The Newly Identified Q Motif of DEAD Box Heicases IS Involved in Adenine Recognition

Tanner, N. Kyle

doi:10.4161/cc.2.1.296

Cited by 60 publications

(60 citation statements)

References 20 publications

(22 reference statements)

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“…Other nucleotides might compete for the binding site but are not efficiently hydrolyzed and do not stimulate RNA unwinding by DEAD box proteins (Du et al, 2002;Franca et al, 2007;Garcia and Uhlenbeck, 2008). It has therefore been suggested that the Q-motif also contributes to positioning of the nucleotide for hydrolysis (Tanner, 2003;Tanner et al, 2003). The phenylalanine of the Q-motif stacks with the adenine base that is also contacted by an aromatic or hydrophobic side chain from motif VI (Bono et al, 2006).…”

Section: Nucleotide Bindingmentioning

confidence: 99%

“…Residues from motifs I and II contact the triphosphate part of the nucleotide directly and through water and Mg 2q (Andersen et al, 2006;Bono et al, 2006;Sengoku et al, 2006;von Moeller et al, 2009). In addition, motif VI from the C-terminal RecA-like domain interacts with the triphosphate in the closed conformation (Bono et al, 2006;Sengoku et al, 2006;von Moeller et al, 2009 , 1982), the Q-motif upstream of motif I is unique to DEAD box proteins (Tanner, 2003;Tanner et al, 2003). Its highly conserved glutamine interacts with the adenine base and provides specificity for adenine nucleotides.…”

Section: Nucleotide Bindingmentioning

confidence: 99%

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The mechanism of ATP-dependent RNA unwinding by DEAD box proteins

Hilbert

Karow²,

Klostermeier³

2009

BCHM

143

171

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DEAD box proteins catalyze the ATP-dependent unwinding of double-stranded RNA (dsRNA). In addition, they facilitate protein displacement and remodeling of RNA or RNA/protein complexes. Their hallmark feature is local destabilization of RNA duplexes. Here, we summarize current data on the DEAD box protein mechanism and present a model for RNA unwinding that integrates recent data on the effect of ATP analogs and mutations on DEAD box protein activity. DEAD box proteins share a conserved helicase core with two flexibly linked RecAlike domains that contain all helicase signature motifs. Variable flanking regions contribute to substrate binding and modulate activity. In the presence of ATP and RNA, the helicase core adopts a compact, closed conformation with extensive interdomain contacts and high affinity for RNA. In the closed conformation, the RecA-like domains form a catalytic site for ATP hydrolysis and a continuous RNA binding site. A kink in the backbone of the bound RNA locally destabilizes the duplex. Rearrangement of this initial complex generates a hydrolysisand unwinding-competent state. From this complex, the first RNA strand can dissociate. After ATP hydrolysis and phosphate release, the DEAD box protein returns to a low-affinity state for RNA. Dissociation of the second RNA strand and reopening of the cleft in the helicase core allow for further catalytic cycles.

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Section: Nucleotide Bindingmentioning

confidence: 99%

Section: Nucleotide Bindingmentioning

confidence: 99%

The mechanism of ATP-dependent RNA unwinding by DEAD box proteins

Hilbert

Karow²,

Klostermeier³

2009

BCHM

143

171

View full text Add to dashboard Cite

show abstract

“…Helicase motifs involved in ATP binding are located at the interface between two RecA-like domains [43,46,47,95,96,101] in the structures of SF1 and SF2 helicases [48, [102][103][104]. Figure 2.2 shows the conserved sequence of the motifs (Q, I, Ia, II, III, IV, V, and VI) of the SF1 helicase family and their location in PcrA.…”

Section: Helicase Motifsmentioning

confidence: 99%

Erratum to: Structure and Mechanisms of SF1 DNA Helicases

Raney

Byrd

Aarattuthodiyil

2012

Advances in Experimental Medicine and Biology

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Superfamily I is a large and diverse group of monomeric and dimeric helicases defined by a set of conserved sequence motifs. Members of this class are involved in essential processes in both DNA and RNA metabolism in all organisms. In addition to conserved amino acid sequences, they also share a common structure containing two RecA-like motifs involved in ATP binding and hydrolysis and nucleic acid binding and unwinding. Unwinding is facilitated by a "pin" structure which serves to split the incoming duplex. This activity has been measured using both ensemble and single-molecule conditions. SF1 helicase activity is modulated through interactions with other proteins.

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“…Based on mutational analyses and sequence comparisons, the Q-motif has been defined as a stretch of nine amino acids with an almost invariant (99%) glutamine (Benz et al, 1999;Tanner, 2003;Tanner et al, 2003). Crystal structures of helicase/nucleotide complexes showed that the glutamine side chain directly binds to the adenine base of the nucleotide via a double hydrogen bond ( Figure 1B).…”

Section: Introductionmentioning

confidence: 99%

Changing nucleotide specificity of the DEAD-box helicase Hera abrogates communication between the Q-motif and the P-loop

Strohmeier¹,

Hertel²,

Diederichsen³

et al. 2011

Biological Chemistry

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DEAD-box proteins disrupt or remodel RNA and protein/ RNA complexes at the expense of ATP. The catalytic core is composed of two flexibly connected RecA-like domains. The N-terminal domain contains most of the motifs involved in nucleotide binding and serves as a minimalistic model for helicase/nucleotide interactions. A single conserved glutamine in the so-called Q-motif has been suggested as a conformational sensor for the nucleotide state. To reprogram the Thermus thermophilus RNA helicase Hera for use of oxo-ATP instead of ATP and to investigate the sensor function of the Q-motif, we analyzed helicase activity of Hera Q28E. Crystal structures of the Hera N-terminal domain Q28E mutant (TthDEAD_Q28E) in apo-and ligand-bound forms show that Q28E does change specificity from adenine to 8-oxoadenine. However, significant structural changes accompany the Q28E mutation, which prevent the P-loop from adopting its catalytically active conformation and explain the lack of helicase activity of Hera_Q28E with either ATP or 8-oxo-ATP as energy sources. 8-Oxo-adenosine, 8-oxo-AMP, and 8-oxo-ADP weakly bind to TthDEAD_Q28E but in noncanonical modes. These results indicate that the Q-motif not only senses the nucleotide state of the helicase but could also stabilize a catalytically competent conformation of the Ploop and other helicase signature motifs.

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The Newly Identified Q Motif of DEAD Box Heicases IS Involved in Adenine Recognition

Cited by 60 publications

References 20 publications

The mechanism of ATP-dependent RNA unwinding by DEAD box proteins

The mechanism of ATP-dependent RNA unwinding by DEAD box proteins

Erratum to: Structure and Mechanisms of SF1 DNA Helicases

Changing nucleotide specificity of the DEAD-box helicase Hera abrogates communication between the Q-motif and the P-loop

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