The KH module has an αβ fold

Morelli, Massimo; Stier, Günter; Gibson, Toby J.; Joseph, Catherine; Musco, Giovanna; Pastore, Annalisa; Travé, Gilles

doi:10.1016/0014-5793(94)01422-w

Cited by 36 publications

(9 citation statements)

References 23 publications

(29 reference statements)

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“…Combining these results with the results presented by Ito et al (1994) and comparisons with the closely spaced domains in HBP (McKnight et al, 1992) and FMRl allows a reasonably precise definition of the nucleic acid binding domain. Thus, a KH domain includes about 70 amino acids, which is consistent with what was found from structure determination of HBP KH-domain 5 (Castiglione-Morelli et al, 1995;Musco et al, 1996) but considerably larger than previous estimates (Siomi et al, 1993a(Siomi et al, , 1994(Siomi et al, , 1995Dreyfuss et al, 1993;Gibson et al, 1993;Buckanovich et al, 1993;Duncan et al, 1994) (see below).…”

Section: Localisation Of the Poly(rc) Binding Domain(s) Of Hnrnp-k Ansupporting

confidence: 90%

“…4 B ; results not shown). The most pronounced difference was observed for the truncated domain 3 from hnRNP-K (Figs 3 and 4B, construct F) where washing at 1 M NaCl reduced the binding significantly and essentially all the bound poly(rC) was lost in the 5 M wash, suggesting that its reduced poly(rC) binding may be caused by a decrease in the stability of the truncated domain rather than to an inability to recognise poly(rC), consistent with observations by others (Castiglione-Morelli et al, 1995). Surprisingly, the isolated domains showed a higher salt resistance than did the complete proteins (Fig.…”

Section: Stability Of the Protein-nucleic-acid Complexes In High Saltsupporting

confidence: 88%

“…Based on our observations of hnRNP-K and the repeated sequences found in HBP (McKnight et al, 1992), we later extended this to cover 65-70 amino acids . NMR studies of KH-domain 5 from HBP recently revealed that this extension is required for structural stability of the domain (Castiglione-Morelli et al, 1995).…”

Section: Hagen Denmarkmentioning

confidence: 99%

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Characterisation of the Nucleic‐Acid‐Binding Activity of KH Domains Different Properties of Different Domains

Dejgaard

Leffers

1996

European Journal of Biochemistry

118

114

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The KH module is a sequence motif recently identified in a number of diversified RNA-binding proteins and suggested to be the functional element responsible for RNA binding. So far, however, this hypothesis has not received direct experimental support. We have expressed the three KH-domains from heterogeneous nuclear ribonucleoprotein K (hnRNP-K), the poly(C)-binding proteins PCBP-1 and PCBP-2, the first three to four domains from the high-density binding protein HBP, the one and a half domain from the archaeon Halobacterium halobium ORF139 and one and a half domain of the fragile-X protein FMRl in Escherichia coli and analysed their nucleic-acid-binding properties in vitro. The results showed that the in vitro poly(rC)-binding activity of hnRNP-K can be assigned to KH-domain 3, whereas both domains 1 and 3 in the PCBPs bind poly(rC). In addition, all these domains exhibit binding activity towards other nucleic acids, albeit at a significantly lower level. The first KH domain from the FMRl protein binds poly(rG) and single-stranded and double-stranded DNA. The N-terminal three or four domains from HBP bind poly(rG) and, at a much lower level, single-stranded and double-stranded DNA. Thus, single KH domains are discrete and independent nucleic-acid-binding units. Moreover, different KH domains bind different nucleic acids, suggesting that KH domains are composed of a conserved, weakly nucleic-acid-binding, structure that is fine tuned, by sequence variation, resulting in sequencespecific nucleic-acid-binding entities.

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Section: Localisation Of the Poly(rc) Binding Domain(s) Of Hnrnp-k Ansupporting

confidence: 90%

Section: Stability Of the Protein-nucleic-acid Complexes In High Saltsupporting

confidence: 88%

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Characterisation of the Nucleic‐Acid‐Binding Activity of KH Domains Different Properties of Different Domains

Dejgaard

Leffers

1996

European Journal of Biochemistry

118

114

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“…Yet it is usually assumed that a module is a domain, i.e. that it is able to fold autonomously into a well defined structure and that it cannot be cut down any further without losing its ability to fold properly [3,4]. For most modules this is the case, therefore the increased availability of newly sequenced proteins and the analysis of their module organization has given a significant boost to structural biology.…”

Section: Introductionmentioning

confidence: 99%

When a module is not a domain: the case of the REJ module and the redefinition of the architecture of polycystin-1

Schröder

Fraternali

Quan

et al. 2011

Biochemical Journal

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Synopsis The extracellular region of a group of cell surface receptors known as the polycystic kidney disease 1 family, comprising amongst others polycystin-1, has been controversially described as containing four fibronectin type III (FNIII) domains or one REJ module in the same portion of polypeptide. Stimulated by recent atomic force microscopy work we re-examined the similarity of these four domains with a FNIII sequence profile showing the evolutionary relationship. Two of the predicted domains could be expressed in bacteria and refolded to give protein suitable for biophysical study and one of these expressed solubly. Circular dichroism spectroscopy showed that both domains contain a significant amount of β-sheet, in good agreement with theoretical predictions. Confirmation of independent folding as a domain is obtained from highly cooperative thermal and urea unfolding curves. Excellent dispersion of peaks in the high field region of one dimensional NMR spectra confirms the presence of a hydrophobic core. Analytical ultracentrifugation and analytical gel filtration agree very well with the narrow linewidths in the NMR spectra that at least one of the domains is monomeric. Based on this combined theoretical and experimental analysis we show that the extracellular portion of polycystin-1 does indeed contain β-sheet domains, very likely fibronectin type III, and that consequently the REJ module is not a single domain.

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“…A; Bycroft et al, ), and one KH motif‐containing protein, human vigilin (Fig. C; Castiglone Morelli et al, ), each contain a three‐stranded antiparallel β‐sheet with two or three helices packed against one face to form an α/β structure, albeit with different topology. Furthermore, a topological variant of the canonical KH domain has been observed in the ribosomal protein S3 from T. thermophilus (Carter et al, ; Grishin, ).…”

Section: Rna‐binding Structural Motifs and Domainsmentioning

confidence: 99%

Overview of Protein Structural and Functional Folds

2004

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This overview provides an illustrated, comprehensive survey of some commonly observed protein-fold families and structural motifs, chosen for their functional significance. It opens with descriptions and definitions of the various elements of protein structure and associated terminology. Following is an introduction into web-based structural bioinformatics that includes surveys of interactive web servers for protein fold or domain annotation, protein-structure databases, protein-structure-classification databases, structural alignments of proteins, and molecular graphics programs available for personal computers. The rest of the overview describes selected families of protein folds in terms of their secondary, tertiary, and quaternary structural arrangements, including ribbon-diagram examples, tables of representative structures with references, and brief explanations pointing out their respective biological and functional significance.

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The KH module has an αβ fold

Cited by 36 publications

References 23 publications

Characterisation of the Nucleic‐Acid‐Binding Activity of KH Domains Different Properties of Different Domains

Characterisation of the Nucleic‐Acid‐Binding Activity of KH Domains Different Properties of Different Domains

When a module is not a domain: the case of the REJ module and the redefinition of the architecture of polycystin-1

Overview of Protein Structural and Functional Folds

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