Major Domain Swiveling Revealed by the Crystal Structures of Complexes of E. coli Rep Helicase Bound to Single-Stranded DNA and ADP

Korolev, Sergey; Hsieh, John; Gauss, George H.; Lohman, Timothy M.; Waksman, Gabriel

doi:10.1016/s0092-8674(00)80525-5

Cited by 484 publications

(617 citation statements)

References 43 publications

Supporting

Mentioning

576

Contrasting

Unclassified

Order By: Relevance

“…One of the remarkable features of all three available helicase structures (Subramanya et al, 1996;Korolev et al, 1997;Yao et al, 605…”

Section: Resultsmentioning

confidence: 99%

“…One of the remarkable features of all three available helicase structures (Subramanya et al, 1996;Korolev et al, 1997;Yao et al, 1997) is the juxtaposition of two RecA-like domains to form a groove that contains elements of the nucleotide binding site. To gain further insight into the relative orientation of these domains in both Rep/PcrA helicase and HCV helicase, the two RecA-like domains of Rep were super-imposed onto the two RecA-like domains of HCV helicase.…”

Section: Resultsmentioning

confidence: 99%

“…Indeed, when domain 1A alone was used to super-impose the Rep and HCV helicase structures, the domains 2A of each structure differ (Korolev et al, 1997). The structure of the open conformer of Rep is virtually identical to that of PcrA (Subramanya et al, 1996).…”

Section: B La Imentioning

confidence: 99%

See 2 more Smart Citations

Comparisons between the structures of HCV and Rep helicases reveal structural similarities between SF1 and SF2 super‐families of helicases

et al. 1998

Self Cite

View full text Add to dashboard Cite

Three helicase structures have been determined recently: that of the DNA helicase PcrA, that of the hepatitis C virus RNA helicase, and that of the Escherichia coli DNA helicase Rep. PcrA and Rep belong to the same super-family of helicases (SFI) and are structurally very similar. In contrast, the HCV helicase belongs to a different super-family of helicases, SF2, and shows little sequence homology with the PcrA/Rep helicases. Yet, the HCV helicase is structurally similar to Rep/PcrA, suggesting preservation of structural scaffolds and relationships between helicase motifs across these two super-families. The comparison study presented here also reveals the existence of a new helicase motif in the SF1 family of helicases.Keywords: HCV, helicase; helicase motif; Rep; structure Helicases are enzymes that unwind duplex DNA or RNA in reactions coupled to nucleoside 5' triphosphate (NTP) binding and hydrolysis, and play central roles in processes affecting nucleic acids (Lohman & Bjomson, 1996). On the basis of amino acid sequence homology, helicases have been classified into five superfamilies (Gorbalenya & Koonin, 1993). Although the overall sequence homology is low, conserved regions or "helicase" motifs within each family have been identified (Gorbalenya et al., 1989). However, homology across families is very weak and limited to the signature sequences that are required for NTP binding (helicase motifs I and 11) (Koonin & Dolja, 1993). With the exception of these NTP binding sequences, it has not been clear prior to the structural comparisons reported here whether the other motifs share common functional roles.Recently, structural information on three helicases has been reported at atomic resolution. The first view of a DNA-helicase, that of the PcrA helicase from Bacillus stearothemzophilus, revealed a two-domain structure (domains 1 and 2), with each domain consisting of two subdomains (lA, lB, 2A, and 2B) (Subramanya et al., 1996). While subdomains 1B and 2B are mostly a-helical and are formed by large insertions within subdomains 1A and 2A (Fig. lA) (Fig. IA). The second view of a helicase was that of the RNA helicase domain of the NS3 protein of hepatitis C virus (HCV) (Yao et al., 1997) (Fig. 1B). The HCV helicase consists of three distinct domains, two of which are RecA structural homologues. The third domain is mostly a-helical, and is formed by the C-terminal region of the sequence. Finally, a third view of a DNA helicase structure was recently obtained: that of the Rep DNA helicase bound to single-stranded DNA (ss-DNA) (Korolev et al., 1997). The asymmetric unit of the Rep/ss-DNA crystals contained two molecules that differ markedly by a large reorientation of the subdomain structure. Although one of the molecules (the open conformer) is very similar in structure to the PcrA DNA-helicase (Fig. lA), the other molecule (the closed form) has undergone a swiveling motion of its 2B domain, corresponding to a 130" rotation around the hinge region that connects domains 2A and 2B.In an attempt to deter...

show abstract

“…One of the remarkable features of all three available helicase structures (Subramanya et al, 1996;Korolev et al, 1997;Yao et al, 605…”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Comparisons between the structures of HCV and Rep helicases reveal structural similarities between SF1 and SF2 super‐families of helicases

et al. 1998

Self Cite

View full text Add to dashboard Cite

show abstract

“…SF1 includes three families (Rep/UrvD, Pif1/RecD, and Upf1 like) [86] and can be divided into groups based on the direction of translocation on ssDNA: 3 -5 for SF1A helicases and 5 -3 for SF1B helicases [43]. Some of the well-characterized SF1A helicases are PcrA, Rep, and UvrD T [87][88][89][90][91][92]. Well-characterized members of SF1B include RecD and Dda [93,94] (He et al, in press).…”

Section: Superfamily 1 Helicasesmentioning

confidence: 99%

“…Motif IV supplies a stacking platform (conserved Y) for the adenine base [88] as well as direct contact with the -phosphate, suggesting that it may be involved directly in hydrolysis of the NTP [89].…”

Section: Motif IVmentioning

confidence: 99%

Erratum to: Structure and Mechanisms of SF1 DNA Helicases

Raney

Byrd

Aarattuthodiyil

2012

Advances in Experimental Medicine and Biology

View full text Add to dashboard Cite

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.

show abstract

Peeling by binding or twisting by cranking: Models for promoter opening and transcription initiation by RNA polymerase II

Fiedler

Timmers

2000

Bioessays

View full text Add to dashboard Cite

The precise, sequence‐specific regulation of RNA synthesis is the primary mechanism underlying differential gene expression. This general statement applies to both prokaryotic and eukaryotic organisms, as well as to their viral pathogens. Thus, it is not surprising that genomes use a substantial portion of their protein‐coding content to regulate the process of RNA synthesis. Transcriptional regulation in bacterial systems is particularly well understood. In this essay, we build on this knowledge and propose two opposing models to describe promoter opening and transcription initiation in the eukaryotic RNA polymerase II system. Promoter opening in the “twisting by cranking” model is based on changes in the trajectory of DNA. In contrast, invasion of single‐standed DNA‐binding proteins between the DNA strands drives the reaction in the “peeling by binding” model. BioEssays 22:316–326, 2000. © 2000 John Wiley & Sons, Inc.

show abstract

Major Domain Swiveling Revealed by the Crystal Structures of Complexes of E. coli Rep Helicase Bound to Single-Stranded DNA and ADP

Cited by 484 publications

References 43 publications

Comparisons between the structures of HCV and Rep helicases reveal structural similarities between SF1 and SF2 super‐families of helicases

Comparisons between the structures of HCV and Rep helicases reveal structural similarities between SF1 and SF2 super‐families of helicases

Erratum to: Structure and Mechanisms of SF1 DNA Helicases

Peeling by binding or twisting by cranking: Models for promoter opening and transcription initiation by RNA polymerase II

Contact Info

Product

Resources

About