6SJX | pdb_00006sjx

Precursor structure of the self-processing module of iron-regulated FrpC of N. Meningitidis with calcium ions

PDB DOI: https://doi.org/10.2210/pdb6SJX/pdb
BMRB: 34424
BMRB: 26530

Classification: METAL BINDING PROTEIN
Organism(s): Neisseria meningitidis serogroup C
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2019-08-14 Released: 2020-02-26
Deposition Author(s): Kuban, V., Macek, P., Hritz, J., Nechvatalova, K., Nedbalcova, K., Faldyna, M., Zidek, L., Bumba, L.
Funding Organization(s): Grant Agency of the Czech Republic, European Regional Development Fund, Other government, Other private, Ministry of Education, Youth and Sports of the Czech Republic

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 20
Conformers Submitted: 14
Selection Criteria: structures with the least restraint violations

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structural Basis of Ca 2+ -Dependent Self-Processing Activity of Repeat-in-Toxin Proteins.

Kuban, V., Macek, P., Hritz, J., Nechvatalova, K., Nedbalcova, K., Faldyna, M., Sebo, P., Zidek, L., Bumba, L.

(2020) mBio 11

PubMed: 32184239 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/mBio.00226-20
Primary Citation Related Structures:
6SJW, 6SJX

PubMed Abstract:
The posttranslational Ca ²⁺-dependent "clip-and-link" activity of large r epeat-in- t o x in (RTX) proteins starts by Ca ²⁺-dependent structural rearrangement of a highly conserved self-processing module (SPM). Subsequently, an internal aspartate-proline (Asp-Pro) peptide bond at the N-terminal end of SPM breaks, and the liberated C-terminal aspartyl residue can react with a free ε-amino group of an adjacent lysine residue to form a new isopeptide bond. Here, we report a solution structure of the calcium-loaded SPM (Ca-SPM) derived from the FrpC protein of Neisseria meningitidis The Ca-SPM structure defines a unique protein architecture and provides structural insight into the autocatalytic cleavage of the Asp-Pro peptide bond through a "twisted-amide" activation. Furthermore, in-frame deletion of the SPM domain from the ApxIVA protein of Actinobacillus pleuropneumoniae attenuated the virulence of this porcine pathogen in a pig respiratory challenge model. We hypothesize that the Ca ²⁺-dependent clip-and-link activity represents an unconventional strategy for Gram-negative pathogens to adhere to the host target cell surface. IMPORTANCE The Ca ²⁺-dependent clip-and-link activity of large repeat-in-toxin (RTX) proteins is an exceptional posttranslational process in which an internal domain called a self-processing module (SPM) mediates Ca ²⁺-dependent processing of a highly specific aspartate-proline (Asp-Pro) peptide bond and covalent linkage of the released aspartyl to an adjacent lysine residue through an isopeptide bond. Here, we report the solution structures of the Ca ²⁺-loaded SPM (Ca-SPM) defining the mechanism of the autocatalytic cleavage of the Asp414-Pro415 peptide bond of the Neisseria meningitidis FrpC exoprotein. Moreover, deletion of the SPM domain in the ApxIVA protein, the FrpC homolog of Actinobacillus pleuropneumoniae , resulted in attenuation of virulence of the bacterium in a pig infection model, indicating that the Ca ²⁺-dependent clip-and-link activity plays a role in the virulence of Gram-negative pathogens.

Organizational Affiliation

Central European Institute of Technology, Masaryk University, Brno, Czech Republic.

Macromolecule Content

Total Structure Weight: 19.45 kDa
Atom Count: 1,360
Modeled Residue Count: 182
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-regulated protein FrpC	A	182	Neisseria meningitidis serogroup C	Mutation(s): 0 Gene Names: frpC
UniProt
Find proteins for P55127 (Neisseria meningitidis serogroup C) Explore P55127 Go to UniProtKB: P55127
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55127
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 20
Conformers Submitted: 14
Selection Criteria: structures with the least restraint violations

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-02-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Grant Agency of the Czech Republic	Czech Republic	19-15175S
European Regional Development Fund	Czech Republic	CZ.1.05/1.1.00/02.0068
Other government	Czech Republic	LM2015042
Other private	Czech Republic	LM2015064
Other private	Czech Republic	LM2015043
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LQ1601