2JOB

Solution structure of an antilipopolysaccharide factor from shrimp and its possible Lipid A binding site


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 60 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

NMR structure of rALF-Pm3, an anti-lipopolysaccharide factor from shrimp: Model of the possible lipid A-binding site

Yang, Y.Boze, H.Chemardin, P.Padilla, A.Moulin, G.Tassanakajon, A.Pugniere, M.Roquet, F.Destoumieux-Garzon, D.Gueguen, Y.Bachere, E.Aumelas, A.

(2009) Biopolymers 91: 207-220

  • DOI: 10.1002/bip.21119
  • Primary Citation of Related Structures:  
    2JOB

  • PubMed Abstract: 
  • The anti-lipopolysaccharide factor ALF-Pm3 is a 98-residue protein identified in hemocytes from the black tiger shrimp Penaeus monodon. It was expressed in Pichia pastoris from the constitutive glyceraldehyde-3-phosphate dehydrogenase promoter as a folded and (15)N uniformly labeled rALF-Pm3 protein ...

    The anti-lipopolysaccharide factor ALF-Pm3 is a 98-residue protein identified in hemocytes from the black tiger shrimp Penaeus monodon. It was expressed in Pichia pastoris from the constitutive glyceraldehyde-3-phosphate dehydrogenase promoter as a folded and (15)N uniformly labeled rALF-Pm3 protein. Its 3D structure was established by NMR and consists of three alpha-helices packed against a four-stranded beta-sheet. The C(34)-C(55) disulfide bond was shown to be essential for the structure stability. By using surface plasmon resonance, we demonstrated that rALF-Pm3 binds to LPS, lipid A and to OM-174, a soluble analogue of lipid A. Biophysical studies of rALF-Pm3/LPS and rALF-Pm3/OM-174 complexes indicated rather high molecular sized aggregates, which prevented us to experimentally determine by NMR the binding mode of these lipids to rALF-Pm3. However, on the basis of striking structural similarities to the FhuA/LPS complex, we designed an original model of the possible lipid A-binding site of ALF-Pm3. Such a binding site, located on the ALF-Pm3 beta-sheet and involving seven charged residues, is well conserved in ALF-L from Limulus polyphemus and in ALF-T from Tachypleus tridentatus. In addition, our model is in agreement with experiments showing that beta-hairpin synthetic peptides corresponding to ALF-L beta-sheet bind to LPS. Delineating lipid A-binding site of ALFs will help go further in the de novo design of new antibacterial or LPS-neutralizing drugs.


    Organizational Affiliation

    CNRS UMR5048, INSERM, U554, Université Montpellier 1 et 2, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, Cedex 9, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
antilipopolysaccharide factorA102Penaeus monodonMutation(s): 0 
Gene Names: ALFPm3
UniProt
Find proteins for A5A3I5 (Penaeus monodon)
Explore A5A3I5 
Go to UniProtKB:  A5A3I5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5A3I5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 60 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2JOB Olderado

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-09
    Changes: Data collection, Database references, Derived calculations