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PDBsum entry 1rtc
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Glycosidase PDB id
1rtc

 

 

 

 

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Contents
Protein chain
268 a.a. *
Waters ×48
* Residue conservation analysis
PDB id:
1rtc
Name: Glycosidase
Title: The structure of recombinant ricin a chain at 2.3 angstroms
Structure: Ricin. Chain: a. Engineered: yes
Source: Ricinus communis. Castor bean. Organism_taxid: 3988. Organ: bean
Resolution:
2.30Å     R-factor:   0.230    
Authors: D.Mlsna,A.F.Monzingo,B.J.Katzin,S.Ernst,J.D.Robertus
Key ref:
D.Mlsna et al. (1993). Structure of recombinant ricin A chain at 2.3 A. Protein Sci, 2, 429-435. PubMed id: 8453380 DOI: 10.1002/pro.5560020315
Date:
29-Oct-92     Release date:   31-Oct-93    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02879  (RICI_RICCO) -  Ricin from Ricinus communis
Seq:
Struc: 		 
Seq:
Struc: 		576 a.a.
268 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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.

 

 
DOI no: 10.1002/pro.5560020315 Protein Sci 2:429-435 (1993)
PubMed id: 8453380  
 
 
Structure of recombinant ricin A chain at 2.3 A.
D.Mlsna, A.F.Monzingo, B.J.Katzin, S.Ernst, J.D.Robertus.
 
  ABSTRACT  
 
The plant cytotoxin ricin is a heterodimer with a cell surface binding (B) chain and an enzymatically active A chain (RTA) known to act as a specific N-glycosidase. RTA must be separated from B chain to attack rRNA. The X-ray structure of ricin has been solved recently; here we report the structure of the isolated A chain expressed from a clone in Escherichia coli. This structure of wild-type rRTA has and will continue to serve as the parent compound for difference Fouriers used to assess the structure of site-directed mutants designed to analyze the mechanism of this medically and commercially important toxin. The structure of the recombinant protein, rRTA, is virtually identical to that seen previously for A chain in the heterodimeric toxin. Some minor conformational changes due to interactions with B chain and to crystal packing differences are described. Perhaps the most significant difference is the presence in rRTA of an additional active site water. This molecule is positioned to act as the ultimate nucleophile in the depurination reaction mechanism proposed by Monzingo and Robertus (1992, J. Mol. Biol. 227, 1136-1145).
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Superposition of the refined models of ricin Aand rRTA. Recom- binant RTA, as refinedin this study is shown in the heavy ondsasa Ca trace. The refined ricin A chain (Ru- tenber et al., 1991) is shown in thin bonds. 		Figure 5.
Fig. 5. The active site of ricin. The conforma- of ricin A is shown in light bonds and that f rRTA n heavy bonds.
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1993, 2, 429-435) copyright 1993.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21455295 Y.P.Pang, J.G.Park, S.Wang, A.Vummenthala, R.K.Mishra, J.E.McLaughlin, R.Di, J.N.Kahn, N.E.Tumer, L.Janosi, J.Davis, and C.B.Millard (2011).
Small-molecule inhibitor leads of ribosome-inactivating proteins developed using the doorstop approach.
  PLoS One, 6, e17883.  
19920175 M.C.Ho, M.B.Sturm, S.C.Almo, and V.L.Schramm (2009).
Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins.
  Proc Natl Acad Sci U S A, 106, 20276-20281.
PDB codes: 3hio 3hiq 3his 3hit 3hiv 3hiw
19073700 P.H.Too, M.K.Ma, A.N.Mak, Y.T.Wong, C.K.Tung, G.Zhu, S.W.Au, K.B.Wong, and P.C.Shaw (2009).
The C-terminal fragment of the ribosomal P protein complexed to trichosanthin reveals the interaction between the ribosome-inactivating protein and the ribosome.
  Nucleic Acids Res, 37, 602-610.
PDB codes: 2jdl 2jjr 2vs6
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.  
17243169 A.Chambery, M.Pisante, A.Di Maro, E.Di Zazzo, M.Ruvo, S.Costantini, G.Colonna, and A.Parente (2007).
Invariant Ser211 is involved in the catalysis of PD-L4, type I RIP from Phytolacca dioica leaves.
  Proteins, 67, 209-218.  
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.  
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.  
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.  
11337416 K.Nielsen, and R.S.Boston (2001).
RIBOSOME-INACTIVATING PROTEINS: A Plant Perspective.
  Annu Rev Plant Physiol Plant Mol Biol, 52, 785-816.  
  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.  
  10739256 Y.X.Wang, J.Jacob, P.T.Wingfield, I.Palmer, S.J.Stahl, J.D.Kaufman, P.L.Huang, P.L.Huang, S.Lee-Huang, and D.A.Torchia (2000).
Anti-HIV and anti-tumor protein MAP30, a 30 kDa single-strand type-I RIP, shares similar secondary structure and beta-sheet topology with the A chain of ricin, a type-II RIP.
  Protein Sci, 9, 138-144.  
10097145 R.Baluna, J.Rizo, B.E.Gordon, V.Ghetie, and E.S.Vitetta (1999).
Evidence for a structural motif in toxins and interleukin-2 that may be responsible for binding to endothelial cells and initiating vascular leak syndrome.
  Proc Natl Acad Sci U S A, 96, 3957-3962.  
  9521107 D.K.Fryxell, S.L.Gawlak, R.W.Dodge, and C.B.Siegall (1998).
Identification of a specific tyrosine residue in Bryodin 1 distinct from the active site but required for full catalytic and cytotoxic activity.
  Protein Sci, 7, 318-324.  
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.  
8539247 T.Kohno, T.Senda, H.Narumi, S.Kimura, and Y.Mitsui (1995).
Crystallization and preliminary crystallographic analysis of recombinant abrin-a A-chain with ribosome inactivating activity.
  Proteins, 23, 126-127.  
8052614 K.N.Morris, and I.G.Wool (1994).
Analysis of the contribution of an amphiphilic alpha-helix to the structure and to the function of ricin A chain.
  Proc Natl Acad Sci U S A, 91, 7530-7533.  
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.

 

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