PDBsum entry 1hwp

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Hydrolase PDB id
Protein chains
252 a.a. *
263 a.a. *
Waters ×20
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Ebulin complexed with pteroic acid, trigonal crystal form
Structure: Ebulin. Chain: a. Synonym: ebulin a chain. Other_details: n-glycosidase. Ebulin. Chain: b. Synonym: ebulin b chain. Other_details: galactoside specific lectin
Source: Sambucus ebulus. Organism_taxid: 28503. Tissue: leaf. Tissue: leaf
Biol. unit: Tetramer (from PQS)
3.10Å     R-factor:   0.219     R-free:   0.317
Authors: J.M.Pascal,P.J.Day,A.F.Monzingo,S.R.Ernst,J.D.Robertus
Key ref:
J.M.Pascal et al. (2001). 2.8-A crystal structure of a nontoxic type-II ribosome-inactivating protein, ebulin l. Proteins, 43, 319-326. PubMed id: 11288182 DOI: 10.1002/prot.1043
09-Jan-01     Release date:   24-Jan-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9AVR2  (Q9AVR2_SAMEB) -  rRNA N-glycosidase
564 a.a.
252 a.a.
Protein chain
Pfam   ArchSchema ?
Q9AVR2  (Q9AVR2_SAMEB) -  rRNA N-glycosidase
564 a.a.
263 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.  - 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: 10.1002/prot.1043 Proteins 43:319-326 (2001)
PubMed id: 11288182  
2.8-A crystal structure of a nontoxic type-II ribosome-inactivating protein, ebulin l.
J.M.Pascal, P.J.Day, A.F.Monzingo, S.R.Ernst, J.D.Robertus, R.Iglesias, Y.Pérez, J.M.Férreras, L.Citores, T.Girbés.
Ebulin l is a type-II ribosome-inactivating protein (RIP) isolated from the leaves of Sambucus ebulus L. As with other type-II RIP, ebulin is a disulfide-linked heterodimer composed of a toxic A chain and a galactoside-specific lectin B chain. A normal level of ribosome-inactivating N-glycosidase activity, characteristic of the A chain of type-II RIP, has been demonstrated for ebulin l. However, ebulin is considered a nontoxic type-II RIP due to a reduced cytotoxicity on whole cells and animals as compared with other toxic type-II RIP like ricin. The molecular cloning, amino acid sequence, and the crystal structure of ebulin l are presented and compared with ricin. Ebulin l is shown to bind an A-chain substrate analogue, pteroic acid, in the same manner as ricin. The galactoside-binding ability of ebulin l is demonstrated crystallographically with a complex of the B chain with galactose and with lactose. The negligible cytotoxicity of ebulin l is apparently due to a reduced affinity for galactosides. An altered mode of galactoside binding in the 2gamma subdomain of the lectin B chain primarily causes the reduced affinity.
  Selected figure(s)  
Figure 2.
Figure 2. Section of the 2.8-Å electron density for the trigonal model. A 2Fo-Fc map with sigmaA-weighted phases. The map is contoured at 1.3 .
Figure 7.
Figure 7. Comparison of the galactoside-binding, 2 subdomains of ebulin (top) and ricin (bottom). Galactose is bound to ebulin. Lactose is bound to ricin. In both pictures, the galactose moiety is numbered at significant carbons of the sugar ring. All contacts with lactose in ricin are made with the galactose moiety. The glucose moiety (GLC) extends into the solvent. The GLC extension ( -1,4 linkage) from the C1 hydroxyl of the galactose moiety in ricin is not possible for the C1 hydroxyl of galactose in ebulin, because of steric interference with 254 N.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2001, 43, 319-326) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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
19056784 M.L.DeMarco, and R.J.Woods (2009).
Atomic-resolution conformational analysis of the GM3 ganglioside in a lipid bilayer and its implications for ganglioside-protein recognition at membrane surfaces.
  Glycobiology, 19, 344-355.  
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
16122386 B.Pils, R.R.Copley, and J.Schultz (2005).
Variation in structural location and amino acid conservation of functional sites in protein domain families.
  BMC Bioinformatics, 6, 210.  
  16508080 R.Mikeska, R.Wacker, R.Arni, T.P.Singh, A.Mikhailov, A.Gabdoulkhakov, W.Voelter, and C.Betzel (2005).
Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 17-25.
PDB codes: 1pum 1puu
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
14686924 A.Chambery, A.Di Maro, M.M.Monti, F.Stirpe, and A.Parente (2004).
Volkensin from Adenia volkensii Harms (kilyambiti plant), a type 2 ribosome-inactivating protein.
  Eur J Biochem, 271, 108-117.  
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
12467648 F.J.Arias, P.Antolín, Torre, B.Barriuso, R.Iglesias, M.A.Rojo, J.M.Ferreras, E.Benvenuto, E.Méndez, and T.Girbés (2003).
Musarmins: three single-chain ribosome-inactivating protein isoforms from bulbs of Muscari armeniacum L. and Miller.
  Int J Biochem Cell Biol, 35, 61-78.  
12565707 F.J.Hou, H.Xu, and W.Y.Liu (2003).
Simultaneous existence of cinnamomin (a type II RIP) and small amount of its free A- and B-chain in mature seeds of camphor tree.
  Int J Biochem Cell Biol, 35, 455-464.  
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.  
11836254 R.P.Kruger, H.C.Winter, N.Simonson-Leff, J.A.Stuckey, I.J.Goldstein, and J.E.Dixon (2002).
Cloning, expression, and characterization of the Galalpha 1,3Gal high affinity lectin from the mushroom Marasmius oreades.
  J Biol Chem, 277, 15002-15005.  
11785761 Y.Bourne, and B.Henrissat (2001).
Glycoside hydrolases and glycosyltransferases: families and functional modules.
  Curr Opin Struct Biol, 11, 593-600.  
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.