The Crystal Structure of Helicobacter Cysteine-rich Protein C at 2.0 Å Resolution: Similar Peptide-binding Sites in TPR and SEL1-like Repeat Proteins

Lüthy, Lucas; Grütter, Markus G.; Mittl, Peer R. E.

doi:10.1016/j.jmb.2004.04.055

Cited by 35 publications

(73 citation statements)

References 56 publications

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“…Homology modeling of Hp0160, Hp0211, Hp0235, Hp0519, and Hp1117 started with a multiple sequence alignment including the protein sequences of the template structures HcpB (1KLX) [57] and HcpC (1OUV) [58] using program CLUSTALW. Due to the modular architecture of Hcps, different superpositions of HcpB and HcpC are possible and meaningful.…”

Section: Methodsmentioning

confidence: 99%

“…slr homologs were identified in ten fully sequenced genomes of closely related e-proteobacterial genera using the COG database. A multiple sequence alignment was generated by aligning SLR protein sequences to crystal structures of H. pylori SLR proteins Hp0336 [57] and Hp1098 [58] using EXPRESSO (http://igs-server.cnrs-mrs.fr/ Tcoffee/tcoffee_cgi/index.cgi), which aligns pairs of structures with SAP while sequence-structure pairs are aligned with FUGUE. The resulting collection of pairwise alignments was combined into a multiple sequence alignment with the T-COFFEE algorithm.…”

Section: Author Summarymentioning

confidence: 99%

“…To examine adaptive evolution in the Japanese hp0519 lineage in a protein structure-function context, we applied several methods for comparative secondary structure analysis and modeled Hp0519 three-dimensional structure on the experimentally determined crystal structures of its homologs HcpB (Hp0336) [57] and HcpC (Hp1098) [58]. Twenty four of 26 (92%) sites under positive selection were in regions near but not overlapping the predicted SLRs, with 19 of 26 (73%) Figure 2A; bar scale indicates number of nucleotide substitutions per codon.…”

Section: Mapping Of Adaptive Substitutions On Slr Protein Structurementioning

confidence: 99%

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Helicobacter pylori Evolution: Lineage-Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes

et al. 2005

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Geographic partitioning is postulated to foster divergence of Helicobacter pylori populations as an adaptive response to local differences in predominant host physiology. H. pylori's ability to establish persistent infection despite host inflammatory responses likely involves active management of host defenses using bacterial proteins that may themselves be targets for adaptive evolution. Sequenced H. pylori genomes encode a family of eight or nine secreted proteins containing repeat motifs that are characteristic of the eukaryotic Sel1 regulatory protein, whereas the related Campylobacter and Wolinella genomes each contain only one or two such ''Sel1-like repeat'' (SLR) genes (''slr genes''). Signatures of positive selection (ratio of nonsynonymous to synonymous mutations, d N /d S ¼ x . 1) were evident in the evolutionary history of H. pylori slr gene family expansion. Sequence analysis of six of these slr genes (hp0160, hp0211, hp0235, hp0519, hp0628, and hp1117) from representative East Asian, European, and African H. pylori strains revealed that all but hp0628 had undergone positive selection, with different amino acids often selected in different regions. Most striking was a divergence of Japanese and Korean alleles of hp0519, with Japanese alleles having undergone particularly strong positive selection (x J . 25), whereas alleles of other genes from these populations were intermingled. Homology-based structural modeling localized most residues under positive selection to SLR protein surfaces. Rapid evolution of certain slr genes in specific H. pylori lineages suggests a model of adaptive change driven by selection for fine-tuning of host responses, and facilitated by geographic isolation. Characterization of such local adaptations should help elucidate how H. pylori manages persistent infection, and potentially lead to interventions tailored to diverse human populations.

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Section: Methodsmentioning

confidence: 99%

Section: Author Summarymentioning

confidence: 99%

Section: Mapping Of Adaptive Substitutions On Slr Protein Structurementioning

confidence: 99%

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Helicobacter pylori Evolution: Lineage-Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes

et al. 2005

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“…Heat denaturation curves were obtained by measuring the CD signal at 222 nm with temperatures increasing from 20 C to 95 C (data pitch, 1 nm; heating rate, 1 C/min; response time, 10 s; bandwidth, 1 nm). GdnHCl-induced denaturation measurements were performed after overnight incubation at 20 C with increasing concentrations of GdnHCl (99.5% purity, Fluka) in phosphate buffered saline (pH 7.4).…”

Section: Circular Dichroism Spectroscopymentioning

confidence: 99%

Structure‐based optimization of designed Armadillo‐repeat proteins

et al. 2012

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The armadillo domain is a right-handed super-helix of repeating units composed of three a-helices each. Armadillo repeat proteins (ArmRPs) are frequently involved in protein-protein interactions, and because of their modular recognition of extended peptide regions they can serve as templates for the design of artificial peptide binding scaffolds. On the basis of sequential and structural analyses, different consensus-designed ArmRPs were synthesized and show high thermodynamic stabilities, compared to naturally occurring ArmRPs. We determined the crystal structures of four full-consensus ArmRPs with three or four identical internal repeats and two different designs for the N-and C-caps. The crystal structures were refined at resolutions ranging from 1.80 to 2.50 Å for the above mentioned designs. A redesign of our initial caps was required to obtain well diffracting crystals. However, the structures with the redesigned caps caused domain swapping events between the N-caps. To prevent this domain swap, 9 and 6 point mutations were introduced in the N-and C-caps, respectively. Structural and biophysical analysis showed that this subsequent redesign of the N-cap prevented domain swapping and improved the thermodynamic stability of the proteins. We systematically investigated the best cap combinations. We conclude that designed ArmRPs with optimized caps are intrinsically stable and well-expressed monomeric proteins and that the high-resolution structures provide excellent structural templates for the continuation of the design of sequence-specific modular peptide recognition units based on armadillo repeats.

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“…The packing angles of repeats are similar to those observed in the H. pylori cysteine-rich protein C (HcpC, PDB id 1OUV) [16], comprised of 267 residues (following signal-peptide cleavage) and sharing 47-53% sequence similarity (25-33% sequence identity) with c5321 (the highest structural homology with proteins in the PDB). An important difference between the two proteins resides in the inter-repeat disulfide bonds stabilizing the super-helical packing in HcpC, not present in c5321.…”

Section: Resultsmentioning

confidence: 55%

Crystal structure of c5321: a protective antigen present in uropathogenic Escherichia coli strains displaying an SLR fold

et al. 2013

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BackgroundIncreasing rates of antimicrobial resistance among uropathogens led, among other efforts, to the application of subtractive reverse vaccinology for the identification of antigens present in extraintestinal pathogenic E. coli (ExPEC) strains but absent or variable in non-pathogenic strains, in a quest for a broadly protective Escherichia coli vaccine. The protein coded by locus c5321 from CFT073 E. coli was identified as one of nine potential vaccine candidates against ExPEC and was able to confer protection with an efficacy of 33% in a mouse model of sepsis. c5321 (known also as EsiB) lacks functional annotation and structurally belongs to the Sel1-like repeat (SLR) family. Herein, as part of the general characterization of this potential antigen, we have focused on its structural properties.ResultsWe report the 1.74 Å-resolution crystal structure of c5321 from CFT073 E. coli determined by Se-Met SAD phasing. The structure is composed of 11 SLR units in a topological organisation that highly resembles that found in HcpC from Helicobacter pylori, with the main difference residing in how the super-helical fold is stabilised. The stabilising effect of disulfide bridges in HcpC is replaced in c5321 by a strengthening of the inter-repeat hydrophobic core. A metal-ion binding site, uncharacteristic of SLR proteins, is detected between SLR units 3 and 4 in the region of the inter-repeat hydrophobic core. Crystal contacts are observed between the C-terminal tail of one molecule and the C-terminal amphipathic groove of a neighbouring one, resembling interactions between ligand and proteins containing tetratricopeptide-like repeats.ConclusionsThe structure of antigen c5321 presents a mode of stabilization of the SLR fold different from that observed in close homologs of known structure. The location of the metal-ion binding site and the observed crystal contacts suggest a potential role in regulation of conformational flexibility and interaction with yet unidentified target proteins, respectively. These findings open new perspectives in both antigen design and for the identification of a functional role for this protective antigen.

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The Crystal Structure of Helicobacter Cysteine-rich Protein C at 2.0 Å Resolution: Similar Peptide-binding Sites in TPR and SEL1-like Repeat Proteins

Cited by 35 publications

References 56 publications

Helicobacter pylori Evolution: Lineage-Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes

Helicobacter pylori Evolution: Lineage-Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes

Structure‐based optimization of designed Armadillo‐repeat proteins

Crystal structure of c5321: a protective antigen present in uropathogenic Escherichia coli strains displaying an SLR fold

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