spacer
spacer
Go to PDB code: 
protein links
Hydrolase PDB id
1ift
Jmol
Contents
Protein chain
258 a.a. *
Waters ×100
* Residue conservation analysis
PDB id:
1ift
Name: Hydrolase
Title: Ricin a-chain (recombinant)
Structure: Ricin. Chain: a. Fragment: a chain. Engineered: yes. Mutation: yes
Source: Ricinus communis. Castor bean. Organism_taxid: 3988
Resolution:
1.80Å     R-factor:   0.216    
Authors: S.A.Weston,A.D.Tucker,D.R.Thatcher,D.J.Derbyshire, R.A.Pauptit
Key ref: S.A.Weston et al. (1994). X-ray structure of recombinant ricin A-chain at 1.8 A resolution. J Mol Biol, 244, 410-422. PubMed id: 7990130 DOI: 10.1006/jmbi.1994.1739
Date:
05-Jul-96     Release date:   14-Jan-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02879  (RICI_RICCO) -  Ricin
Seq:
Struc: 		 
Seq:
Struc: 		576 a.a.
258 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: 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.1994.1739 J Mol Biol 244:410-422 (1994)
PubMed id: 7990130  
 
 
X-ray structure of recombinant ricin A-chain at 1.8 A resolution.
S.A.Weston, A.D.Tucker, D.R.Thatcher, D.J.Derbyshire, R.A.Pauptit.
 
  ABSTRACT  
 
Ricin is a potent plant toxin which acts by removing a specific adenine residue from the ribosome. The X-ray crystal structure of a new, tetragonal crystal form of the recombinant ricin A-chain diffracting to 1.8 A resolution has been determined via molecular replacement methods and refined to a crystallographic R-factor of 18.6%. The higher resolution electron density allowed improvements to be made upon previously published models, resulting in an increase in the assigned secondary structure of the protein. The enzyme adopts the same global conformation in this crystal form with differences in detail due only partly to crystal packing. The active site superimposes closely with those of previously published models but the locations of the active-site water molecules differ in this structure. To address the current mechanistic model, an additional two structures are presented: recombinant ricin A-chain complexed with the substrate analogue formycin monophosphate as well as with adenosine monophosphate, which is cleaved by the crystalline enzyme. The formycin monophosphate displaces a putative catalytic water molecule. This supports the notion that the analogue does not bind in a transition state conformation and that contacts from other elements of the 28 S RNA natural substrate are required to achieve full reactivity. The structure of the adenosine monophosphate complex suggests a mechanism for the release of the adenine product via of the side-chain Tyr80. The structures suggest that Glu177 is better positioned for the activation of the catalytic water molecule than Arg180.
 

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
19627120 S.Ding, C.Gao, and L.Q.Gu (2009).
Capturing single molecules of immunoglobulin and ricin with an aptamer-encoded glass nanopore.
  Anal Chem, 81, 6649-6655.  
19292477 X.P.Li, J.C.Chiou, M.Remacha, J.P.Ballesta, and N.E.Tumer (2009).
A two-step binding model proposed for the electrostatic interactions of ricin a chain with ribosomes.
  Biochemistry, 48, 3853-3863.  
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.  
17986339 J.H.Carra, C.A.McHugh, S.Mulligan, L.M.Machiesky, A.S.Soares, and C.B.Millard (2007).
Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site.
  BMC Struct Biol, 7, 72.
PDB codes: 2p8n 2pjn 2pjo 2r2x 2r3d
16998874 L.J.Peek, R.N.Brey, and C.R.Middaugh (2007).
A rapid, three-step process for the preformulation of a recombinant ricin toxin A-chain vaccine.
  J Pharm Sci, 96, 44-60.  
17916187 S.C.Allen, K.A.Moore, C.J.Marsden, V.Fülöp, K.G.Moffat, J.M.Lord, G.Ladds, and L.M.Roberts (2007).
The isolation and characterization of temperature-dependent ricin A chain molecules in Saccharomyces cerevisiae.
  FEBS J, 274, 5586-5599.
PDB codes: 2vc3 2vc4
  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
15889996 C.J.Marsden, D.C.Smith, L.M.Roberts, and J.M.Lord (2005).
Ricin: current understanding and prospects for an antiricin vaccine.
  Expert Rev Vaccines, 4, 229-237.  
15905278 C.L.Zhou, A.T.Zemla, D.Roe, M.Young, M.Lam, J.S.Schoeniger, and R.Balhorn (2005).
Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin.
  Bioinformatics, 21, 3089-3096.  
15340172 C.A.McHugh, R.F.Tammariello, C.B.Millard, and J.H.Carra (2004).
Improved stability of a protein vaccine through elimination of a partially unfolded state.
  Protein Sci, 13, 2736-2743.  
14686928 C.J.Marsden, V.Fülöp, P.J.Day, and J.M.Lord (2004).
The effect of mutations surrounding and within the active site on the catalytic activity of ricin A chain.
  Eur J Biochem, 271, 153-162.
PDB codes: 1uq4 1uq5
15075327 M.E.Fraser, M.Fujinaga, M.M.Cherney, A.R.Melton-Celsa, E.M.Twiddy, A.D.O'Brien, and M.N.James (2004).
Structure of shiga toxin type 2 (Stx2) from Escherichia coli O157:H7.
  J Biol Chem, 279, 27511-27517.
PDB codes: 1r4p 1r4q
15489170 R.F.Fischetti, D.J.Rodi, D.B.Gore, and L.Makowski (2004).
Wide-angle X-ray solution scattering as a probe of ligand-induced conformational changes in proteins.
  Chem Biol, 11, 1431-1443.  
12592009 C.C.Correll, and K.Swinger (2003).
Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution.
  RNA, 9, 355-363.
PDB code: 1msy
12832768 S.Fermani, G.Falini, A.Ripamonti, A.Bolognesi, L.Polito, and F.Stirpe (2003).
Crystallization and preliminary X-ray diffraction analysis of two ribosome-inactivating proteins: lychnin and dianthin 30.
  Acta Crystallogr D Biol Crystallogr, 59, 1227-1229.  
11389598 K.S.Tanaka, X.Y.Chen, Y.Ichikawa, P.C.Tyler, R.H.Furneaux, and V.L.Schramm (2001).
Ricin A-chain inhibitors resembling the oxacarbenium ion transition state.
  Biochemistry, 40, 6845-6851.  
11551434 M.A.Olson (2001).
Electrostatic effects on the free-energy balance in folding a ribosome-inactivating protein.
  Biophys Chem, 91, 219-229.  
11418185 S.Tang, L.Xie, F.Hou, W.Y.Liu, and K.Ruan (2001).
Non-specific deadenylation and deguanylation of naked RNA catalyzed by ricin under acidic condition.
  Biochim Biophys Acta, 1519, 192-198.  
11685244 X.Yang, T.Gérczei, L.T.Glover, and C.C.Correll (2001).
Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping.
  Nat Struct Biol, 8, 968-973.
PDB codes: 1jbr 1jbs 1jbt
  11152136 J.M.Word, R.C.Bateman, B.K.Presley, S.C.Lovell, and D.C.Richardson (2000).
Exploring steric constraints on protein mutations using MAGE/PROBE.
  Protein Sci, 9, 2251-2259.  
  10493577 I.V.Kurinov, D.E.Myers, J.D.Irvin, and F.M.Uckun (1999).
X-ray crystallographic analysis of the structural basis for the interactions of pokeweed antiviral protein with its active site inhibitor and ribosomal RNA substrate analogs.
  Protein Sci, 8, 1765-1772.
PDB codes: 1qcg 1qci 1qcj
9876120 M.A.Olson, and L.Cuff (1999).
Free energy determinants of binding the rRNA substrate and small ligands to ricin A-chain.
  Biophys J, 76, 28-39.  
9708998 X.Y.Chen, T.M.Link, and V.L.Schramm (1998).
Ricin A-chain: kinetics, mechanism, and RNA stem-loop inhibitors.
  Biochemistry, 37, 11605-11613.  
9552157 X.Yan, P.Day, T.Hollis, A.F.Monzingo, E.Schelp, J.D.Robertus, G.W.Milne, and S.Wang (1998).
Recognition and interaction of small rings with the ricin A-chain binding site.
  Proteins, 31, 33-41.  
9037714 M.A.Olson (1997).
Ricin A-chain structural determinant for binding substrate analogues: a molecular dynamics simulation analysis.
  Proteins, 27, 80-95.  
  9667869 V.L.Schramm (1997).
Enzymatic N-riboside scission in RNA and RNA precursors.
  Curr Opin Chem Biol, 1, 323-331.  
8631323 J.A.Chaddock, A.F.Monzingo, J.D.Robertus, J.M.Lord, and L.M.Roberts (1996).
Major structural differences between pokeweed antiviral protein and ricin A-chain do not account for their differing ribosome specificity.
  Eur J Biochem, 235, 159-166.  
8604301 M.Orita, F.Nishikawa, T.Kohno, T.Senda, Y.Mitsui, E.Yaeta, T.Kazunari, and S.Nishikawa (1996).
High-resolution NMR study of a GdAGA tetranucleotide loop that is an improved substrate for ricin, a cytotoxic plant protein.
  Nucleic Acids Res, 24, 611-618.  
8780513 P.J.Day, S.R.Ernst, A.E.Frankel, A.F.Monzingo, J.M.Pascal, M.C.Molina-Svinth, and J.D.Robertus (1996).
Structure and activity of an active site substitution of ricin A chain.
  Biochemistry, 35, 11098-11103.
PDB codes: 1obs 1obt
  8527834 R.C.Jackson (1995).
Update on computer-aided drug design.
  Curr Opin Biotechnol, 6, 646-651.  
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.