Three-dimensional structure of the E. coli DMA-binding protein FIS

Kostrewa, Dirk; Granzin, Joachim; Koch, Christian A.; Choe, Huhn; Raghunathan, Srinivasan; Wolf, Wojciech M.; Labahn, Jörg; Kahmann, Regine

doi:10.1038/349178a0

Cited by 171 publications

(131 citation statements)

References 26 publications

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“…58 (A backbone overlay of the 10 lowest energy NMR structures is shown.) Subsequently, this motif has been identified in a wide variety of proteins, including other dimeric helical bundles (FIS DNA-binding protein 116 and Rop mutant 68 ), intramolecularly folded helical bundles (FAS death domain 117 and N-terminal domain of the δ subunit of the ATPsynthase 118 ), and β-sheet proteins (the IgG fold 119 ), and multimeric proteins with both α/β structures (p53 tetramerization domain 120 ). Glu7 is not involved in stabilizing the native state of α 2 D. Superposition of the 10 lowest energy NMR-derived structures (left panel) shows that Glu7 adopts multiple conformations typical of solvent-exposed residues (hydrophobic core residues in gray).…”

Section: Resultsmentioning

confidence: 99%

De NovoDesign of Helical Bundles as Models for Understanding Protein Folding and Function

et al. 2000

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De novo protein design has proven to be a powerful tool for understanding protein folding, structure, and function. In this Account, we highlight aspects of our research on the design of dimeric, four-helix bundles. Dimeric, four-helix bundles are found throughout nature, and the history of their design in our laboratory illustrates our hierarchic approach to protein design. This approach has been successfully applied to create a completely native-like protein. Structural and mutational analysis allowed us to explore the determinants of native protein structure. These determinants were then applied to the design of a dinuclear metal-binding protein that can now serve as a model for this important class of proteins.Protein folding is an important and multifaceted scientific problem. 1-8 One facet of this problem involves the prediction of three-dimensional structure from amino acid sequence, an endeavor the importance of which has been highlighted by the recent release of gene sequences of many whole organisms. As the size of the protein structural database expands, it will be increasingly possible to assign amino acid sequences to a given structural family on the basis of the homology of their sequences with proteins of known structure. Another facet of the folding problem is the delineation of the kinetic mechanism by which an unfolded protein chain undergoes the transition from a random coil with an astronomical number of configurations to a uniquely folded structure. A final facet of the protein folding problem is to understand, at the atomic level, the detailed physicochemical features that kinetically and thermodynamically direct the formation of an unique, cooperatively folded, native structure. This latter endeavor is particularly important as it lays the groundwork for the design of novel inhibitors of natural proteins as well as the construction of novel proteins and related biopolymers not found in nature.De novo protein design is an approach to the protein folding problem that critically tests our understanding of all these facets of this problem. 9,10 This method involves the design of a sequence that is intended to fold into a predetermined three-dimensional structure without the sequence being patterned after any natural protein. Through an iterative process of design and rigorous characterization, the principles governing protein folding and function can be evaluated. Thus, "failures" highlight gaps in our understanding, whereas "successes" confirm the principles used in the design and often provide simple model systems to further

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Section: Resultsmentioning

confidence: 99%

De NovoDesign of Helical Bundles as Models for Understanding Protein Folding and Function

et al. 2000

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“…However, the N-terminal 24 residues are disordered in the crystal structure, although they may be involved in DNA binding and recognition. The helix-turn-helix motif protrudes from each monomer and is related in sequence and structure to other prokaryotic helix-turn-helix-containing proteins (rms deviation of 0.51 A on Ca atoms when compared with A cro repressor; Kostrewa et al, 1991). However, FIS has six positively charged residues in the recognition helix which is different to other helix-turn-helix proteins, and suggests that FIS recognizes DNA predominantly through non-specific interactions.…”

Section: Helix-turn-helix Proteinsmentioning

confidence: 97%

“…The crystal structure of the factor for inversion stimulation (FIS, 98 amino acids) from E. coli has recently been determined (Kostrewa et al, 1991). FIS stimulates site-specific recombination by binding as a dimer to consensus 1 5-bp enhancer sequences.…”

Section: Helix-turn-helix Proteinsmentioning

confidence: 99%

“…However, FIS has six positively charged residues in the recognition helix which is different to other helix-turn-helix proteins, and suggests that FIS recognizes DNA predominantly through non-specific interactions. Based on the separation distance between the FIS helix-turn-helix structures (24 A) which is shorter than that required for binding to successive major grooves of ideal B-DNA (34 A), a model of DNA interaction involving DNA bending has been proposed (Kostrewa et al, 1991). A DNA bend of approx.…”

Section: Helix-turn-helix Proteinsmentioning

confidence: 99%

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Structural aspects of protein-DNA recognition

Freemont

Lane

Sanderson

1991

Biochemical Journal

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“…This figure was prepared using Molscript (Kradis, 1991). B: Amino-acid sequence for the wild-type Fis protein and secondary structures of wildtype Fis (WT) (Kostrewa et al, 1991;Yuan et al, 1991). Fis mutant L y~~~G l u (K36E) in hexagonal form ( Safo et al, 1997), and Fis mutant Pro26Ala (P26A-a for monomer a and P26A-b for monomer b ) as defined by PROCHECK (Laskowski et al, 1993).…”

Section: Overall Structure Of Pro26alamentioning

confidence: 99%

Conversion of a β‐strand to anα‐helix induced by a single‐site mutation observed in the crystal structure of fis mutant pro²⁶Ala

Yang

Corselli

et al. 1998

Protein Science

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The conversion from an a-helix to a P-strand has received extensive attention since this structural change may induce many amyloidogenic proteins to self-assemble into fibrils and cause fatal diseases. Here we report the conversion of a peptide segment from a P-strand to an a-helix by a single-site mutation as observed in the crystal structure of Fis mutant Pro26Ala determined at 2.0 8, resolution. Pro26 in Fis occurs at the point where a flexible extended P-hairpin arm leaves the core structure. Thus it can be classified as a "hinge proline" located at the C-terminal end of the P2-strand and the N-terminal cap of the A a-helix. The replacement of Pro26 to alanine extends the A a-helix for two additional turns in one of the dimeric subunits; therefore, the structure of the peptide from residues 22 to 26 is converted from a P-strand to an a-helix. This result confirms the structural importance of the proline residue located at the hinge region and may explain the mutant's reduced ability to activate Hin-catalyzed DNA inversion. The peptide (residues 20 to 26) in the second monomer subunit presumably retains its P-strand conformation in the crystal; therefore, this peptide shows a "chameleon-like'' character since it can adopt either an a-helix or a P-strand structure in different environments. The structure of Pro26Ala provides an additional example where not only the protein sequence, but also non-local interactions determine the secondary structure of proteins.

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Three-dimensional structure of the E. coli DMA-binding protein FIS

Cited by 171 publications

References 26 publications

De NovoDesign of Helical Bundles as Models for Understanding Protein Folding and Function

De NovoDesign of Helical Bundles as Models for Understanding Protein Folding and Function

Structural aspects of protein-DNA recognition

Conversion of a β‐strand to anα‐helix induced by a single‐site mutation observed in the crystal structure of fis mutant pro²⁶Ala

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Three-dimensional structure of the E. coli DMA-binding protein FIS

Cited by 171 publications

References 26 publications

De NovoDesign of Helical Bundles as Models for Understanding Protein Folding and Function

De NovoDesign of Helical Bundles as Models for Understanding Protein Folding and Function

Structural aspects of protein-DNA recognition

Conversion of a β‐strand to anα‐helix induced by a single‐site mutation observed in the crystal structure of fis mutant pro26Ala

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Conversion of a β‐strand to anα‐helix induced by a single‐site mutation observed in the crystal structure of fis mutant pro²⁶Ala