Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.03 kDa 
• Atom Count: 487 
• Modelled Residue Count: 60 
• Deposited Residue Count: 60 
• Unique protein chains: 1

2K35

Hydramacin-1: Structure and antibacterial activity of a peptide from the basal metazoan Hydra

• PDB DOI: 10.2210/pdb2K35/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Hydra
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2008-04-22 Released: 2008-11-18 
• Deposition Author(s): Jung, S., Dingley, A.J., Stanisak, M., Gelhaus, C., Bosch, T., Podschun, R., Leippe, M., Gr tzinger, J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 25 
• Selection Criteria: target function 

Literature

Hydramacin-1, structure and antibacterial activity of a protein from the Basal metazoan hydra.

Jung, S., Dingley, A.J., Augustin, R., Anton-Erxleben, F., Stanisak, M., Gelhaus, C., Gutsmann, T., Hammer, M.U., Podschun, R., Bonvin, A.M., Leippe, M., Bosch, T.C., Grotzinger, J.

(2009) J Biol Chem 284: 1896-1905

• PubMed: 19019828 
• DOI: 10.1074/jbc.M804713200
• Primary Citation of Related Structures:  
  2K35


• PubMed Abstract: 
  

Hydramacin-1 is a novel antimicrobial protein recently discovered during investigations of the epithelial defense of the ancient metazoan Hydra. The amino acid sequence of hydramacin-1 shows no sequence homology to any known antimicrobial proteins. Determination of the solution structure revealed that hydramacin-1 possesses a disulfide bridge-stabilized alphabeta motif. This motif is the common scaffold of the knottin protein fold. The structurally closest relatives are the scorpion oxin-like superfamily. Within this superfamily hydramacin-1 establishes a new family of proteins that all share antimicrobial activity. Hydramacin-1 is potently active against Gram-positive and Gram-negative bacteria including multi-resistant human pathogenic strains. It leads to aggregation of bacteria as an initial step of its bactericidal mechanism. Aggregated cells are connected via electron-dense contacts and adopt a thorn apple-like morphology. Analysis of the hydramacin-1 structure revealed an unusual distribution of amino acid side chains on the surface. A belt of positively charged residues is sandwiched by two hydrophobic areas. Based on this characteristic surface feature and on biophysical analysis of protein-membrane interactions, we propose a model that describes the aggregation effect exhibited by hydramacin-1.

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Organizational Affiliation: 

Institute of Biochemistry and Institute of Zoology, Zoophysiology, Christian-Albrechts-University of Kiel, Olshausenstrasse 40, 24098 Kiel, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hydramacin-1	A	60	Hydra	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B3RFR8 (Hydra vulgaris) Explore B3RFR8  Go to UniProtKB:  B3RFR8

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 25 
• Selection Criteria: target function 
• OLDERADO: 2K35 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-04-22 
• Released Date: 2008-11-18 
Deposition Author(s): Jung, S., Dingley, A.J., Stanisak, M., Gelhaus, C., Bosch, T., Podschun, R., Leippe, M., Gr tzinger, J.

Revision History  

• Version 1.0: 2008-11-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Database references, Derived calculations