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PDBsum entry 2q3n

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protein ligands Protein-protein interface(s) links
Plant protein PDB id
2q3n
Jmol
Contents
Protein chains
247 a.a. *
261 a.a. *
Ligands
NAG ×3
* Residue conservation analysis
PDB id:
2q3n
Name: Plant protein
Title: Agglutinin from abrus precatorius (apa-i)
Structure: Agglutinin-1 a chain. Chain: a. Fragment: residues 21-280. Agglutinin-1 b chain. Chain: b. Fragment: residues 281-547
Source: Abrus precatorius. Indian licorice. Organism_taxid: 3816. Organism_taxid: 3816
Resolution:
3.50Å     R-factor:   0.201     R-free:   0.255
Authors: A.Bagaria,K.Surendranath,U.A.Ramagopal,S.Ramakumar,A.A.Karan
Key ref:
A.Bagaria et al. (2006). Structure-function analysis and insights into the reduced toxicity of Abrus precatorius agglutinin I in relation to abrin. J Biol Chem, 281, 34465-34474. PubMed id: 16772301 DOI: 10.1074/jbc.M601777200
Date:
30-May-07     Release date:   26-Jun-07    
Supersedes: 2amz
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9M6E9  (AGGL_ABRPR) -  Agglutinin-1
Seq:
Struc:
 
Seq:
Struc:
547 a.a.
247 a.a.
Protein chain
Pfam   ArchSchema ?
Q9M6E9  (AGGL_ABRPR) -  Agglutinin-1
Seq:
Struc:
 
Seq:
Struc:
547 a.a.
261 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.3.2.2.22  - rRNA N-glycosylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     negative regulation of translation   1 term 
  Biochemical function     rRNA N-glycosylase activity     1 term  

 

 
DOI no: 10.1074/jbc.M601777200 J Biol Chem 281:34465-34474 (2006)
PubMed id: 16772301  
 
 
Structure-function analysis and insights into the reduced toxicity of Abrus precatorius agglutinin I in relation to abrin.
A.Bagaria, K.Surendranath, U.A.Ramagopal, S.Ramakumar, A.A.Karande.
 
  ABSTRACT  
 
Abrin and agglutinin-I from the seeds of Abrus precatorius are type II ribosome-inactivating proteins that inhibit protein synthesis in eukaryotic cells. The two toxins share a high degree of sequence similarity; however, agglutinin-I is weaker in its activity. We compared the kinetics of protein synthesis inhibition by abrin and agglutinin-I in two different cell lines and found that approximately 200-2000-fold higher concentration of agglutinin-I is needed for the same degree of inhibition. Like abrin, agglutinin-I also induced apoptosis in the cells by triggering the intrinsic mitochondrial pathway, although at higher concentrations as compared with abrin. The reason for the decreased toxicity of agglutinin-I became apparent on the analysis of the crystal structure of agglutinin-I obtained by us in comparison with that of the reported structure of abrin. The overall protein folding of agglutinin-I is similar to that of abrin-a with a single disulfide bond holding the toxic A subunit and the lectin-like B-subunit together, constituting a heterodimer. However, there are significant differences in the secondary structural elements, mostly in the A chain. The substitution of Asn-200 in abrin-a with Pro-199 in agglutinin-I seems to be a major cause for the decreased toxicity of agglutinin-I. This perhaps is not a consequence of any kink formation by a proline residue in the helical segment, as reported by others earlier, but due to fewer interactions that proline can possibly have with the bound substrate.
 
  Selected figure(s)  
 
Figure 9.
FIGURE 9. 2F[o] - F[c] omit maps around the Pro-199, Tyr-73, and Tyr-112 residues (contoured at 1 ) are shown here.
Figure 10.
FIGURE 10. A view down the crystallographic 2-fold axis of the APA-I heterotetramer (A-B heterodimer). The schematic representation shows the interacting A and A' subunits of two A-B dimer, and the arrow shows the putative tetramerization interface. The three arginine residues, namely Arg-125, Arg-134, and Arg-181, are shown by ball and stick, and the corresponding symmetry related residues have been omitted for clarity. The disulfide bonds linking chain A and chain B are shown by ball and stick model. The active site cleft is away from the tetramerization interface.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 34465-34474) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20433687 J.Cheng, T.H.Lu, C.L.Liu, and J.Y.Lin (2010).
A biophysical elucidation for less toxicity of agglutinin than abrin-a from the seeds of Abrus precatorius in consequence of crystal structure.
  J Biomed Sci, 17, 34.
PDB code: 2zr1
19768210 D.Pauly, S.Kirchner, B.Stoermann, T.Schreiber, S.Kaulfuss, R.Schade, R.Zbinden, M.A.Avondet, M.B.Dorner, and B.G.Dorner (2009).
Simultaneous quantification of five bacterial and plant toxins from complex matrices using a multiplexed fluorescent magnetic suspension assay.
  Analyst, 134, 2028-2039.  
18798567 L.Maveyraud, H.Niwa, V.Guillet, D.I.Svergun, P.V.Konarev, R.A.Palmer, W.J.Peumans, P.Rougé, E.J.Van Damme, C.D.Reynolds, and L.Mourey (2009).
Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra.
  Proteins, 75, 89.
PDB codes: 3c9z 3ca0 3ca1 3ca3 3ca4 3ca5 3ca6 3cah
18955274 V.Ramnath, P.S.Rekha, G.Kuttan, and R.Kuttan (2009).
Regulation of Caspase-3 and Bcl-2 Expression in Dalton's Lymphoma Ascites Cells by Abrin.
  Evid Based Complement Alternat Med, 6, 233-238.  
18353919 K.Surendranath, and A.A.Karande (2008).
A neutralizing antibody to the a chain of abrin inhibits abrin toxicity both in vitro and in vivo.
  Clin Vaccine Immunol, 15, 737-743.  
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 code is shown on the right.