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PDBsum entry 1abr

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protein ligands Protein-protein interface(s) links
Glycosidase/carbohydrate PDB id
1abr
Jmol
Contents
Protein chains
251 a.a. *
267 a.a. *
Ligands
NDG-NGZ-MAN-MAN-
BMA
NDG-NDG-BGC-MAN-
BMA
Waters ×600
* Residue conservation analysis
PDB id:
1abr
Name: Glycosidase/carbohydrate
Title: Crystal structure of abrin-a
Structure: Abrin-a. Chain: a. Engineered: yes. Abrin-a. Chain: b. Engineered: yes
Source: Abrus precatorius. Indian licorice. Organism_taxid: 3816.
Biol. unit: Dimer (from PQS)
Resolution:
2.14Å     R-factor:   0.189    
Authors: T.H.Tahirov,T.-H.Lu,Y.-C.Liaw,S.-C.Chu,J.-Y.Lin
Key ref:
T.H.Tahirov et al. (1995). Crystal structure of abrin-a at 2.14 A. J Mol Biol, 250, 354-367. PubMed id: 7608980 DOI: 10.1006/jmbi.1995.0382
Date:
11-Nov-94     Release date:   07-Feb-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11140  (ABRA_ABRPR) -  Abrin-a
Seq:
Struc:
 
Seq:
Struc:
528 a.a.
251 a.a.*
Protein chain
Pfam   ArchSchema ?
P11140  (ABRA_ABRPR) -  Abrin-a
Seq:
Struc:
 
Seq:
Struc:
528 a.a.
267 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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: 10.1006/jmbi.1995.0382 J Mol Biol 250:354-367 (1995)
PubMed id: 7608980  
 
 
Crystal structure of abrin-a at 2.14 A.
T.H.Tahirov, T.H.Lu, Y.C.Liaw, Y.L.Chen, J.Y.Lin.
 
  ABSTRACT  
 
The crystal structure of abrin-a, a type II ribosome-inactivating protein from the seeds of Abrus precatorius, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of ricin. The structure has been refined at 2.14 A to a R-factor of 18.9%. The root-mean-square deviations of bond lengths and angles from the standard values are 0.013 A and 1.82 degrees, respectively. The overall protein folding is similar to that of ricin, but there are differences in the secondary structure, mostly of the A-chain. Several parts of the molecular surface differ significantly; some of them are quite near the active site cleft, and probably influence ribosome recognition. The positions of invariant active site residues remain the same, except the position of Tyr74. Two water molecules of hydrogen-bonded active site residues have been located in the active site cleft. Both of them may be responsible for hydrolyzing the N-C glycosidic bond. The current abrin-a structure is lactose free; this is probably essential for abrin-a crystallization. The B-chain is a glycoprotein, and the positions of several sugar residues of two sugar chains linked to earlier predicted glycosylation sites were determined. One of the sugar chains is a bridge between two neighboring molecules, since one of its mannose residues is connected to the galactose binding site of the neighboring molecule. Another sugar chain covers the surface of the B-chain.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. The electron density of the first sugar chain using the (Fo - Fc ) omit map contoured at 2.5 s.
Figure 9.
Figure 9. Ramachandranplot of abrin-a. All residues of the A- and B-chains are included. The glycine residues are shown as triangles. The percentage of residues with (f, 8) conformational angles in the most favoured regions (A, B, L) is 86.0%. In additional allowed regions (0a, 0b, 0l, 0p) this percentage is 13.3%, and in the generously allowed regions (a,b,l,p) it is 0.7%. Proline, glycine and the end residues are excluded from percentage calculations. In the generously allowed regions, the labelled residues Asp35 belong to the A-chain, and Val2 and Ser5 belong to the B-chain.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1995, 250, 354-367) copyright 1995.  
  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
19214704 R.Liu, W.Jiang, and Y.Zhou (2010).
Identifying protein-protein interaction sites in transient complexes with temperature factor, sequence profile and accessible surface area.
  Amino Acids, 38, 263-270.  
19292877 H.Hemmi, A.Kuno, S.Ito, R.Suzuki, T.Hasegawa, and J.Hirabayashi (2009).
NMR studies on the interaction of sugars with the C-terminal domain of an R-type lectin from the earthworm Lumbricus terrestris.
  FEBS J, 276, 2095-2105.  
19100814 J.Pohleven, N.Obermajer, J.Sabotic, S.Anzlovar, K.Sepcińá, J.Kos, B.Kralj, B.Strukelj, and J.Brzin (2009).
Purification, characterization and cloning of a ricin B-like lectin from mushroom Clitocybe nebularis with antiproliferative activity against human leukemic T cells.
  Biochim Biophys Acta, 1790, 173-181.  
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
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.  
18215161 P.V.Castilho, L.S.Goto, L.M.Roberts, and A.P.Araújo (2008).
Isolation and characterization of four type 2 ribosome inactivating pulchellin isoforms from Abrus pulchellus seeds.
  FEBS J, 275, 948-959.  
17404804 T.Wang, Y.S.Zou, D.W.Zhu, A.Azzi, W.Y.Liu, and S.X.Lin (2008).
Cinnamomin: separation, crystallization and preliminary X-ray diffraction study.
  Amino Acids, 34, 239-243.  
17470286 X.Hou, M.Chen, L.Chen, E.J.Meehan, J.Xie, and M.Huang (2007).
X-ray sequence and crystal structure of luffaculin 1, a novel type 1 ribosome-inactivating protein.
  BMC Struct Biol, 7, 29.
PDB code: 2oqa
16772301 A.Bagaria, K.Surendranath, U.A.Ramagopal, S.Ramakumar, and A.A.Karande (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.
PDB codes: 2amz 2q3n
15906321 A.J.Bordner, and R.Abagyan (2005).
Statistical analysis and prediction of protein-protein interfaces.
  Proteins, 60, 353-366.  
15720394 A.L.Silva, L.S.Goto, A.R.Dinarte, D.Hansen, R.A.Moreira, L.M.Beltramini, and A.P.Araújo (2005).
Pulchellin, a highly toxic type 2 ribosome-inactivating protein from Abrus pulchellus. Cloning heterologous expression of A-chain and structural studies.
  FEBS J, 272, 1201-1210.  
15687495 J.M.Mancheño, H.Tateno, I.J.Goldstein, M.Martínez-Ripoll, and J.A.Hermoso (2005).
Structural analysis of the Laetiporus sulphureus hemolytic pore-forming lectin in complex with sugars.
  J Biol Chem, 280, 17251-17259.
PDB codes: 1w3a 1w3f 1w3g
15774467 V.Mishra, S.Bilgrami, R.S.Sharma, P.Kaur, S.Yadav, R.Krauspenhaar, C.Betzel, W.Voelter, C.R.Babu, and T.P.Singh (2005).
Crystal structure of himalayan mistletoe ribosome-inactivating protein reveals the presence of a natural inhibitor and a new functionally active sugar-binding site.
  J Biol Chem, 280, 20712-20721.
PDB code: 1yf8
16227292 X.Shi, K.Brauburger, and R.M.Elliott (2005).
Role of N-linked glycans on bunyamwera virus glycoproteins in intracellular trafficking, protein folding, and virus infectivity.
  J Virol, 79, 13725-13734.  
15182350 A.G.Kourmanova, O.J.Soudarkina, S.Olsnes, and J.V.Kozlov (2004).
Cloning and characterization of the genes encoding toxic lectins in mistletoe (Viscum album L).
  Eur J Biochem, 271, 2350-2360.  
15756471 H.Hemmi, A.Kuno, S.Ito, R.Suzuki, S.Kaneko, T.Hasegawa, J.Hirabayashi, and K.Kasai (2004).
(1)H, (13)C, and (15)N chemical shift assignment of the C-terminal 15 kDa domain of a novel galactose-binding protein from the earthworm Lumbricus terrestris.
  J Biomol NMR, 30, 377-378.  
15382229 M.J.Bernett, T.Somasundaram, and M.Blaber (2004).
An atomic resolution structure for human fibroblast growth factor 1.
  Proteins, 57, 626-634.
PDB code: 1rg8
15388944 R.Suzuki, Z.Fujimoto, A.Kuno, J.Hirabayashi, K.Kasai, and T.Hasegawa (2004).
Crystallization and preliminary X-ray crystallographic studies of the C-terminal domain of galactose-binding lectin EW29 from the earthworm Lumbricus terrestris.
  Acta Crystallogr D Biol Crystallogr, 60, 1895-1896.  
15194688 T.Uchida, T.Yamasaki, S.Eto, H.Sugawara, G.Kurisu, A.Nakagawa, M.Kusunoki, and T.Hatakeyama (2004).
Crystal structure of the hemolytic lectin CEL-III isolated from the marine invertebrate Cucumaria echinata: implications of domain structure for its membrane pore-formation mechanism.
  J Biol Chem, 279, 37133-37141.
PDB code: 1vcl
15583377 V.Mishra, A.S.Ethayathulla, R.S.Sharma, S.Yadav, R.Krauspenhaar, C.Betzel, C.R.Babu, and T.P.Singh (2004).
Structure of a novel ribosome-inactivating protein from a hemi-parasitic plant inhabiting the northwestern Himalayas.
  Acta Crystallogr D Biol Crystallogr, 60, 2295-2304.
PDB code: 1pc8
12823544 H.Niwa, A.G.Tonevitsky, I.I.Agapov, S.Saward, U.Pfüller, and R.A.Palmer (2003).
Crystal structure at 3 A of mistletoe lectin I, a dimeric type-II ribosome-inactivating protein, complexed with galactose.
  Eur J Biochem, 270, 2739-2749.
PDB code: 1oql
12611897 J.Morlon-Guyot, M.Helmy, S.Lombard-Frasca, D.Pignol, G.Piéroni, and B.Beaumelle (2003).
Identification of the ricin lipase site and implication in cytotoxicity.
  J Biol Chem, 278, 17006-17011.  
14627732 S.R.Brych, J.Kim, T.M.Logan, and M.Blaber (2003).
Accommodation of a highly symmetric core within a symmetric protein superfold.
  Protein Sci, 12, 2704-2718.
PDB codes: 1jy0 1m16 1nzk 1p63
12364335 M.Tenno, A.Saeki, F.J.Kézdy, A.P.Elhammer, and A.Kurosaka (2002).
The lectin domain of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 1 is involved in O-glycosylation of a polypeptide with multiple acceptor sites.
  J Biol Chem, 277, 47088-47096.  
11722556 L.Xie, B.Z.Wang, R.G.Hu, H.B.Ji, L.Zhang, and W.Y.Liu (2001).
Structural and functional studies of cinnamomin, a new type II ribosome-inactivating protein isolated from the seeds of the camphor tree.
  Eur J Biochem, 268, 5723-5733.  
11375527 N.Manoj, A.A.Jeyaprakash, J.V.Pratap, S.S.Komath, R.Kenoth, M.J.Swamy, and M.Vijayan (2001).
Crystallization and preliminary X-ray studies of snake gourd lectin: homology with type II ribosome-inactivating proteins.
  Acta Crystallogr D Biol Crystallogr, 57, 912-914.  
11714927 S.R.Brych, S.I.Blaber, T.M.Logan, and M.Blaber (2001).
Structure and stability effects of mutations designed to increase the primary sequence symmetry within the core region of a beta-trefoil.
  Protein Sci, 10, 2587-2599.
PDB codes: 1jqz 1jt3 1jt4 1jt5 1jt7 1jtc
10636890 C.L.Liu, C.C.Tsai, S.C.Lin, L.I.Wang, C.I.Hsu, M.J.Hwang, and J.Y.Lin (2000).
Primary structure and function analysis of the Abrus precatorius agglutinin A chain by site-directed mutagenesis. Pro(199) Of amphiphilic alpha-helix H impairs protein synthesis inhibitory activity.
  J Biol Chem, 275, 1897-1901.  
10930837 K.Panneerselvam, S.C.Lin, C.L.Liu, Y.C.Liaw, J.Y.Lin, and T.H.Lu (2000).
Crystallization of agglutinin from the seeds of Abrus precatorius.
  Acta Crystallogr D Biol Crystallogr, 56, 898-899.  
10944358 M.Li, Y.P.Wang, J.J.Chai, K.Y.Wang, and R.C.Bi (2000).
Molecular-replacement studies of Trichosanthes kirilowii lectin 1: a structure belonging to the family of type 2 ribosome-inactivating proteins.
  Acta Crystallogr D Biol Crystallogr, 56, 1073-1075.  
10328267 J.K.Dattagupta, A.Podder, C.Chakrabarti, U.Sen, D.Mukhopadhyay, S.K.Dutta, and M.Singh (1999).
Refined crystal structure (2.3 A) of a double-headed winged bean alpha-chymotrypsin inhibitor and location of its second reactive site.
  Proteins, 35, 321-331.
PDB code: 2wbc
10095769 M.de Sousa, L.M.Roberts, and J.M.Lord (1999).
Restoration of lectin activity to an inactive abrin B chain by substitution and mutation of the 2 gamma subdomain.
  Eur J Biochem, 260, 355-361.  
9345620 C.S.Wright (1997).
New folds of plant lectins.
  Curr Opin Struct Biol, 7, 631-636.  
  8844840 B.Hazes (1996).
The (QxW)3 domain: a flexible lectin scaffold.
  Protein Sci, 5, 1490-1501.  
8768899 D.F.Wyss, and G.Wagner (1996).
The structural role of sugars in glycoproteins.
  Curr Opin Biotechnol, 7, 409-416.  
8856055 S.H.Lin, L.P.Chow, Y.L.Chen, Y.C.Liaw, J.K.Chen, and J.Y.Lin (1996).
Probing the domain structure of abrin-a by tryptic digestion.
  Eur J Biochem, 240, 564-569.  
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.