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Protein synthesis inhibitor PDB id
1pag
Jmol
Contents
Protein chains
262 a.a. *
Ligands
FMP ×2
Waters ×78
* Residue conservation analysis
PDB id:
1pag
Name: Protein synthesis inhibitor
Title: The 2.5 angstroms structure of pokeweed antiviral protein
Structure: Pokeweed antiviral protein. Chain: a, b. Engineered: yes
Source: Phytolacca americana. American pokeweed. Organism_taxid: 3527
Resolution:
2.80Å     R-factor:   0.200    
Authors: A.F.Monzingo,E.J.Collins,S.R.Ernst,J.D.Irvin,J.D.Robertus
Key ref: A.F.Monzingo et al. (1993). The 2.5 A structure of pokeweed antiviral protein. J Mol Biol, 233, 705-715. PubMed id: 8411176 DOI: 10.1006/jmbi.1993.1547
Date:
19-Oct-92     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P10297  (RIP1_PHYAM) -  Antiviral protein I
Seq:
Struc: 		313 a.a.
262 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     defense response   4 terms 
  Biochemical function     hydrolase activity     2 terms  

 

 
DOI no: 10.1006/jmbi.1993.1547 J Mol Biol 233:705-715 (1993)
PubMed id: 8411176  
 
 
The 2.5 A structure of pokeweed antiviral protein.
A.F.Monzingo, E.J.Collins, S.R.Ernst, J.D.Irvin, J.D.Robertus.
 
  ABSTRACT  
 
The pokeweed antiviral protein (PAP), isolated from the leaves of Phytolacca americana, is one of a family of plant and bacterial ribosome-inhibiting proteins (RIPs) which act as specific N-glycosidases on rRNA. Here we report the three-dimensional structure of PAP determined to 2.5 A resolution by X-ray crystallography. After 14 rounds of refinement, the R factor is 0.17 for 5.0 to 2.5 A data. The protein is homologous with the A chain of ricin and exhibits a very similar folding pattern. The positions of key active site residues are also similar. We also report the 2.8 A structure of PAP complexed with a substrate analog, formycin 5'-monophosphate. As seen previously in ricin, the formycin ring is stacked between invariant tyrosines 72 and 123. Arg179 bonds to N-3 which is thought to be important in catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17286798 U.Baykal, and N.E.Tumer (2007).
The C-terminus of pokeweed antiviral protein has distinct roles in transport to the cytosol, ribosome depurination and cytotoxicity.
  Plant J, 49, 995.  
16972795 A.Chambery, A.de Donato, A.Bolognesi, L.Polito, F.Stirpe, and A.Parente (2006).
Sequence determination of lychnin, a type 1 ribosome-inactivating protein from Lychnis chalcedonica seeds.
  Biol Chem, 387, 1261-1266.  
16238796 K.Szalai, I.Schöll, E.Förster-Waldl, L.Polito, A.Bolognesi, E.Untersmayr, A.B.Riemer, G.Boltz-Nitulescu, F.Stirpe, and E.Jensen-Jarolim (2005).
Occupational sensitization to ribosome-inactivating proteins in researchers.
  Clin Exp Allergy, 35, 1354-1360.  
15304562 K.A.Hudak, B.A.Parikh, R.Di, M.Baricevic, M.Santana, M.Seskar, and N.E.Tumer (2004).
Generation of pokeweed antiviral protein mutations in Saccharomyces cerevisiae: evidence that ribosome depurination is not sufficient for cytotoxicity.
  Nucleic Acids Res, 32, 4244-4256.  
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.  
11876649 E.D.Deeks, J.P.Cook, P.J.Day, D.C.Smith, L.M.Roberts, and J.M.Lord (2002).
The low lysine content of ricin A chain reduces the risk of proteolytic degradation after translocation from the endoplasmic reticulum to the cytosol.
  Biochemistry, 41, 3405-3413.  
12358434 K.A.Hudak, J.D.Bauman, and N.E.Tumer (2002).
Pokeweed antiviral protein binds to the cap structure of eukaryotic mRNA and depurinates the mRNA downstream of the cap.
  RNA, 8, 1148-1159.  
11288182 J.M.Pascal, P.J.Day, A.F.Monzingo, S.R.Ernst, J.D.Robertus, R.Iglesias, Y.Pérez, J.M.Férreras, L.Citores, and T.Girbés (2001).
2.8-A crystal structure of a nontoxic type-II ribosome-inactivating protein, ebulin l.
  Proteins, 43, 319-326.
PDB codes: 1hwm 1hwn 1hwo 1hwp
10652330 F.Rajamohan, M.J.Pugmire, I.V.Kurinov, and F.M.Uckun (2000).
Modeling and alanine scanning mutagenesis studies of recombinant pokeweed antiviral protein.
  J Biol Chem, 275, 3382-3390.  
10727935 J.E.Krawetz, and R.S.Boston (2000).
Substrate specificity of a maize ribosome-inactivating protein differs across diverse taxa.
  Eur J Biochem, 267, 1966-1974.  
10771444 M.Chen, X.Ye, J.Cai, and Y.Lin (2000).
Crystallization and preliminary crystallographic study of cucurmosin, a ribosome-inactivating protein from the sarcocarp of Cucurbita moschata.
  Acta Crystallogr D Biol Crystallogr, 56, 665-666.  
10478456 E.Honjo, and K.Watanabe (1999).
Expression of mature pokeweed antiviral protein with or without C-terminal extrapeptide in Escherichia coli as a fusion with maltose-binding protein.
  Biosci Biotechnol Biochem, 63, 1291-1294.  
  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
  10595542 I.V.Kurinov, F.Rajamohan, T.K.Venkatachalam, and F.M.Uckun (1999).
X-ray crystallographic analysis of the structural basis for the interaction of pokeweed antiviral protein with guanine residues of ribosomal RNA.
  Protein Sci, 8, 2399-2405.
PDB code: 1d6a
10329776 Y.R.Yuan, Y.N.He, J.P.Xiong, and Z.X.Xia (1999).
Three-dimensional structure of beta-momorcharin at 2.55 A resolution.
  Acta Crystallogr D Biol Crystallogr, 55, 1144-1151.
PDB code: 1cf5
10571185 Y.X.Wang, N.Neamati, J.Jacob, I.Palmer, S.J.Stahl, J.D.Kaufman, P.L.Huang, P.L.Huang, H.E.Winslow, Y.Pommier, P.T.Wingfield, S.Lee-Huang, A.Bax, and D.A.Torchia (1999).
Solution structure of anti-HIV-1 and anti-tumor protein MAP30: structural insights into its multiple functions.
  Cell, 99, 433-442.
PDB code: 1d8v
9761837 H.M.Li, Z.H.Zeng, Z.Hu, and D.C.Wang (1998).
Crystallization and preliminary crystallographic analyses of pokeweed antiviral protein from seeds.
  Acta Crystallogr D Biol Crystallogr, 54, 137-139.  
9649321 J.K.Suh, C.J.Hovde, and J.D.Robertus (1998).
Shiga toxin attacks bacterial ribosomes as effectively as eucaryotic ribosomes.
  Biochemistry, 37, 9394-9398.  
9924987 J.Xu, A.X.Meng, K.L.Hefferon, I.G.Ivanov, and M.G.Abouhaidar (1998).
Effect of N-terminal deletions on the activity of pokeweed antiviral protein expressed in E. coli.
  Biochimie, 80, 1069-1076.  
18726259 Z.Zeng, L.Jin, H.Li, Z.Hu, and D.Wang (1998).
Crystal structure of pokeweed antiviral protein from seeds ofPhytolacca americana at 0.25 nm.
  Sci China C Life Sci, 41, 413-418.  
9108070 N.E.Tumer, D.J.Hwang, and M.Bonness (1997).
C-terminal deletion mutant of pokeweed antiviral protein inhibits viral infection but does not depurinate host ribosomes.
  Proc Natl Acad Sci U S A, 94, 3866-3871.  
8564542 E.M.Marcotte, A.F.Monzingo, S.R.Ernst, R.Brzezinski, and J.D.Robertus (1996).
X-ray structure of an anti-fungal chitosanase from streptomyces N174.
  Nat Struct Biol, 3, 155-162.
PDB code: 1chk
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.  
  11725098 L.P.Chow, M.Kamo, J.Y.Lin, S.H.Wang, Y.Ueno, and A.Tsugita (1996).
Amino Acid Sequence of Trichoanguina, a Ribosomal-Inactivating Protein from Trichosanthes anguinea Seeds.
  J Biomed Sci, 3, 178-186.  
8548448 M.A.Batalia, A.F.Monzingo, S.Ernst, W.Roberts, and J.D.Robertus (1996).
The crystal structure of the antifungal protein zeamatin, a member of the thaumatin-like, PR-5 protein family.
  Nat Struct Biol, 3, 19-23.
PDB code: 1du5
8749853 D.Frishman, and P.Argos (1995).
Knowledge-based protein secondary structure assignment.
  Proteins, 23, 566-579.  
7862664 E.J.Collins, D.N.Garboczi, M.N.Karpusas, and D.C.Wiley (1995).
The three-dimensional structure of a class I major histocompatibility complex molecule missing the alpha 3 domain of the heavy chain.
  Proc Natl Acad Sci U S A, 92, 1218-1221.
PDB code: 1tmc
7561975 M.A.Olson, J.P.Scovill, and D.C.Hack (1995).
Simulation analysis of formycin 5'-monophosphate analog substrates in the ricin A-chain active site.
  J Comput Aided Mol Des, 9, 226-236.  
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.  
7667309 Y.Hur, D.J.Hwang, O.Zoubenko, C.Coetzer, F.M.Uckun, and N.E.Tumer (1995).
Isolation and characterization of pokeweed antiviral protein mutations in Saccharomyces cerevisiae: identification of residues important for toxicity.
  Proc Natl Acad Sci U S A, 92, 8448-8452.  
7925458 H.Ago, J.Kataoka, H.Tsuge, N.Habuka, E.Inagaki, M.Noma, and M.Miyano (1994).
X-ray structure of a pokeweed antiviral protein, coded by a new genomic clone, at 0.23 nm resolution. A model structure provides a suitable electrostatic field for substrate binding.
  Eur J Biochem, 225, 369-374.
PDB code: 1apa
8202351 J.A.Chaddock, J.M.Lord, M.R.Hartley, and L.M.Roberts (1994).
Pokeweed antiviral protein (PAP) mutations which permit E.coli growth do not eliminate catalytic activity towards prokaryotic ribosomes.
  Nucleic Acids Res, 22, 1536-1540.  
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.