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PDBsum entry 1m2t

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protein ligands Protein-protein interface(s) links
Ribosome inhibitor, hydrolase PDB id
1m2t
Jmol
Contents
Protein chains
248 a.a. *
262 a.a. *
Ligands
NAG ×6
FUC ×2
ADE
GOL ×8
Waters ×503
* Residue conservation analysis
PDB id:
1m2t
Name: Ribosome inhibitor, hydrolase
Title: Mistletoe lectin i from viscum album in complex with adenine monophosphate. Crystal structure at 1.9 a resolution
Structure: Mistletoe lectin i a chain. Chain: a. Synonym: beta-galactoside specific lectin i a chain. Mla. M rrna n-glycosidase. Mistletoe lectin i b chain. Chain: b. Synonym: lectin chain a isoform 1
Source: Viscum album. European mistletoe. Organism_taxid: 3972. Organ: leaf. Organ: leaf
Biol. unit: Dimer (from PQS)
Resolution:
1.89Å     R-factor:   0.210     R-free:   0.240
Authors: R.Krauspenhaar,W.Rypniewski,N.Kalkura,K.Moore,L.Delucas,S.St A.Mikhailov,W.Voelter,C.Betzel
Key ref:
R.Krauspenhaar et al. (2002). Crystallisation under microgravity of mistletoe lectin I from Viscum album with adenine monophosphate and the crystal structure at 1.9 A resolution. Acta Crystallogr D Biol Crystallogr, 58, 1704-1707. PubMed id: 12351890 DOI: 10.1107/S0907444902014270
Date:
25-Jun-02     Release date:   24-Jun-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P81446  (ML1_VISAL) -  Beta-galactoside-specific lectin 1
Seq:
Struc:
 
Seq:
Struc:
564 a.a.
248 a.a.*
Protein chain
Pfam   ArchSchema ?
P81446  (ML1_VISAL) -  Beta-galactoside-specific lectin 1
Seq:
Struc:
 
Seq:
Struc:
564 a.a.
262 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 50 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: 10.1107/S0907444902014270 Acta Crystallogr D Biol Crystallogr 58:1704-1707 (2002)
PubMed id: 12351890  
 
 
Crystallisation under microgravity of mistletoe lectin I from Viscum album with adenine monophosphate and the crystal structure at 1.9 A resolution.
R.Krauspenhaar, W.Rypniewski, N.Kalkura, K.Moore, L.DeLucas, S.Stoeva, A.Mikhailov, W.Voelter, C.h.Betzel.
 
  ABSTRACT  
 
The crystal structure of the ribosome-inactivating protein (RIP) mistletoe lectin I (ML-I) from Viscum album in complex with adenine has been refined to 1.9 A resolution. High quality crystals of the ML-I complex were obtained by the method of vapour diffusion using the high density protein crystal growth system (HDPCG) on the international space station, mission ISS 6A. Hexagonal crystals were grown during three months under microgravity conditions. Diffraction data to 1.9A were collected applying synchrotron radiation and cryo- techniques. The structure was refined subsequently to analyse the structure of ML-I and particularly the active site conformation, complexed by adenine that mimics the RNA substrate binding.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Cartoon plot of ML­I. The three domains of the A­chain are labeled I, II & III and coloured orange, green and turquoise. The helices of the secondary structure are labeled with capital letters, b­sheets in lowercase. For the B­ chain the domains I and II are coloured according to their subdomains: The linker region l1 and l2 are shown in orange, the homologous subdomains a, b, g are numbered in ascending order and coloured yellow, green and blue. The disulphide bond connecting the two chains is shown as dashed line. Dashed red circles indicate the active site region AZ at the A chain and the galactose­binding sites G1 and G2 in the B chain. The N and C terminus are indicated with N and "C".
Figure 3.
Figure 3 Stereo view of the active site of ML­I in native conformation as well in complex with adenine. Native ML­I is shown in yellow and with bound adenine in blue. Hydrogen bonds and water molecules are coloured according to the residues. The catalytic key residues for the N­glycosidase activity are: Tyr76A, Tyr115A, Glu177A and Arg168A.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 1704-1707) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
  16820678 M.E.Fraser, M.M.Cherney, P.Marcato, G.L.Mulvey, G.D.Armstrong, and M.N.James (2006).
Binding of adenine to Stx2, the protein toxin from Escherichia coli O157:H7.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 627-630.
PDB code: 2ga4
  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
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
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.