner, D.M.; Rodela, E.; Mittelmeier, T.M.; Byrd, A.; Bolger, T.A.
The DEAD-box RNA helicase Ded1 has a role in the translational response to TORC1 inhibition
Mol. Biol. Cell
30
2171-2184
2019
Saccharomyces cerevisiae (P06634), Saccharomyces cerevisiae ATCC 204508 (P06634)
EXTERNAL LINKS (specific for EC-Number 3.6.4.13)
Transporter Classification Database (TCDB): 1.I.1.1.3, 1.G.3.1.7, 3.A.18.1.1, 1.A.53.1.5, 1.A.85.1.6, 1.A.53.1.7, 1.G.3.1.2, 1.G.3.1.1, 3.A.22.1.1, 1.A.53.1.11, 1.A.53.1.6
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