OB-fold domains: a snapshot of the evolution of sequence, structure and function

Arcus, Vickery L.

doi:10.1016/s0959-440x(02)00392-5

Cited by 203 publications

(183 citation statements)

References 41 publications

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“…In addition, two extended loops L23 and L45 display weak electron density associated with high B factor values, indicating that they are flexible and͞or mobile. They line the positively charged track, and they may clamp nucleic acids on the nsp9 surface after conformational change, as observed in other OB-fold proteins (32). In other members of the OB-fold superfamily, each monomer has its own, autonomous single-stranded nucleic acid-binding site.…”

Section: Resultsmentioning

confidence: 93%

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The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world

Egloff

Ferrón

Campanacci

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

285

328

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The recently identified etiological agent of the severe acute respiratory syndrome (SARS) belongs to Coronaviridae (CoV), a family of viruses replicating by a poorly understood mechanism. Here, we report the crystal structure at 2.7-Å resolution of nsp9, a hitherto uncharacterized subunit of the SARS-CoV replicative polyproteins. We show that SARS-CoV nsp9 is a single-stranded RNA-binding protein displaying a previously unreported, oligosaccharide͞oligo-nucleotide fold-like fold. The presence of this type of protein has not been detected in the replicative complexes of RNA viruses, and its presence may reflect the unique and complex CoV viral replication͞transcription machinery.I n 2003, a human coronavirus (CoV) was identified as the causative agent of a form of atypical pneumonia: severe acute respiratory syndrome-CoV (SARS-CoV) (1-5). Coronaviridae have the longest known single-stranded (ss)RNA genome (27-31.5 kb), with a complex genetic organization and sophisticated replication͞transcription cycle (6, 7). Twenty-eight proteins are predicted to be encoded by the SARS-CoV genome (8, 9). The nonstructural (nsp) or ''replicase'' proteins of CoVs are derived from an unusually large replicase gene of Ͼ20 kb that consists of two large ORFs (ORFs 1a and 1b). Translation of this replicase gene from the incoming genomic RNA is the first step in CoV genome expression and includes a Ϫ1 ribosomal frameshift to express the ORF1b-encoded polypeptide. Translation products are the pp1a polyprotein (Ͼ4,000 amino acids) and the C-terminally extended pp1ab polyprotein (Ͼ7,000 amino acids), which are both cleaved by two or three ORF1a-encoded viral proteinases (10). Most of these replicase cleavage products assemble into a membrane-associated viral replication͞ transcription complex. Among other components, this complex includes a set of relatively small polypeptides (nsp6 to nsp11) encoded by the 3Ј region of ORF1a, for which no predicted nor proven function has been assigned. For the mouse hepatitis CoV, several of these cleavage products were reported to colocalize with other components of the viral replication complex in the perinuclear region of the infected cell (11), suggesting their involvement (directly or indirectly) in viral RNA metabolism.As part of a viral structural genomics program (12), we have cloned the 28 gene products of SARS-CoV and expressed them either as full-length proteins or as (predicted) functional domains. The determination of the three-dimensional structures of these gene products is expected to facilitate and accelerate discovery of drugs against this emerging and life-threatening pathogen. Furthermore, structural homology search is becoming a powerful method to infer biochemical and͞or biological function of previously uncharacterized proteins. We report here the crystal structure of nsp9, one the SARS-CoV uncharacterized nonstructural protein, as well as evidence for its function as an ssDNA͞RNA-binding protein. Materials and MethodsCrystallization, Structure Determination, and Refinement. SARS...

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Section: Resultsmentioning

confidence: 93%

“…Second, the short six-stranded ␤-barrel of nsp9 includes an opened fivestranded barrel reminiscent of the five-stranded ␤-barrel of the oligosaccharide͞oligonucleotide-binding (OB)-fold proteins. The latter proteins form a superfamily in which two-thirds of the members are nucleic acid-binding proteins (32).…”

Section: Resultsmentioning

confidence: 99%

The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world

Egloff

Ferrón

Campanacci

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

285

328

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“…The OB-fold is found in all existent species from archaea to mammals, and these domains commonly bind oligonucleotides (RNA and DNA) or oligosaccharides, although protein binding and enzymatic activities have also been described (15). The OB-fold consists of a five-stranded ␤-barrel capped with an N-terminal ␣-helix, and ligand-binding sites are adaptable, often involving the face of the ␤-barrel and combinations of the variable loops.…”

Section: Discussionmentioning

confidence: 99%

“…The OB-fold consists of a five-stranded ␤-barrel capped with an N-terminal ␣-helix, and ligand-binding sites are adaptable, often involving the face of the ␤-barrel and combinations of the variable loops. Nucleic acid binding usually involves the L2 and L4 loops, whereas the L3 and L4 loops have been described to bind oligosaccharide in the shigella-like toxin (15). In the SSL7 interaction with IgA, the L1 and L4 loops provide the major binding contacts, and the capping ␣-helix of the OB-fold is also involved (Figs.…”

Section: Discussionmentioning

confidence: 99%

Structural basis for evasion of IgA immunity by Staphylococcus aureus revealed in the complex of SSL7 with Fc of human IgA1

Ramsland

Willoughby

Trist

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

106

102

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Infection by Staphylococcus aureus can result in severe conditions such as septicemia, toxic shock, pneumonia, and endocarditis with antibiotic resistance and persistent nasal carriage in normal individuals being key drivers of the medical impact of this virulent pathogen. In both virulent infection and nasal colonization, S. aureus encounters the host immune system and produces a wide array of factors that frustrate host immunity. One in particular, the prototypical staphylococcal superantigen-like protein SSL7, potently binds IgA and C5, thereby inhibiting immune responses dependent on these major immune mediators. We report here the three-dimensional structure of the complex of SSL7 with Fc of human IgA1 at 3.2 Å resolution. Two SSL7 molecules interact with the Fc (one per heavy chain) primarily at the junction between the C␣2 and C␣3 domains. The binding site on each IgA chain is extensive, with SSL7 shielding most of the lateral surface of the C␣3 domain. However, the SSL7 molecules are positioned such that they should allow binding to secretory IgA. The key IgA residues interacting with SSL7 are also bound by the leukocyte IgA receptor, Fc␣RI (CD89), thereby explaining how SSL7 potently inhibits IgAdependent cellular effector functions mediated by Fc␣RI, such as phagocytosis, degranulation, and respiratory burst. Thus, the ability of S. aureus to subvert IgA-mediated immunity is likely to facilitate survival in mucosal environments such as the nasal passage and may contribute to systemic infections.Staphylococcus aureus is an important human pathogen causing conditions ranging from minor superficial skin infections to life-threatening syndromes, including sepsis, toxic shock syndrome, osteomyelitis, pneumonitis, and endocarditis. It is carried without symptoms in at least 20% of individuals (1, 2). The emergence in the 1960s of pandemic penicillin-resistant S. aureus has been followed by a variety of hospital-associated and community-associated methicillin-resistant strains (HA-and CA-MRSA) (2, 3). The increased prevalence of MRSA infections and corresponding rise in life-threatening syndromes have made it imperative to elucidate the mechanisms of pathogenesis for S. aureus. The interaction between S. aureus and the host is complex and is mediated by an array of bacterial proteins that both mediate the various pathologies and modify the immune system of the host (4-10).SSL7 (formerly named SET1) is the first described member of a new family of putative S. aureus toxins, the staphylococcal superantigen-like (SSL) proteins (11, 12), related to the staphylococcal enterotoxins (SEs) or superantigens (13). The SSL proteins have Ϸ30% sequence identity with toxic shock syndrome 1 (TSST-1) and 25% or less identity with other SEs. Despite the sequence differences, the SSL proteins have a typical SE tertiary structure consisting of a distinct oligonucleotide/oligosaccharide binding (OB-fold) linked to a ␤-grasp domain (14 -16).Similar to the se genes, the ssl genes are located in a pathogenicity island (SaPIn2) and ...

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“…Common properties of SSBs include stoichiometric, sequence nonspecific binding to ssDNA, highaffinity and (typically) cooperative binding to ssDNA, weak or nonexistent affinity for dsDNA, and the ability to stimulate cognate replication and recombination enzymes. SSBs all contain one or more copies of the oligonucleotide/oligosaccharide-binding (OB) fold motif (Arcus 2002;Bochkarev and Bochkareva 2004). SSB sequences are divergent, however, and their tertiary structures vary dramatically between species.…”

Section: Properties Of Dna-pairing Proteinsmentioning

confidence: 99%

DNA-Pairing and Annealing Processes in Homologous Recombination and Homology-Directed Repair

Morrical

2015

Cold Spring Harb Perspect Biol

116

127

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The formation of heteroduplex DNA is a central step in the exchange of DNA sequences via homologous recombination, and in the accurate repair of broken chromosomes via homology-directed repair pathways. In cells, heteroduplex DNA largely arises through the activities of recombination proteins that promote DNA-pairing and annealing reactions. Classes of proteins involved in pairing and annealing include RecA-family DNA-pairing proteins, single-stranded DNA (ssDNA)-binding proteins, recombination mediator proteins, annealing proteins, and nucleases. This review explores the properties of these pairing and annealing proteins, and highlights their roles in complex recombination processes including the double Holliday junction (DhJ) formation, synthesis-dependent strand annealing, and singlestrand annealing pathways-DNA transactions that are critical both for genome stability in individual organisms and for the evolution of species.

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OB-fold domains: a snapshot of the evolution of sequence, structure and function

Cited by 203 publications

References 41 publications

The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world

The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world

Structural basis for evasion of IgA immunity by Staphylococcus aureus revealed in the complex of SSL7 with Fc of human IgA1

DNA-Pairing and Annealing Processes in Homologous Recombination and Homology-Directed Repair

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