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PDBsum entry 2mll

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protein ligands Protein-protein interface(s) links
Ribosome PDB id
2mll
Jmol
Contents
Protein chains
241 a.a. *
255 a.a. *
Ligands
NAG ×3
Waters ×215
* Residue conservation analysis
PDB id:
2mll
Name: Ribosome
Title: Mistletoe lectin i from viscum album
Structure: Protein (ribosome-inactivating protein type ii). Chain: a. Protein (ribosome-inactivating protein type ii). Chain: b
Source: Viscum album. European mistletoe. Organism_taxid: 3972. Organism_taxid: 3972
Biol. unit: Tetramer (from PQS)
Resolution:
2.70Å     R-factor:   0.251     R-free:   0.319
Authors: R.Krauspenhaar,S.Eschenburg,M.Perbandt,V.Kornilov,N.Konareva I.Mikailova,S.Stoeva,R.Wacker,T.Maier,T.P.Singh,A.Mikhailov W.Voelter,C.Betzel
Key ref: R.Krauspenhaar et al. (1999). Crystal structure of mistletoe lectin I from Viscum album. Biochem Biophys Res Commun, 257, 418-424. PubMed id: 10198229 DOI: 10.1006/bbrc.1999.0470
Date:
16-Mar-99     Release date:   20-Mar-00    
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.
241 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
* PDB and UniProt seqs differ at 46 residue positions (black crosses)

 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/bbrc.1999.0470 Biochem Biophys Res Commun 257:418-424 (1999)
PubMed id: 10198229  
 
 
Crystal structure of mistletoe lectin I from Viscum album.
R.Krauspenhaar, S.Eschenburg, M.Perbandt, V.Kornilov, N.Konareva, I.Mikailova, S.Stoeva, R.Wacker, T.Maier, T.Singh, A.Mikhailov, W.Voelter, C.Betzel.
 
  ABSTRACT  
 
The crystal structure of the ribosome-inactivating protein (RIP) mistletoe lectin I (ML-I) from Viscum album has been solved by molecular replacement techniques. The structure has been refined to a crystallographic R-factor of 24.5% using X-ray diffraction data to 2.8 A resolution. The heterodimeric 63-kDa protein consists of a toxic A subunit which exhibits RNA-glycosidase activity and a galactose-specific lectin B subunit. The overall protein fold is similar to that of ricin from Ricinus communis; however, unlike ricin, ML-I is already medically applied as a component of a commercially available misteltoe extract with immunostimulating potency and for the treatment of human cancer. The three-dimensional structure reported here revealed structural details of this pharmaceutically important protein. The comparison to the structure of ricin gives more insights into the functional mechanism of this protein, provides structural details for further protein engineering studies, and may lead to the development of more effective therapeutic RIPs.
 

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.  
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.  
19111067 R.R.Thangudu, M.Manoharan, N.Srinivasan, F.Cadet, R.Sowdhamini, and B.Offmann (2008).
Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families.
  BMC Struct Biol, 8, 55.  
16183566 E.G.De Mejía, and V.I.Prisecaru (2005).
Lectins as bioactive plant proteins: a potential in cancer treatment.
  Crit Rev Food Sci Nutr, 45, 425-445.  
15562516 N.Rekha, S.M.Machado, C.Narayanan, A.Krupa, and N.Srinivasan (2005).
Interaction interfaces of protein domains are not topologically equivalent across families within superfamilies: Implications for metabolic and signaling pathways.
  Proteins, 58, 339-353.  
  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
15635663 R.Wacker, S.Stoeva, C.Betzel, and W.Voelter (2005).
Complete structure determination of N-acetyl-D-galactosamine-binding mistletoe lectin-3 from Viscum album L. album.
  J Pept Sci, 11, 289-302.  
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
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.  
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
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.  
10479774 E.M.Williamson (1999).
Selected bibliography
  Phytother Res, 13, 545-548.  
10504411 J.Eck, M.Langer, B.Möckel, K.Witthohn, H.Zinke, and H.Lentzen (1999).
Characterization of recombinant and plant-derived mistletoe lectin and their B-chains.
  Eur J Biochem, 265, 788-797.  
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.