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PDBsum entry 1pc8

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1pc8
Jmol
Contents
Protein chains
240 a.a. *
255 a.a. *
Ligands
NAG
NDG-NAG
NAG-NAG-BMA
NAG-NAG
Waters ×13
* Residue conservation analysis
PDB id:
1pc8
Name: Hydrolase
Title: Crystal structure of a novel form of mistletoe lectin from h viscum album l. At 3.8a resolution
Structure: Himalayan mistletoe ribosome-inactivating protein chain: a. Synonym: mistletoe lectin. Himalayan mistletoe ribosome-inactivating protein chain: b. Synonym: mistletoe lectin. Ec: 3.2.2.22
Source: Viscum album. European mistletoe. Organism_taxid: 3972. Strain: himalayan v.Album. Strain: himalayan v.Album
Biol. unit: Dimer (from PQS)
Resolution:
3.80Å     R-factor:   0.231     R-free:   0.271
Authors: V.Mishra,A.S.Ethayathulla,M.Paramasivam,G.Singh,S.Yadav,P.Ka R.S.Sharma,C.R.Babu,T.P.Singh
Key ref:
V.Mishra et al. (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. PubMed id: 15583377 DOI: 10.1107/S0907444904023534
Date:
16-May-03     Release date:   22-Jun-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q6ITZ3  (ML4_VISAL) -  Beta-galactoside-specific lectin 4
Seq:
Struc:
 
Seq:
Struc:
520 a.a.
240 a.a.
Protein chain
Pfam   ArchSchema ?
Q6ITZ3  (ML4_VISAL) -  Beta-galactoside-specific lectin 4
Seq:
Struc:
 
Seq:
Struc:
520 a.a.
255 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: 10.1107/S0907444904023534 Acta Crystallogr D Biol Crystallogr 60:2295-2304 (2004)
PubMed id: 15583377  
 
 
Structure of a novel ribosome-inactivating protein from a hemi-parasitic plant inhabiting the northwestern Himalayas.
V.Mishra, A.S.Ethayathulla, R.S.Sharma, S.Yadav, R.Krauspenhaar, C.Betzel, C.R.Babu, T.P.Singh.
 
  ABSTRACT  
 
This is the first report of the structural studies of a novel ribosome-inactivating protein (RIP) obtained from the Himalayan mistletoe (Viscum album) (HmRip). HmRip is a type II heterodimeric protein consisting of a toxic enzyme (A-chain) with an active site for ribosome inactivation and a lectin subunit (B-chain) with well defined sugar-binding sites. The crystal structure of HmRip has been determined at 3.8 A resolution and refined to a crystallographic R factor of 0.228 (R(free) = 0.271). A comparison of this structure with other type II RIPs reveals the presence of distinct structural features in the active site of the A-chain and in the 2gamma sugar-binding site of the B-chain. The conformation of the side chain of Tyr110, which is a conserved active-site residue in the A subunit, is strikingly different from those observed in other mistletoe RIPs, indicating its unique substrate-binding preference. The deletion of two important residues from the kink region after Ala231 in the 2gamma subdomain of the B-chain results in a significantly different conformation of the sugar-binding pocket. A ribosome-recognition site has also been identified in HmRip. The site is a shallow cavity, with the conserved residues Arg51, Asp70, Thr72 and Asn73 involved in the binding. The conformations of the antigenic epitopes of residues 1-20, 85-103 and 206-223 differ from those observed in other type II RIPs, resulting in the distinct antigenicity and pharmacological properties of HmRip.
 
  Selected figure(s)  
 
Figure 5.
Figure 5 Overall fold of the B-chain (yellow) showing the location of the 2 [gamma] sugar-binding site (red) in the B2 domain and the 1 [alpha] sugar-binding site (blue) in the B1 domain. The sugar-binding residues are also shown as a ball-and-stick model. The figure was drawn with MOLSCRIPT (Merritt & Murphy, 1994 [Merritt, E. A. & Murphy, M. E. P. (1994). Acta Cryst. D50, 869-873.]-[bluearr.gif] ) and RASTER3D (Kraulis, 1991 [Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]-[bluearr.gif] ).
Figure 8.
Figure 8 The ribosome-recognition site has its roof represented by the highly antigenic peptide (red). The ribosome-binding residues are shown as a ball-and-stick model. (b) GRASP (Nicholls et al., 1991 [Nicholls, A., Sharp, K. & Honig, B. (1991). Proteins, 11, 281-296.]-[bluearr.gif] ) figure showing a shallow cavity representing the ribosome-recognition site and a well defined cleft corresponding to the N-glycosidase activity site, connected by a shallow channel. The ribosome-binding residues are shown in cyan and key active-site residues are shown in yellow. (c) Superposition of the C^ [alpha] traces of HmRip (yellow), ML-I (pink) and ricin (blue), showing the highly variable nature of the antigenic peptide that results in different architectures of the ribosome-recognition sites.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 2295-2304) copyright 2004.  
  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.  
18316789 A.Savidor, R.S.Donahoo, O.Hurtado-Gonzales, M.L.Land, M.B.Shah, K.H.Lamour, and W.H.McDonald (2008).
Cross-species global proteomics reveals conserved and unique processes in Phytophthora sojae and Phytophthora ramorum.
  Mol Cell Proteomics, 7, 1501-1516.  
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
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
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.