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PDBsum entry 1g24

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protein Protein-protein interface(s) links
Transferase PDB id
1g24
Jmol
Contents
Protein chains
211 a.a. *
Waters ×869
* Residue conservation analysis
PDB id:
1g24
Name: Transferase
Title: The crystal structure of exoenzyme c3 from clostridium botulinum
Structure: Exoenzyme c3. Chain: a, b, c, d. Synonym: mono-adp-ribosyltransferase c3. Engineered: yes
Source: Clostridium botulinum. Organism_taxid: 1491. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.70Å     R-factor:   0.240     R-free:   0.265
Authors: S.Han,A.S.Arvai,S.B.Clancy,J.A.Tainer
Key ref:
S.Han et al. (2001). Crystal structure and novel recognition motif of rho ADP-ribosylating C3 exoenzyme from Clostridium botulinum: structural insights for recognition specificity and catalysis. J Mol Biol, 305, 95. PubMed id: 11114250 DOI: 10.1006/jmbi.2000.4292
Date:
16-Oct-00     Release date:   18-Dec-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P15879  (ARC3_CBDP) -  Mono-ADP-ribosyltransferase C3
Seq:
Struc:
251 a.a.
211 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     viral reproduction   3 terms 
  Biochemical function     transferase activity     3 terms  

 

 
DOI no: 10.1006/jmbi.2000.4292 J Mol Biol 305:95 (2001)
PubMed id: 11114250  
 
 
Crystal structure and novel recognition motif of rho ADP-ribosylating C3 exoenzyme from Clostridium botulinum: structural insights for recognition specificity and catalysis.
S.Han, A.S.Arvai, S.B.Clancy, J.A.Tainer.
 
  ABSTRACT  
 
Clostridium botulinum C3 exoenzyme inactivates the small GTP-binding protein family Rho by ADP-ribosylating asparagine 41, which depolymerizes the actin cytoskeleton. C3 thus represents a major family of the bacterial toxins that transfer the ADP-ribose moiety of NAD to specific amino acids in acceptor proteins to modify key biological activities in eukaryotic cells, including protein synthesis, differentiation, transformation, and intracellular signaling. The 1.7 A resolution C3 exoenzyme structure establishes the conserved features of the core NAD-binding beta-sandwich fold with other ADP-ribosylating toxins despite little sequence conservation. Importantly, the central core of the C3 exoenzyme structure is distinguished by the absence of an active site loop observed in many other ADP-ribosylating toxins. Unlike the ADP-ribosylating toxins that possess the active site loop near the central core, the C3 exoenzyme replaces the active site loop with an alpha-helix, alpha3. Moreover, structural and sequence similarities with the catalytic domain of vegetative insecticidal protein 2 (VIP2), an actin ADP-ribosyltransferase, unexpectedly implicates two adjacent, protruding turns, which join beta5 and beta6 of the toxin core fold, as a novel recognition specificity motif for this newly defined toxin family. Turn 1 evidently positions the solvent-exposed, aromatic side-chain of Phe209 to interact with the hydrophobic region of Rho adjacent to its GTP-binding site. Turn 2 evidently both places the Gln212 side-chain for hydrogen bonding to recognize Rho Asn41 for nucleophilic attack on the anomeric carbon of NAD ribose and holds the key Glu214 catalytic side-chain in the adjacent catalytic pocket. This proposed bipartite ADP-ribosylating toxin turn-turn (ARTT) motif places the VIP2 and C3 toxin classes into a single ARTT family characterized by analogous target protein recognition via turn 1 aromatic and turn 2 hydrogen-bonding side-chain moieties. Turn 2 centrally anchors the catalytic Glu214 within the ARTT motif, and furthermore distinguishes the C3 toxin class by a conserved turn 2 Gln and the VIP2 binary toxin class by a conserved turn 2 Glu for appropriate target side-chain hydrogen-bonding recognition. Taken together, these structural results provide a molecular basis for understanding the coupled activity and recognition specificity for C3 and for the newly defined ARTT toxin family, which acts in the depolymerization of the actin cytoskeleton. This beta5 to beta6 region of the toxin fold represents an experimentally testable and potentially general recognition motif region for other ADP-ribosylating toxins that have a similar beta-structure framework.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Proposed structure-based mechanism for ADP-ribosylation of Rho. The schematic drawing for the mechanism shows the roles of C3 residues Gln212, Glu214, and a hydrophobic pocket composed of Phe127, Met178, Val180 and Phe183. Glu214 evidently plays an important role in stabilizing the intermediate oxocarbenium ion. Gln212 likely recognizes Asn41 of Rho and places the carboxyamide group near the N-glycosidic bond for ADP-ribosylation.
Figure 5.
Figure 5. (a) Stereo view of the C3 recognition specificity region (residues 203-214) (orange) showing the symmetry-related interaction (pink) near the NAD-binding pocket. Phe209 is positioned into the hydrophobic pocket composed of Phe49, Trp58, Ile124. Protein side-chains and water molecules are shown in ball and stick representation. The residues belong to symmetry-related molecules are illustrated in gray. (b) Schematic drawing of the proposed role of residue Phe209 and Gln212 in C3. The solvent-exposed Phe209 (black) in T1 may be involved in a hydrophobic interaction with Rho. Gln212 (green) in T2 may recognize Asn41 (orange) of Rho. The catalytic Glu214 side-chain (magenta) is positioned to form a hydrogen bond with Gly211 backbone. (c) Schematic drawing of the proposed role of residue Phe423 and Glu426 in VIP2. The solvent-exposed Phe423 (black) in T1 may be involved in a hydrophobic interaction with actin and Glu426 (cyan) in T2 may recognize Arg177 (orange) of actin. The catalytic Glu428 side-chain (magenta) forms a hydrogen bond with Ser425 backbone.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 305, 95-0) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21193903 I.Just, A.Rohrbeck, S.C.Huelsenbeck, and M.Hoeltje (2011).
Therapeutic effects of Clostridium botulinum C3 exoenzyme.
  Naunyn Schmiedebergs Arch Pharmacol, 383, 247-252.  
19840027 J.Fahrer, J.Kuban, K.Heine, G.Rupps, E.Kaiser, E.Felder, R.Benz, and H.Barth (2010).
Selective and specific internalization of clostridial C3 ADP-ribosyltransferases into macrophages and monocytes.
  Cell Microbiol, 12, 233-247.  
20106667 M.O.Hottiger, P.O.Hassa, B.Lüscher, H.Schüler, and F.Koch-Nolte (2010).
Toward a unified nomenclature for mammalian ADP-ribosyltransferases.
  Trends Biochem Sci, 35, 208-219.  
19849782 F.F.White, N.Potnis, J.B.Jones, and R.Koebnik (2009).
The type III effectors of Xanthomonas.
  Mol Plant Pathol, 10, 749-766.  
19824793 M.R.Popoff, and P.Bouvet (2009).
Clostridial toxins.
  Future Microbiol, 4, 1021-1064.  
  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.  
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
18349144 J.Baysarowich, K.Koteva, D.W.Hughes, L.Ejim, E.Griffiths, K.Zhang, M.Junop, and G.D.Wright (2008).
Rifamycin antibiotic resistance by ADP-ribosylation: Structure and diversity of Arr.
  Proc Natl Acad Sci U S A, 105, 4886-4891.
PDB code: 2hw2
18369192 J.Ménétrey, G.Flatau, P.Boquet, A.Ménez, and E.A.Stura (2008).
Structural basis for the NAD-hydrolysis mechanism and the ARTT-loop plasticity of C3 exoenzymes.
  Protein Sci, 17, 878-886.
PDB codes: 2c89 2c8a 2c8b 2c8c 2c8d 2c8e 2c8f
19061375 S.Lord-Fontaine, F.Yang, Q.Diep, P.Dergham, S.Munzer, P.Tremblay, and L.McKerracher (2008).
Local Inhibition of Rho Signaling by Cell-Permeable Recombinant Protein BA-210 Prevents Secondary Damage and Promotes Functional Recovery following Acute Spinal Cord Injury.
  J Neurotrauma, 25, 1309-1322.  
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.  
16931513 A.R.Morrison, J.Moss, L.A.Stevens, J.E.Evans, C.Farrell, E.Merithew, D.G.Lambright, D.L.Greiner, J.P.Mordes, A.A.Rossini, and R.Bortell (2006).
ART2, a T cell surface mono-ADP-ribosyltransferase, generates extracellular poly(ADP-ribose).
  J Biol Chem, 281, 33363-33372.  
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.  
  16511307 S.Kernstock, F.Koch-Nolte, J.Mueller-Dieckmann, M.S.Weiss, and C.Mueller-Dieckmann (2006).
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of human ARH3, the first eukaryotic protein-ADP-ribosylhydrolase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 224-227.  
16905096 S.M.Margarit, W.Davidson, L.Frego, and C.E.Stebbins (2006).
A steric antagonism of actin polymerization by a salmonella virulence protein.
  Structure, 14, 1219-1229.
PDB codes: 2gwj 2gwk 2gwl 2gwm
16177825 A.Pautsch, M.Vogelsgesang, J.Tränkle, C.Herrmann, and K.Aktories (2005).
Crystal structure of the C3bot-RalA complex reveals a novel type of action of a bacterial exoenzyme.
  EMBO J, 24, 3670-3680.
PDB codes: 2a78 2a9k
16099990 C.J.O'Neal, M.G.Jobling, R.K.Holmes, and W.G.Hol (2005).
Structural basis for the activation of cholera toxin by human ARF6-GTP.
  Science, 309, 1093-1096.
PDB codes: 2a5d 2a5f 2a5g
15933034 J.H.Paul, S.J.Williamson, A.Long, R.N.Authement, D.John, A.M.Segall, F.L.Rohwer, M.Androlewicz, and S.Patterson (2005).
Complete genome sequence of phiHSIC, a pseudotemperate marine phage of Listonella pelagia.
  Appl Environ Microbiol, 71, 3311-3320.  
15809419 K.P.Holbourn, J.M.Sutton, H.R.Evans, C.C.Shone, and K.R.Acharya (2005).
Molecular recognition of an ADP-ribosylating Clostridium botulinum C3 exoenzyme by RalA GTPase.
  Proc Natl Acad Sci U S A, 102, 5357-5362.
PDB codes: 1wca 2bov
16107839 R.Jørgensen, A.R.Merrill, S.P.Yates, V.E.Marquez, A.L.Schwan, T.Boesen, and G.R.Andersen (2005).
Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry.
  Nature, 436, 979-984.
PDB codes: 1zm2 1zm3 1zm4 1zm9
15353562 H.Barth, K.Aktories, M.R.Popoff, and B.G.Stiles (2004).
Binary bacterial toxins: biochemistry, biology, and applications of common Clostridium and Bacillus proteins.
  Microbiol Mol Biol Rev, 68, 373.  
15272191 H.R.Evans, D.E.Holloway, J.M.Sutton, J.Ayriss, C.C.Shone, and K.R.Acharya (2004).
C3 exoenzyme from Clostridium botulinum: structure of a tetragonal crystal form and a reassessment of NAD-induced flexure.
  Acta Crystallogr D Biol Crystallogr, 60, 1502-1505.
PDB code: 1uzi
15311272 J.Sun, A.W.Maresso, J.J.Kim, and J.T.Barbieri (2004).
How bacterial ADP-ribosylating toxins recognize substrates.
  Nat Struct Mol Biol, 11, 868-876.  
15458407 L.H.Coye, and C.M.Collins (2004).
Identification of SpyA, a novel ADP-ribosyltransferase of Streptococcus pyogenes.
  Mol Microbiol, 54, 89-98.  
12721285 C.Bourgeois, I.Okazaki, E.Cavanaugh, M.Nightingale, and J.Moss (2003).
Identification of regulatory domains in ADP-ribosyltransferase-1 that determine transferase and NAD glycohydrolase activities.
  J Biol Chem, 278, 26351-26355.  
12925212 G.Scott, S.Leopardi, L.Parker, L.Babiarz, M.Seiberg, and R.Han (2003).
The proteinase-activated receptor-2 mediates phagocytosis in a Rho-dependent manner in human keratinocytes.
  J Invest Dermatol, 121, 529-541.  
12933793 H.R.Evans, J.M.Sutton, D.E.Holloway, J.Ayriss, C.C.Shone, and K.R.Acharya (2003).
The crystal structure of C3stau2 from Staphylococcus aureus and its complex with NAD.
  J Biol Chem, 278, 45924-45930.
PDB codes: 1ojq 1ojz
12807879 J.Sun, and J.T.Barbieri (2003).
Pseudomonas aeruginosa ExoT ADP-ribosylates CT10 regulator of kinase (Crk) proteins.
  J Biol Chem, 278, 32794-32800.  
12077446 C.Mueller-Dieckmann, T.Scheuermann, K.Wursthorn, J.Schröder, F.Haag, G.E.Schulz, and F.Koch-Nolte (2002).
Expression, purification, crystallization and preliminary X-ray analysis of rat ecto-ADP-ribosyltransferase 2 (ART2.2).
  Acta Crystallogr D Biol Crystallogr, 58, 1211-1213.  
  11847234 C.Wilde, H.Barth, P.Sehr, L.Han, M.Schmidt, I.Just, and K.Aktories (2002).
Interaction of the Rho-ADP-ribosylating C3 exoenzyme with RalA.
  J Biol Chem, 277, 14771-14776.  
11814347 C.Wilde, I.Just, and K.Aktories (2002).
Structure-function analysis of the Rho-ADP-ribosylating exoenzyme C3stau2 from Staphylococcus aureus.
  Biochemistry, 41, 1539-1544.  
12070318 G.Glowacki, R.Braren, K.Firner, M.Nissen, M.Kühl, P.Reche, F.Bazan, M.Cetkovic-Cvrlje, E.Leiter, F.Haag, and F.Koch-Nolte (2002).
The family of toxin-related ecto-ADP-ribosyltransferases in humans and the mouse.
  Protein Sci, 11, 1657-1670.  
12221101 J.C.Marvaud, B.G.Stiles, A.Chenal, D.Gillet, M.Gibert, L.A.Smith, and M.R.Popoff (2002).
Clostridium perfringens iota toxin. Mapping of the Ia domain involved in docking with Ib and cellular internalization.
  J Biol Chem, 277, 43659-43666.  
12029083 J.Ménétrey, G.Flatau, E.A.Stura, J.B.Charbonnier, F.Gas, J.M.Teulon, M.H.Le Du, P.Boquet, and A.Menez (2002).
NAD binding induces conformational changes in Rho ADP-ribosylating clostridium botulinum C3 exoenzyme.
  J Biol Chem, 277, 30950-30957.
PDB codes: 1gze 1gzf
12399599 Y.Kamata, H.Hoshi, H.Choki, and S.Kozaki (2002).
Characterization of a neutralizing monoclonal antibody against botulinum ADP-ribosyltransferase, C3 exoenzyme.
  J Vet Med Sci, 64, 767-771.  
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.

 

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