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Lectin PDB-id
1hev
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Protein chain
43 a.a. *

* Residue conservation analysis
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PDB id: 1hev
Name: Lectin
Title: Hevein: the nmr assignment and an assessment of solution- state folding for the agglutinin-toxin motif

Structure:
Hevein. Chain: a. Engineered: yes

Source:
Hevea brasiliensis. Organism_taxid: 3981

UniProt:
P02877 (HEVE_HEVBR) Pfam   ArchSchema ?
Seq: 204 a.a.
Struc: 43 a.a.
Key:    PfamA domain
 Secondary structure  CATH domain

Resolution:
not givenÅ

NMR structure:
6 models

Authors:
N.H.Andersen,B.Cao

Key ref:
N.H.Andersen et al. (1993). Hevein: NMR assignment and assessment of solution-state folding for the agglutinin-toxin motif.. Biochemistry, 32, 1407-1422. [PubMed id: 8431421] [DOI: 10.1021/bi00057a004]

Date:
14-Jan-93

Release date:
31-Jan-94
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    Key reference    
 
 
DOI no: 10.1021/bi00057a004 Biochemistry 32:1407-1422 (1993)
PubMed id: 8431421  
 
 
Hevein: NMR assignment and assessment of solution-state folding for the agglutinin-toxin motif.
N.H.Andersen, B.Cao, A.Rodríguez-Romero, B.Arreguin.
 
  ABSTRACT  
 
The first high-resolution solution-state structure of a member of the toxin-agglutinin folding motif with the WGA disulfide linkage is presented. The 1H NMR spectrum of hevein has been 100% assigned from residue 2 through residue 43, the C-terminus, using two-dimensional correlation and NOE spectroscopy. During the course of the NOESY analysis, the three-dimensional structural features of hevein were derived, using nonstereospecific distance constraints (with tight bounds) for XPLOR simulated annealing followed by unconstrained relaxation in the CHARMm force field, at two levels of long-range constraint density. In addition, a large number of low-bound-only constraints, corresponding to unobserved NOE's, were used in both refinements. The first structure elucidation employed a total of 180 distance constraints (60 of which were medium or long range, i/i+n with n < or = 2). The second refinement employed 244 (101 medium or long range) constraints: some conformation-insensitive intraresidue constraints were deleted, two misassigned long-range constraints were corrected, and 41 new i/i+n (n > or = 2) constraints were added. The average bounds precisions of the two refinements were comparable (+/- 0.44 A) and significantly tighter than those that result when a universal low bound corresponding to the sum of the van der Waals radii was used. (The more conservative treatment of NOE's gave the same final structure but required a higher constraint density before assignment errors would stand out during the refinement.) Constraint density also has a significant influence on convergence and accuracy using tight constraints. The study demonstrates that convergence within an ensemble of solution structures is not a dependable criterion for either the accuracy or precision of the derived structure. The best fitting conformers from the refinement at the higher constraint density bear a greater similarity to the solid-state structure of the domains of wheat germ agglutinin (0.95 A rmsd over residues 2-32) than to the recently reported 2.8-A X-ray structure of hevein (1.25 A rmsd over residues 2-32, 2.83 A rmsd over residues 2-42). The consensus conformer from the solution data is defined to a backbone rmsd of < 0.6 A over the full sequence for which NMR data could be collected.(ABSTRACT TRUNCATED AT 400 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20135044 J.L.Barneto, M.Avalos, R.Babiano, P.Cintas, J.L.Jiménez, and J.C.Palacios (2010).
A new model for mapping the peptide backbone: predicting proton chemical shifts in proteins.
  Org Biomol Chem, 8, 857-863.  
19596697 J.R.Cort, Z.Liu, G.M.Lee, K.N.Huggins, S.Janes, K.Prickett, and N.H.Andersen (2009).
Solution state structures of human pancreatic amylin and pramlintide.
  Protein Eng Des Sel, 22, 497-513.  
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
16156796 M.Iijima, T.Hashimoto, Y.Matsuda, T.Nagai, Y.Yamano, T.Ichi, T.Osaki, and S.Kawabata (2005).
Comprehensive sequence analysis of horseshoe crab cuticular proteins and their involvement in transglutaminase-dependent cross-linking.
  FEBS J, 272, 4774-4786.  
14675430 E.J.Van Damme, A.Barre, P.Rougé, and W.J.Peumans (2004).
Potato lectin: an updated model of a unique chimeric plant protein.
  Plant J, 37, 34-45.  
15039554 T.Fujii, M.Hayashida, M.Hamasu, M.Ishiguro, and Y.Hata (2004).
Structures of two lectins from the roots of pokeweed (Phytolacca americana).
  Acta Crystallogr D Biol Crystallogr, 60, 665-673.
PDB codes: 1uha 1uln
14661954 F.Barbault, C.Landon, M.Guenneugues, J.P.Meyer, V.Schott, J.L.Dimarcq, and F.Vovelle (2003).
Solution structure of Alo-3: a new knottin-type antifungal peptide from the insect Acrocinus longimanus.
  Biochemistry, 42, 14434-14442.
PDB code: 1q3j
14635132 F.P.Wang, Q.Li, Y.Zhou, M.G.Li, and X.Xiao (2003).
The C-terminal module of Chi1 from Aeromonas caviae CB101 has a function in substrate binding and hydrolysis.
  Proteins, 53, 908-916.  
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
12784603 M.Kaomek, K.Mizuno, T.Fujimura, P.Sriyotha, and J.R.Cairns (2003).
Cloning, expression, and characterization of an antifungal chitinase from Leucaena leucocephala de Wit.
  Biosci Biotechnol Biochem, 67, 667-676.  
11959852 N.Fujitani, S.Kawabata, T.Osaki, Y.Kumaki, M.Demura, K.Nitta, and K.Kawano (2002).
Structure of the antimicrobial peptide tachystatin A.
  J Biol Chem, 277, 23651-23657.
PDB code: 1cix
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.  
12019263 Y.Kamikubo, Y.Okumura, and D.J.Loskutoff (2002).
Identification of the disulfide bonds in the recombinant somatomedin B domain of human vitronectin.
  J Biol Chem, 277, 27109-27119.  
10866795 J.F.Espinosa, J.L.Asensio, J.L.García, J.Laynez, M.Bruix, C.Wright, H.C.Siebert, H.J.Gabius, F.J.Cañada, and J.Jiménez-Barbero (2000).
NMR investigations of protein-carbohydrate interactions binding studies and refined three-dimensional solution structure of the complex between the B domain of wheat germ agglutinin and N,N', N"-triacetylchitotriose.
  Eur J Biochem, 267, 3965-3978.  
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.  
10333739 F.García-Olmedo, A.Molina, J.M.Alamillo, and P.Rodríguez-Palenzuéla (1998).
Plant defense peptides.
  Biopolymers, 47, 479-491.  
9845845 H.D.Chen, C.L.Chen, S.W.Huang, H.F.Kung, and H.C.Chen (1998).
Characterization of latex allergenic components by capillary zone electrophoresis and N-terminal sequence analysis.
  J Biomed Sci, 5, 421-427.  
7607237 J.L.Asensio, F.J.Canada, M.Bruix, A.Rodriguez-Romero, and J.Jimenez-Barbero (1995).
The interaction of hevein with N-acetylglucosamine-containing oligosaccharides. Solution structure of hevein complexed to chitobiose.
  Eur J Biochem, 230, 621-633.  
  8528070 M.Sukumar, J.Rizo, M.Wall, L.A.Dreyfus, Y.M.Kupersztoch, and L.M.Gierasch (1995).
The structure of Escherichia coli heat-stable enterotoxin b by nuclear magnetic resonance and circular dichroism.
  Protein Sci, 4, 1718-1729.
PDB code: 1ehs
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.