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PDBsum entry 1zm2

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protein ligands Protein-protein interface(s) links
Biosynthetic protein/transferase PDB id
1zm2
Jmol
Contents
Protein chains
823 a.a. *
207 a.a. *
Ligands
APR
* Residue conservation analysis
PDB id:
1zm2
Name: Biosynthetic protein/transferase
Title: Structure of adp-ribosylated eef2 in complex with catalytic fragment of eta
Structure: Elongation factor 2. Chain: a, c, e. Fragment: eef2. Synonym: ef-2. Exotoxin a. Chain: b, d, f. Fragment: catalytic domain. Synonym: NAD-dependent adp-ribosyltransferase. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Pseudomonas aeruginosa. Organism_taxid: 287. Gene: eta. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
3.07Å     R-factor:   0.231     R-free:   0.265
Authors: R.Joergensen,A.R.Merrill,S.P.Yates,V.E.Marquez,A.L.Schwan, T.Boesen,G.R.Andersen
Key ref:
R.Jørgensen et al. (2005). Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry. Nature, 436, 979-984. PubMed id: 16107839 DOI: 10.1038/nature03871
Date:
10-May-05     Release date:   24-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P32324  (EF2_YEAST) -  Elongation factor 2
Seq:
Struc:
 
Seq:
Struc:
842 a.a.
823 a.a.*
Protein chains
Pfam   ArchSchema ?
P11439  (TOXA_PSEAE) -  Exotoxin A
Seq:
Struc:
 
Seq:
Struc:
638 a.a.
207 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains B, D, F: E.C.2.4.2.36  - NAD(+)--diphthamide ADP-ribosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NAD+ + diphthamide-[translation elongation factor 2] = nicotinamide + N-(ADP-D-ribosyl)diphthamide-[translation elongation factor 2]
NAD(+)
+ diphthamide-[translation elongation factor 2]
= nicotinamide
+ N-(ADP-D-ribosyl)diphthamide-[translation elongation factor 2]
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     translation   5 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
    Added reference    
 
 
DOI no: 10.1038/nature03871 Nature 436:979-984 (2005)
PubMed id: 16107839  
 
 
Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry.
R.Jørgensen, A.R.Merrill, S.P.Yates, V.E.Marquez, A.L.Schwan, T.Boesen, G.R.Andersen.
 
  ABSTRACT  
 
The bacteria causing diphtheria, whooping cough, cholera and other diseases secrete mono-ADP-ribosylating toxins that modify intracellular proteins. Here, we describe four structures of a catalytically active complex between a fragment of Pseudomonas aeruginosa exotoxin A (ETA) and its protein substrate, translation elongation factor 2 (eEF2). The target residue in eEF2, diphthamide (a modified histidine), spans across a cleft and faces the two phosphates and a ribose of the non-hydrolysable NAD+ analogue, betaTAD. This suggests that the diphthamide is involved in triggering NAD+ cleavage and interacting with the proposed oxacarbenium intermediate during the nucleophilic substitution reaction, explaining the requirement of diphthamide for ADP ribosylation. Diphtheria toxin may recognize eEF2 in a manner similar to ETA. Notably, the toxin-bound betaTAD phosphates mimic the phosphate backbone of two nucleotides in a conformational switch of 18S rRNA, thereby achieving universal recognition of eEF2 by ETA.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: The enzymatic reaction and the eEF2-ETA[c] structure. a, Schematic representation of the ADP-ribosylation reaction with important atoms labelled. The reaction features an S[N]1 mechanism with scission of the glycosidic bond (NC1-NN1) within the NAD^+ substrate b, The toxin (orange) binds to eEF2 domain IV (grey) and a single hairpin in domain III (blue, marked HP). The diphthamide (blue, marked DIPH) and the TAD (black) are shown in ball and stick representation. c, In the eEF2-ETA[c]- TAD structure, the toxin in complex 1 (blue) is rotated 6 compared to complex 3 (orange). d, ADP ribosylation in the crystalline state analysed by native PAGE. Lane 1, eEF2; lane 2, ADPR-eEF2; lane 3, washed eEF2-ETA[c] crystals reacted during NAD^+ soak; lane 4, washed eEF2-ETA[c] crystals soaked without NAD^+. Buffer samples used for washing the crystals either before or after the NAD^+ reaction did not contain eEF2, as analysed by PAGE (not shown).
Figure 5.
Figure 5: Ribosome mimicry by ETA. a, The toxin (orange) and the large helix 44 (H44) in the 40S ribosomal subunit (blue) share overall localization with respect to domain IV of eEF2 (grey). b, The phosphates of TAD (NAD^+) are presented to the eEF2 diphthamide in an orientation markedly similar to the sugar-phosphate backbone of bases A1492 and A1493.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2005, 436, 979-984) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21264238 A.Shapira, M.Gal-Tanamy, L.Nahary, D.Litvak-Greenfeld, R.Zemel, R.Tur-Kaspa, and I.Benhar (2011).
Engineered toxins "zymoxins" are activated by the HCV NS3 protease by removal of an inhibitory protein domain.
  PLoS One, 6, e15916.  
21394738 G.Kaul, G.Pattan, and T.Rafeequi (2011).
Eukaryotic elongation factor-2 (eEF2): its regulation and peptide chain elongation.
  Cell Biochem Funct, 29, 227-234.  
21170356 R.J.Fieldhouse, Z.Turgeon, D.White, and A.R.Merrill (2010).
Cholera- and anthrax-like toxins are among several new ADP-ribosyltransferases.
  PLoS Comput Biol, 6, e1001029.  
20534494 R.T.Kidmose, N.N.Vasiliev, A.B.Chetverin, G.R.Andersen, and C.R.Knudsen (2010).
Structure of the Qbeta replicase, an RNA-dependent RNA polymerase consisting of viral and host proteins.
  Proc Natl Acad Sci U S A, 107, 10884-10889.
PDB code: 3mmp
21203470 V.Roy, K.Ghani, and M.Caruso (2010).
A dominant-negative approach that prevents diphthamide formation confers resistance to Pseudomonas exotoxin a and diphtheria toxin.
  PLoS One, 5, e15753.  
19917080 A.Arita, X.Zhou, T.P.Ellen, X.Liu, J.Bai, J.P.Rooney, A.Kurtz, C.B.Klein, W.Dai, T.J.Begley, and M.Costa (2009).
A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae.
  BMC Genomics, 10, 524.  
  19255877 N.Schwarz, R.Fliegert, S.Adriouch, M.Seman, A.H.Guse, F.Haag, and F.Koch-Nolte (2009).
Activation of the P2X7 ion channel by soluble and covalently bound ligands.
  Purinergic Signal, 5, 139-149.  
20025795 X.Agirrezabala, and J.Frank (2009).
Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu.
  Q Rev Biophys, 42, 159-200.  
19461676 X.Liu, J.Wu, S.Zhang, C.Li, and Q.Huang (2009).
Novel strategies to augment genetically delivered immunotoxin molecular therapy for cancer therapy.
  Cancer Gene Ther, 16, 861-872.  
18454192 A.Arnoldo, J.Curak, S.Kittanakom, I.Chevelev, V.T.Lee, M.Sahebol-Amri, B.Koscik, L.Ljuma, P.J.Roy, A.Bedalov, G.Giaever, C.Nislow, R.A.Merrill, S.Lory, and I.Stagljar (2008).
Identification of small molecule inhibitors of Pseudomonas aeruginosa exoenzyme S using a yeast phenotypic screen.
  PLoS Genet, 4, e1000005.  
18490658 H.Tsuge, M.Nagahama, M.Oda, S.Iwamoto, H.Utsunomiya, V.E.Marquez, N.Katunuma, M.Nishizawa, and J.Sakurai (2008).
Structural basis of actin recognition and arginine ADP-ribosylation by Clostridium perfringens iota-toxin.
  Proc Natl Acad Sci U S A, 105, 7399-7404.
PDB code: 3buz
18953335 I.Häcker, B.Sander, M.M.Golas, E.Wolf, E.Karagöz, B.Kastner, H.Stark, P.Fabrizio, and R.Lührmann (2008).
Localization of Prp8, Brr2, Snu114 and U4/U6 proteins in the yeast tri-snRNP by electron microscopy.
  Nat Struct Mol Biol, 15, 1206-1212.  
18285480 J.Botet, M.Rodríguez-Mateos, J.P.Ballesta, J.L.Revuelta, and M.Remacha (2008).
A chemical genomic screen in Saccharomyces cerevisiae reveals a role for diphthamidation of translation elongation factor 2 in inhibition of protein synthesis by sordarin.
  Antimicrob Agents Chemother, 52, 1623-1629.  
18044731 P.Wolf, K.Alt, P.Bühler, A.Katzenwadel, U.Wetterauer, M.Tacke, and U.Elsässer-Beile (2008).
Anti-PSMA immunotoxin as novel treatment for prostate cancer? High and specific antitumor activity on human prostate xenograft tumors in SCID mice.
  Prostate, 68, 129-138.  
18785839 Q.Deng, and J.T.Barbieri (2008).
Molecular mechanisms of the cytotoxicity of ADP-ribosylating toxins.
  Annu Rev Microbiol, 62, 271-288.  
18276581 R.Jørgensen, A.E.Purdy, R.J.Fieldhouse, M.S.Kimber, D.H.Bartlett, and A.R.Merrill (2008).
Cholix toxin, a novel ADP-ribosylating factor from Vibrio cholerae.
  J Biol Chem, 283, 10671-10678.
PDB codes: 2q5t 2q6m
18583986 R.Jørgensen, Y.Wang, D.Visschedyk, and A.R.Merrill (2008).
The nature and character of the transition state for the ADP-ribosyltransferase reaction.
  EMBO Rep, 9, 802-809.
PDB codes: 2zit 3b78 3b82 3b8h
18391406 S.Kishishita, K.Shimizu, K.Murayama, T.Terada, M.Shirouzu, S.Yokoyama, and N.Kunishima (2008).
Structures of two archaeal diphthine synthases: insights into the post-translational modification of elongation factor 2.
  Acta Crystallogr D Biol Crystallogr, 64, 397-406.
PDB codes: 1wde 1wng
18765564 T.R.Webb, S.H.Cross, L.McKie, R.Edgar, L.Vizor, J.Harrison, J.Peters, and I.J.Jackson (2008).
Diphthamide modification of eEF2 requires a J-domain protein and is essential for normal development.
  J Cell Sci, 121, 3140-3145.  
17446867 D.J.Taylor, J.Nilsson, A.R.Merrill, G.R.Andersen, P.Nissen, and J.Frank (2007).
Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation.
  EMBO J, 26, 2421-2431.
PDB codes: 2p8w 2p8x 2p8y 2p8z
17241198 I.de Bruijn, M.J.de Kock, M.Yang, P.de Waard, T.A.van Beek, and J.M.Raaijmakers (2007).
Genome-based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in Pseudomonas species.
  Mol Microbiol, 63, 417-428.  
17146673 M.Vogelsgesang, A.Pautsch, and K.Aktories (2007).
C3 exoenzymes, novel insights into structure and action of Rho-ADP-ribosylating toxins.
  Naunyn Schmiedebergs Arch Pharmacol, 374, 347-360.  
17082187 R.Søe, R.T.Mosley, M.Justice, J.Nielsen-Kahn, M.Shastry, A.R.Merrill, and G.R.Andersen (2007).
Sordarin derivatives induce a novel conformation of the yeast ribosome translocation factor eEF2.
  J Biol Chem, 282, 657-666.
PDB codes: 2e1r 2npf
17015823 C.Mueller-Dieckmann, S.Kernstock, M.Lisurek, J.P.von Kries, F.Haag, M.S.Weiss, and F.Koch-Nolte (2006).
The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation.
  Proc Natl Acad Sci U S A, 103, 15026-15031.
PDB codes: 2foz 2fp0
16713730 D.Desveaux, A.U.Singer, and J.L.Dangl (2006).
Type III effector proteins: doppelgangers of bacterial virulence.
  Curr Opin Plant Biol, 9, 376-382.  
16956368 K.P.Holbourn, C.C.Shone, and K.R.Acharya (2006).
A family of killer toxins. Exploring the mechanism of ADP-ribosylating toxins.
  FEBS J, 273, 4579-4593.  
16959969 P.O.Hassa, S.S.Haenni, M.Elser, and M.O.Hottiger (2006).
Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going?
  Microbiol Mol Biol Rev, 70, 789-829.  
16406634 S.P.Yates, R.Jørgensen, G.R.Andersen, and A.R.Merrill (2006).
Stealth and mimicry by deadly bacterial toxins.
  Trends Biochem Sci, 31, 123-133.  
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.