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Chitin-binding PDB id
1mmc
Jmol
Contents
Protein chain
30 a.a.
PDB id:
1mmc
Name: Chitin-binding
Title: 1h nmr study of the solution structure of ac-amp2
Structure: Antimicrobial peptide 2. Chain: a. Synonym: ac-amp2
Source: Amaranthus caudatus. Amaranth. Organism_taxid: 3567. Tissue: seed
NMR struc: 26 models
Authors: J.C.Martins,D.Maes,R.Loris,H.A.M.Pepermans,L.Wyns,R.Willem, P.Verheyden
Key ref:
J.C.Martins et al. (1996). H NMR study of the solution structure of Ac-AMP2, a sugar binding antimicrobial protein isolated from Amaranthus caudatus. J Mol Biol, 258, 322-333. PubMed id: 8627629 DOI: 10.1006/jmbi.1996.0253
Date:
25-Oct-95     Release date:   08-Mar-96    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P27275  (AMP_AMACA) -  Antimicrobial peptide 2
Seq:
Struc: 		86 a.a.
30 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cell wall macromolecule catabolic process   2 terms 
  Biochemical function     chitin binding     2 terms  

 

 
DOI no: 10.1006/jmbi.1996.0253 J Mol Biol 258:322-333 (1996)
PubMed id: 8627629  
 
 
H NMR study of the solution structure of Ac-AMP2, a sugar binding antimicrobial protein isolated from Amaranthus caudatus.
J.C.Martins, D.Maes, R.Loris, H.A.Pepermans, L.Wyns, R.Willem, P.Verheyden.
 
  ABSTRACT  
 
The conformation in water of antimicrobial protein 2 from Amaranthus caudatus (Ac-AMP2) was determined using 1H NMR, DIANA and restrained molecular modeling. Ac-AMP2 is a 30 amino acid residue, lectin-like protein that specifically binds to chitin, a polymer of beta-1,4-N-acetyl-D-glucosamine. After sequence specific resonance assignments, a total of 198 distance restraints were collected from 2D NOESY buildup spectra at 500 MHz at pH 2, supplemented by a 2D NOESY spectrum at 600 MHz. The location of the three previously unassigned disulfide bridges was determined from preliminary DIANA structures, using a statistical analysis of intercystinyl distances. The solution structure of Ac-AMP2 is presented as a set of 26 DIANA structures, further refined by restrained molecular dynamics using a simulated annealing protocol in the AMBER force field, with a backbone r.m.s.d. for the well defined Glu3-Cys28 segment of 0.69(+/-0.12) angstroms. The main structural element is an antiparallel beta-sheet from Met13 to Lys23 including a betaI-turn over Gln17-Phel8 with a beta bulge at Gly19. In addition, a beta'I turn over Arg6-Gly7, a beta'III turn over Ser11-Gly12 and a helical turn from Gly24 to Cys28 are identified. This structure is very similar to the equivalent regions of the X-ray structure of wheat germ agglutinin and the NMR structure of hevein.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Average intercystinyl S g --S g distances observed in the set of 48 conformers for each of the three possible disulfide bridge patterns, Cys4-Cys15, Cys9-Cys21, Cys14-Cys28 (I), Cys4-Cys21, Cys9-Cys15, Cys14-Cys28 (II) and Cys4-Cys9, Cys14-Cys28, Cys15-Cys21 (III). 		Figure 5.
Figure 5. Stereo view of the 26 conformers representing the solution conformation of Ac-AMP2 in solution. Conformers 2 to 26 were superimposed for minimum r.m.s.d. of the backbone atoms of residues 3 to 28 with conformer 1. Black lines represent the backbone atoms, gray lines the disulfide bridges. For clarity, the N and C-terminal residues 1-2 and 29-30 are not displayed. The structure features the Cys4-Cys15, Cys9-Cys21 and Cys14-Cys28 disulfide bridges from top to bottom.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 258, 322-333) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21500331 V.Roldós, F.J.Cañada, and J.Jiménez-Barbero (2011).
Carbohydrate-protein interactions: a 3D view by NMR.
  Chembiochem, 12, 990.  
19466694 S.Yokoyama, Y.Iida, Y.Kawasaki, Y.Minami, K.Watanabe, and F.Yagi (2009).
The chitin-binding capability of Cy-AMP1 from cycad is essential to antifungal activity.
  J Pept Sci, 15, 492-497.  
16220560 M.I.Chávez, C.Andreu, P.Vidal, N.Aboitiz, F.Freire, P.Groves, J.L.Asensio, G.Asensio, M.Muraki, F.J.Cañada, and J.Jiménez-Barbero (2005).
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.
  Chemistry, 11, 7060-7074.
PDB codes: 1znt 1zuv 1zwu
15368576 N.Aboitiz, M.Vila-Perelló, P.Groves, J.L.Asensio, D.Andreu, F.J.Cañada, and J.Jiménez-Barbero (2004).
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.
  Chembiochem, 5, 1245-1255.
PDB code: 1t0w
12676931 H.Hemmi, J.Ishibashi, T.Tomie, and M.Yamakawa (2003).
Structural basis for new pattern of conserved amino acid residues related to chitin-binding in the antifungal peptide from the coconut rhinoceros beetle Oryctes rhinoceros.
  J Biol Chem, 278, 22820-22827.
PDB code: 1iyc
11909866 P.Karisola, H.Alenius, J.Mikkola, N.Kalkkinen, J.Helin, O.T.Pentikäinen, S.Repo, T.Reunala, K.Turjanmaa, M.S.Johnson, T.Palosuo, and M.S.Kulomaa (2002).
The major conformational IgE-binding epitopes of hevein (Hev b6.02) are identified by a novel chimera-based allergen epitope mapping strategy.
  J Biol Chem, 277, 22656-22661.  
11298757 J.C.Martins, M.Enassar, R.Willem, J.M.Wieruzeski, G.Lippens, and S.J.Wodak (2001).
Solution structure of the main alpha-amylase inhibitor from amaranth seeds.
  Eur J Biochem, 268, 2379-2389.
PDB code: 1htx
11173474 S.C.Ha, K.Min, J.C.Koo, Y.Kim, D.J.Yun, M.J.Cho, and K.K.Kim (2001).
Crystallization and preliminary crystallographic studies of an antimicrobial protein from Pharbitis nil.
  Acta Crystallogr D Biol Crystallogr, 57, 263-265.  
10903932 J.L.Asensio, F.J.Cañada, H.C.Siebert, J.Laynez, A.Poveda, P.M.Nieto, U.M.Soedjanaamadja, H.J.Gabius, and J.Jiménez-Barbero (2000).
Structural basis for chitin recognition by defense proteins: GlcNAc residues are bound in a multivalent fashion by extended binding sites in hevein domains.
  Chem Biol, 7, 529-543.  
10842338 J.L.Asensio, H.C.Siebert, C.W.von Der Lieth, J.Laynez, M.Bruix, U.M.Soedjanaamadja, J.J.Beintema, F.J.Cañada, H.J.Gabius, and J.Jiménez-Barbero (2000).
NMR investigations of protein-carbohydrate interactions: studies 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.
  Proteins, 40, 218-236.  
10674716 N.F.Dawson, D.J.Craik, A.M.McManus, S.G.Dashper, E.C.Reynolds, G.W.Tregear, L.Otvos, and J.D.Wade (2000).
Chemical synthesis, characterization and activity of RK-1, a novel alpha-defensin-related peptide.
  J Pept Sci, 6, 19-25.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.