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- PDB-1zwu: 30 NMR structures of AcAMP2-like peptide with non natural beta-(2... -

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Basic information

Entry
Database: PDB / ID: 1zwu
Title30 NMR structures of AcAMP2-like peptide with non natural beta-(2-naphthyl)-alanine residue.
ComponentsAMARANTHUS CAUDATUS ANTIMICROBIAL PEPTIDE 2 (ACMP2)
KeywordsANTIMICROBIAL PROTEIN / alpha-helix / anti-parallel beta-sheet.
Function / homology
Function and homology information


chitin binding / defense response to fungus / killing of cells of another organism / defense response to bacterium
Similarity search - Function
Antimicrobial peptide, C6 type, conserved site / Plant C6 type antimicrobial peptide (AMP) signature. / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily
Similarity search - Domain/homology
Antimicrobial peptide 2
Similarity search - Component
MethodSOLUTION NMR / The structures are based on 348 NOE-derived distance constraints, 18 come from cys-cys disulfide bridges
AuthorsChavez, M.I. / Andreu, C. / Vidal, P. / Freire, F. / Aboitiz, N. / Groves, P. / Asensio, J.L. / Asensio, G. / Muraki, M. / Canada, F.J. / Jimenez-Barbero, J.
Citation
Journal: Chemistry / Year: 2005
Title: On the Importance of Carbohydrate-Aromatic Interactions for the Molecular Recognition of Oligosaccharides by Proteins: NMR Studies of the Structure and Binding Affinity of AcAMP2-like Peptides ...Title: On the Importance of Carbohydrate-Aromatic Interactions for the Molecular Recognition of Oligosaccharides by Proteins: NMR Studies of the Structure and Binding Affinity of AcAMP2-like Peptides with Non-Natural Naphthyl and Fluoroaromatic Residues.
Authors: Chavez, M.I. / Andreu, C. / Vidal, P. / Aboitiz, N. / Freire, F. / Groves, P. / Asensio, J.L. / Asensio, G. / Muraki, M. / Canada, F.J. / Jimenez-Barbero, J.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: 1H NMR study of the solution structure of AcAMP2, a sugar binding antimicrobial protein isolated from Amaranthus caudatus.
Authors: Martins, J.C. / Maes, D. / Loris, R. / Pepermans, H.A. / Wyns, L. / Willem, R. / Verheyden, P.
#2: Journal: Protein Pept.Lett. / Year: 2002
Title: The importance of CH/pi interactions to the function of carbohydrate binding proteins
Authors: Muraki, M.
#3: Journal: Chembiochem / Year: 2004
Title: NMR and modeling studies of protein-carbohydrate interactions:synthesis three-dimensional structure, and recognition properties of a minimum hevein domain with binding affinity for chitooligosaccharides.
Authors: Aboitiz, N. / Vila-Perello, M. / Groves, P. / Asensio, J.L. / Andreu, D. / Canada, F.J. / Jimenez-Barbero, J.
#4: Journal: Proteins / Year: 2000
Title: NMR investigations of protein-carbohydrate interactions:synthesis on the relevance of Trp/Tyr variations in lectin binding sites as deduced from titration microcalorimetry and NMR studies on ...Title: NMR investigations of protein-carbohydrate interactions:synthesis on the relevance of Trp/Tyr variations in lectin binding sites as deduced from titration microcalorimetry and NMR studies on hevein domains. Determination of the NMR structure of the complex between pseudohevein and N,N',N"-triacetylchitotriose.
Authors: Asensio, J.L. / Siebert, H.C. / von Der Lieth, C.W. / Laynez, J. / Bruix, M. / Soedjanaamadja, U.M. / Beitema, J.J. / Canada, F.J. / Gabius, H.J. / Jimenez-barbero, J.
#5: Journal: Chem.Biol. / Year: 2000
Title: Structural basis for chitin recognition by defense proteins: GlcNAc residues are bound in a multivalent fashion by extended binding sites in hevein domains.
Authors: Asensio, J.L. / Canada, F.J. / Siebert, H.C. / Laynez, J. / Poveda, A. / Nieto, P.M. / Soedjanaamadja, U.M. / Gabius, H.J. / Jimenez-Barbero, J.
#6: Journal: Protein Eng. / Year: 2000
Title: Chemically Prepared Hevein Domains: Effect of C-Terminal Truncation and the Mutagenesis of Aromatic Residues on Affinity for Chitin
Authors: Muraki, M. / Morii, H. / Harata, K.
History
DepositionJun 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 3, 2011Group: Non-polymer description
Revision 1.4Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMARANTHUS CAUDATUS ANTIMICROBIAL PEPTIDE 2 (ACMP2)


Theoretical massNumber of molelcules
Total (without water)3,2451
Polymers3,2451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 50structures with the least restraint violations
RepresentativeModel #5lowest energy

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Components

#1: Protein/peptide AMARANTHUS CAUDATUS ANTIMICROBIAL PEPTIDE 2 (ACMP2)


Mass: 3244.841 Da / Num. of mol.: 1
Mutation: Phe 18 has been mutated to the non proteinogenic aminoacid beta-(2-naphthyl)-alanine.
Source method: obtained synthetically
Details: The residue Phe 18 of the natural AcAMP2 was changed to beta-(2-naphthyl)-alanine. The aminoacid was manually assembled by solid phase synthesis using Fmoc chemistry using standard protocols.
References: UniProt: P27275

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY

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Sample preparation

DetailsContents: 2.92 mM AcAMP2F18Nal; 20 mM Phosphate buffer; 90% H20, 10% D20
Solvent system: 90% H20, 10% D20
Sample conditionsIonic strength: 100 mM NaCl / pH: 5.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.2Brukercollection
XEASY1.3.13Wuthrichdata analysis
DYANA1.5Guentertstructure solution
Amber5Kollmanrefinement
RefinementMethod: The structures are based on 348 NOE-derived distance constraints, 18 come from cys-cys disulfide bridges
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 30

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