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PDBsum entry 2a5g

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protein ligands metals Protein-protein interface(s) links
Protein transport/transferase PDB id
2a5g
Jmol
Contents
Protein chains
162 a.a. *
185 a.a. *
Ligands
GTP
Metals
_NA
_MG
Waters ×66
* Residue conservation analysis
PDB id:
2a5g
Name: Protein transport/transferase
Title: Cholera toxin a1 subunit bound to arf6(q67l)
Structure: Adp-ribosylation factor 6. Chain: a. Engineered: yes. Mutation: yes. Cholera enterotoxin, a chain. Chain: b. Fragment: cholera toxin a1 subunit. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: arf6. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Vibrio cholerae. Organism_taxid: 666. Gene: ctxa, toxa.
Biol. unit: Dimer (from PQS)
Resolution:
2.66Å     R-factor:   0.202     R-free:   0.265
Authors: C.J.O'Neal,M.G.Jobling,R.K.Holmes,W.G.J.Hol
Key ref:
C.J.O'Neal et al. (2005). Structural basis for the activation of cholera toxin by human ARF6-GTP. Science, 309, 1093-1096. PubMed id: 16099990 DOI: 10.1126/science.1113398
Date:
30-Jun-05     Release date:   16-Aug-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P62330  (ARF6_HUMAN) -  ADP-ribosylation factor 6
Seq:
Struc:
175 a.a.
162 a.a.*
Protein chain
Pfam   ArchSchema ?
P01555  (CHTA_VIBCH) -  Cholera enterotoxin subunit A
Seq:
Struc:
258 a.a.
185 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   19 terms 
  Biological process     protein localization in endosome   26 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
DOI no: 10.1126/science.1113398 Science 309:1093-1096 (2005)
PubMed id: 16099990  
 
 
Structural basis for the activation of cholera toxin by human ARF6-GTP.
C.J.O'Neal, M.G.Jobling, R.K.Holmes, W.G.Hol.
 
  ABSTRACT  
 
The Vibrio cholerae bacterium causes devastating diarrhea when it infects the human intestine. The key event is adenosine diphosphate (ADP)-ribosylation of the human signaling protein GSalpha, catalyzed by the cholera toxin A1 subunit (CTA1). This reaction is allosterically activated by human ADP-ribosylation factors (ARFs), a family of essential and ubiquitous G proteins. Crystal structures of a CTA1:ARF6-GTP (guanosine triphosphate) complex reveal that binding of the human activator elicits dramatic changes in CTA1 loop regions that allow nicotinamide adenine dinucleotide (NAD+) to bind to the active site. The extensive toxin:ARF-GTP interface surface mimics ARF-GTP recognition of normal cellular protein partners, which suggests that the toxin has evolved to exploit promiscuous binding properties of ARFs.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Changes in loop regions of CTA1 between holo-CT (left) and CTA1:ARF6-GTP (right) lead to opening of the active site (green). Loops are colored as in Fig. 1.
Figure 4.
Fig. 4. ARF6-GTP-bound CTA1 in complex with its substrate, NAD^+. (A) A [A]-weighted omit map contoured at 2.5 , showing density surrounding the NAD^+ molecule in the CTA1 active site. (B) Surface representation of the NAD^+-occupied CTA1 active site (green), viewed from the top. The large active-site cleft is open to solvent from the top and from both ends. ARF6-GTP, in yellow, binds to CTA1 (gray) far from the active site (green). The knob (red), formed by active-site loop residues 48 to 52 when CTA1 is ARF-bound, and the ARTT motif (brown) (40) form a surface for potential G[S ]recruitment. (C) Stereoview of contacts between NAD^+ and active site residues (green sticks). Hydrogen bonds are indicated as black dashes. A detailed listing of contacts between NAD^+ and CTA1 atoms is presented in table S4. NAD^+ makes extensive direct interactions with protein atoms but also recruits three waters and a glycerol molecule to mediate hydrogen bonds with the active site. Abbreviations of amino acid residues as in (41).
 
  The above figures are reprinted by permission from the AAAs: Science (2005, 309, 1093-1096) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21170023 A.S.Selyunin, S.E.Sutton, B.A.Weigele, L.E.Reddick, R.C.Orchard, S.M.Bresson, D.R.Tomchick, and N.M.Alto (2011).
The assembly of a GTPase-kinase signalling complex by a bacterial catalytic scaffold.
  Nature, 469, 107-111.
PDB codes: 3pcr 3pcs
21129209 A.F.Neuwald (2010).
Bayesian classification of residues associated with protein functional divergence: Arf and Arf-like GTPases.
  Biol Direct, 5, 66.  
20535822 A.Sircar, S.Chaudhury, K.P.Kilambi, M.Berrondo, and J.J.Gray (2010).
A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19.
  Proteins, 78, 3115-3123.  
20353553 H.R.Ansari, and G.P.Raghava (2010).
Identification of NAD interacting residues in proteins.
  BMC Bioinformatics, 11, 160.  
21152290 I.H.Moal, and P.A.Bates (2010).
SwarmDock and the Use of Normal Modes in Protein-Protein Docking.
  Int J Mol Sci, 11, 3623-3648.  
20607697 M.Eisenstein, A.Ben-Shimon, Z.Frankenstein, and N.Kowalsman (2010).
CAPRI targets T29-T42: proving ground for new docking procedures.
  Proteins, 78, 3174-3181.  
21134634 P.Chavrier, and J.Ménétrey (2010).
Toward a structural understanding of arf family:effector specificity.
  Structure, 18, 1552-1558.  
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.  
20597089 S.J.Fleishman, J.E.Corn, E.M.Strauch, T.A.Whitehead, I.Andre, J.Thompson, J.J.Havranek, R.Das, P.Bradley, and D.Baker (2010).
Rosetta in CAPRI rounds 13-19.
  Proteins, 78, 3212-3218.  
20635420 S.Y.Huang, and X.Zou (2010).
MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19.
  Proteins, 78, 3096-3103.  
19954358 D.Luongo, R.D'Arienzo, P.Bergamo, F.Maurano, and M.Rossi (2009).
Immunomodulation of gut-associated lymphoid tissue: current perspectives.
  Int Rev Immunol, 28, 446-464.  
19644450 T.Isabet, G.Montagnac, K.Regazzoni, B.Raynal, F.El Khadali, P.England, M.Franco, P.Chavrier, A.Houdusse, and J.Ménétrey (2009).
The structural basis of Arf effector specificity: the crystal structure of ARF6 in a complex with JIP4.
  EMBO J, 28, 2835-2845.
PDB code: 2w83
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
18241884 M.E.Yanez, K.V.Korotkov, J.Abendroth, and W.G.Hol (2008).
Structure of the minor pseudopilin EpsH from the Type 2 secretion system of Vibrio cholerae.
  J Mol Biol, 377, 91.
PDB code: 2qv8
18940667 Q.Liu, I.A.Kriksunov, H.Jiang, R.Graeff, H.Lin, H.C.Lee, and Q.Hao (2008).
Covalent and noncovalent intermediates of an NAD utilizing enzyme, human CD38.
  Chem Biol, 15, 1068-1078.
PDB codes: 3dzf 3dzg 3dzh 3dzi 3dzj 3dzk
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
18272180 R.S.Ampapathi, A.L.Creath, D.I.Lou, J.W.Craft, S.R.Blanke, and G.B.Legge (2008).
Order-disorder-order transitions mediate the activation of cholera toxin.
  J Mol Biol, 377, 748-760.  
17976649 A.H.Pande, P.Scaglione, M.Taylor, K.N.Nemec, S.Tuthill, D.Moe, R.K.Holmes, S.A.Tatulian, and K.Teter (2007).
Conformational instability of the cholera toxin A1 polypeptide.
  J Mol Biol, 374, 1114-1128.  
17506703 A.K.Gillingham, and S.Munro (2007).
The small G proteins of the Arf family and their regulators.
  Annu Rev Cell Dev Biol, 23, 579-611.  
17347647 J.Ménétrey, M.Perderiset, J.Cicolari, T.Dubois, N.Elkhatib, F.El Khadali, M.Franco, P.Chavrier, and A.Houdusse (2007).
Structural basis for ARF1-mediated recruitment of ARHGAP21 to Golgi membranes.
  EMBO J, 26, 1953-1962.
PDB code: 2j59
17451437 T.El Hage, C.Merlen, S.Fabrega, and F.Authier (2007).
Role of receptor-mediated endocytosis, endosomal acidification and cathepsin D in cholera toxin cytotoxicity.
  FEBS J, 274, 2614-2629.  
17360489 X.Wang, A.A.Ribeiro, Z.Guan, S.N.Abraham, and C.R.Raetz (2007).
Attenuated virulence of a Francisella mutant lacking the lipid A 4'-phosphatase.
  Proc Natl Acad Sci U S A, 104, 4136-4141.  
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.  
16552056 K.Teter, M.G.Jobling, D.Sentz, and R.K.Holmes (2006).
The cholera toxin A1(3) subdomain is essential for interaction with ADP-ribosylation factor 6 and full toxic activity but is not required for translocation from the endoplasmic reticulum to the cytosol.
  Infect Immun, 74, 2259-2267.  
16782791 P.J.Kundrotas, and E.Alexov (2006).
Electrostatic properties of protein-protein complexes.
  Biophys J, 91, 1724-1736.  
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.  
16142224 E.Jabri (2005).
A toxin activator.
  Nat Struct Mol Biol, 12, 736.  
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.