1CW5

SOLUTION STRUCTURE OF CARNOBACTERIOCIN B2

PDB DOI: 10.2210/pdb1CW5/pdb
BMRB: 4506

Classification: TOXIN
Organism(s): Carnobacterium maltaromaticum
Mutation(s): No

Deposited: 1999-08-25 Released: 1999-09-07
Deposition Author(s): Wang, Y., Henz, M.E., Gallagher, N.L.F., Chai, S., Yan, L.Z., Gibbs, A.C., Stiles, M.E., Wishart, D.S., Vederas, J.C.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 30
Conformers Submitted: 20
Selection Criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON- BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Solution structure of carnobacteriocin B2 and implications for structure-activity relationships among type IIa bacteriocins from lactic acid bacteria.

Wang, Y., Henz, M.E., Gallagher, N.L., Chai, S., Gibbs, A.C., Yan, L.Z., Stiles, M.E., Wishart, D.S., Vederas, J.C.

(1999) Biochemistry 38: 15438-15447

PubMed: 10569926 Search on PubMed
DOI: 10.1021/bi991351x
Primary Citation of Related Structures:
1CW5, 1CW6

PubMed Abstract:

Carnobacteriocin B2 (CbnB2), a type IIa bacteriocin, is a 48 residue antimicrobial peptide from the lactic acid bacterium Carnobacterium pisicola LV17B. Type IIa bacteriocins have a conserved YGNGVXC sequence near the N-terminus and usually contain a disulfide bridge. CbnB2 seemed to be unique in that its two cysteines (Cys9 and Cys14) could be isolated as free thiols [Quadri et al. (1994) J. Biol. Chem. 26, 12204-12211]. To establish the structural consequences of the presence or absence of a disulfide bridge and to investigate if the YGNGVXC sequence is a receptor-binding motif [Fleury et al. (1996) J. Biol. Chem. 271, 14421-14429], the three-dimensional solution structure of CbnB2 was determined by two-dimensional (1)H nuclear magnetic resonance (NMR) techniques. Mass spectroscopic and thiol modification experiments on CbnB2 and on model peptides, in conjunction with activity measurements, were used to verify the redox status of CbnB2. The results show that CbnB2 readily forms a disulfide bond and that this peptide has full antimicrobial activity. NMR results indicate that CbnB2 in trifluoroethanol (TFE) has a well-defined central helical structure (residues 18-39) but a disordered N terminus. Comparison of the CbnB2 structure with the refined solution structure of leucocin A (LeuA), another type IIa bacteriocin, indicates that the central helical structure is conserved between the two peptides despite differences in sequence but that the N-terminal structure (a proposed receptor binding site) is not. This is unexpected because LeuA and CbnB2 exhibit >66% sequence identity in the first 24 residues. This suggests that the N-terminus, which had been proposed [Fleury et al. (1996) J. Biol. Chem. 271, 14421-14429] to be a receptor binding site of type IIa bacteriocins, may not be directly involved and that recognition of the amphiphilic helical portion is the critical feature.

Organizational Affiliation:

Faculty of Pharmacy and Pharmaceutical Sciences, Department of Chemistry, University of Alberta, Edmonton, Canada.

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYPE IIA BACTERIOCIN CARNOBACTERIOCIN B2	A	48	Carnobacterium maltaromaticum	Mutation(s): 0 Gene Names: cbnB2, canCP52
UniProt
Find proteins for P38580 (Carnobacterium maltaromaticum) Explore P38580 Go to UniProtKB: P38580
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38580
Protein Feature View Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 30
Conformers Submitted: 20
Selection Criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON- BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
OLDERADO: 1CW5 Olderado