spacer
spacer

PDBsum entry 1xfx
Go to PDB code: 
protein metals Protein-protein interface(s) links
Lyase/metal binding protein PDB id
1xfx

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
(+ 0 more) 735 a.a.
(+ 0 more) 146 a.a. *
Metals
_MG ×6
_CA ×24
* Residue conservation analysis
PDB id:
1xfx
Name: Lyase/metal binding protein
Title: Crystal structure of anthrax edema factor (ef) in complex with calmodulin in the presence of 10 millimolar exogenously added calcium chloride
Structure: Calmodulin-sensitive adenylate cyclase. Chain: a, b, c, d, e, f. Synonym: atp pyrophosphate-lyase, adenylyl cyclase, edema factor, ef, anthrax edema toxin adenylate cyclase component. Engineered: yes. Calmodulin 2. Chain: o, p, q, r, s, t. Engineered: yes
Source: Bacillus anthracis. Organism_taxid: 1392. Gene: cya. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
3.20Å     R-factor:   0.262     R-free:   0.278
Authors: Y.Shen,N.L.Zhukovskaya,Q.Guo,J.Florian,W.J.Tang
Key ref:
Y.Shen et al. (2005). Calcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor. EMBO J, 24, 929-941. PubMed id: 15719022 DOI: 10.1038/sj.emboj.7600574
Date:
15-Sep-04     Release date:   03-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P40136  (CYAA_BACAN) -  Calmodulin-sensitive adenylate cyclase from Bacillus anthracis
Seq:
Struc: 		 
Seq:
Struc: 		800 a.a.
735 a.a.
Protein chains
Pfam   ArchSchema ?
P0DP23  (CALM1_HUMAN) -  Calmodulin-1 from Homo sapiens
Seq:
Struc: 		149 a.a.
146 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F: E.C.4.6.1.1  - adenylate cyclase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP = 3',5'-cyclic AMP + diphosphate
ATP
 = 3',5'-cyclic AMP
 + diphosphate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1038/sj.emboj.7600574 EMBO J 24:929-941 (2005)
PubMed id: 15719022  
 
 
Calcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor.
Y.Shen, N.L.Zhukovskaya, Q.Guo, J.Florián, W.J.Tang.
 
  ABSTRACT  
 
Edema factor (EF), a key anthrax exotoxin, has an anthrax protective antigen-binding domain (PABD) and a calmodulin (CaM)-activated adenylyl cyclase domain. Here, we report the crystal structures of CaM-bound EF, revealing the architecture of EF PABD. CaM has N- and C-terminal domains and each domain can bind two calcium ions. Calcium binding induces the conformational change of CaM from closed to open. Structures of the EF-CaM complex show how EF locks the N-terminal domain of CaM into a closed conformation regardless of its calcium-loading state. This represents a mechanism of how CaM effector alters the calcium affinity of CaM and uncouples the conformational change of CaM from calcium loading. Furthermore, structures of EF-CaM complexed with nucleotides show that EF uses two-metal-ion catalysis, a prevalent mechanism in DNA and RNA polymerases. A histidine (H351) further facilitates the catalysis of EF by activating a water to deprotonate 3'OH of ATP. Mammalian adenylyl cyclases share no structural similarity with EF and they also use two-metal-ion catalysis, suggesting the catalytic mechanism-driven convergent evolution of two structurally diverse adenylyl cyclases.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Structure of EF -CaM complex. (A) Ribbon diagram of EF in complex with CaM and that of LF. Catalytic core domain, helical domain, N-terminal PABD, and C-terminal PABD of EF are colored in green, yellow, blue, and purple, respectively, and CaM in red. N-terminal PABD, C-terminal PABD, and protease domain of LF are in blue, purple and green, respectively. (B) Comparison of PABDs of EF and LF. The similar secondary structures of the N-terminal / sandwich of PABDs of EF and LF are depicted in blue and dark blue, respectively, and those of the C-terminal five-helix domain of PABD of EF and LF are colored in purple and magenta, respectively. Five loops, L1 -L5, which have significant differences between EF-PABD and LF-PABD, are colored in cyan and yellow, respectively. (C) Sequence alignment of PABD of EF and LF. Identical sequences are colored in yellow and similar sequences are in green. 		Figure 2.
Figure 2 Structures of N-CaM and its interaction with EF. (A) Structures of N-CaM (red) in EF -CaM complex at 1 M calcium, 1 mM calcium, 10 mM calcium concentrations in comparison with the calcium-free N-CaM structure (left, PDB code: 1CFD) and the crystal structure of four calcium-loaded CaM (right, PDB code: 1CLL). Calcium ions are colored in orange. (B) The interaction between N-CaM and the helical domain of EF. The helical domains of EF and N-CaM of the EF -CaM complex at 10 mM calcium concentration are colored in yellow and red, respectively. For comparison, four calcium-loaded CaM is shown in cyan. (C) Detailed hydrogen bonding and salt bridge formed at the interface between helices I and II of N-CaM and helices L and M of EF.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2005, 24, 929-941) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21262847 L.D.Jennings-Antipov, L.Song, and R.J.Collier (2011).
Interactions of anthrax lethal factor with protective antigen defined by site-directed spin labeling.
  Proc Natl Acad Sci U S A, 108, 1868-1873.  
21425348 L.Martínez, T.E.Malliavin, and A.Blondel (2011).
Mechanism of reactant and product dissociation from the anthrax edema factor: A locally enhanced sampling and steered molecular dynamics study.
  Proteins, 79, 1649-1661.  
20534570 E.Laine, C.Goncalves, J.C.Karst, A.Lesnard, S.Rault, W.J.Tang, T.E.Malliavin, D.Ladant, and A.Blondel (2010).
Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor.
  Proc Natl Acad Sci U S A, 107, 11277-11282.  
20438574 I.Zornetta, L.Brandi, B.Janowiak, F.Dal Molin, F.Tonello, R.J.Collier, and C.Montecucco (2010).
Imaging the cell entry of the anthrax oedema and lethal toxins with fluorescent protein chimeras.
  Cell Microbiol, 12, 1435-1445.  
19217845 E.Laine, A.Blondel, and T.E.Malliavin (2009).
Dynamics and energetics: a consensus analysis of the impact of calcium on EF-CaM protein complex.
  Biophys J, 96, 1249-1263.  
19056899 H.M.Taha, J.Schmidt, M.Göttle, S.Suryanarayana, Y.Shen, W.J.Tang, A.Gille, J.Geduhn, B.König, S.Dove, and R.Seifert (2009).
Molecular analysis of the interaction of anthrax adenylyl cyclase toxin, edema factor, with 2'(3')-O-(N-(methyl)anthraniloyl)-substituted purine and pyrimidine nucleotides.
  Mol Pharmacol, 75, 693-703.  
19705488 L.Martínez, E.Laine, T.E.Malliavin, M.Nilges, and A.Blondel (2009).
ATP conformations and ion binding modes in the active site of anthrax edema factor: a computational analysis.
  Proteins, 77, 971-983.  
19266022 S.Rossi Paccani, M.Benagiano, N.Capitani, I.Zornetta, D.Ladant, C.Montecucco, M.M.D'Elios, and C.T.Baldari (2009).
The adenylate cyclase toxins of Bacillus anthracis and Bordetella pertussis promote Th2 cell development by shaping T cell antigen receptor signaling.
  PLoS Pathog, 5, e1000325.  
19560485 W.J.Tang, and Q.Guo (2009).
The adenylyl cyclase activity of anthrax edema factor.
  Mol Aspects Med, 30, 423-430.  
19348766 Y.Zhou, W.Yang, M.M.Lurtz, Y.Chen, J.Jiang, Y.Huang, C.F.Louis, and J.J.Yang (2009).
Calmodulin mediates the Ca2+-dependent regulation of Cx44 gap junctions.
  Biophys J, 96, 2832-2848.  
19528217 Z.Chen, M.Moayeri, D.Crown, S.Emerson, I.Gorshkova, P.Schuck, S.H.Leppla, and R.H.Purcell (2009).
Novel chimpanzee/human monoclonal antibodies that neutralize anthrax lethal factor, and evidence for possible synergy with anti-protective antigen antibody.
  Infect Immun, 77, 3902-3908.  
18620864 D.Chen, M.Misra, L.Sower, J.W.Peterson, G.E.Kellogg, and C.H.Schein (2008).
Novel inhibitors of anthrax edema factor.
  Bioorg Med Chem, 16, 7225-7233.  
18175311 E.Laine, J.D.Yoneda, A.Blondel, and T.E.Malliavin (2008).
The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis.
  Proteins, 71, 1813-1829.  
18765729 J.L.Larabee, K.DeGiusti, J.L.Regens, and J.D.Ballard (2008).
Bacillus anthracis edema toxin activates nuclear glycogen synthase kinase 3beta.
  Infect Immun, 76, 4895-4904.  
18583346 Q.Guo, J.E.Jureller, J.T.Warren, E.Solomaha, J.Florián, and W.J.Tang (2008).
Protein-protein docking and analysis reveal that two homologous bacterial adenylyl cyclase toxins interact with calmodulin differently.
  J Biol Chem, 283, 23836-23845.  
17311351 D.Chen, G.Menche, T.D.Power, L.Sower, J.W.Peterson, and C.H.Schein (2007).
Accounting for ligand-bound metal ions in docking small molecules on adenylyl cyclase toxins.
  Proteins, 67, 593-605.  
  19081825 J.Mogridge (2007).
Defensive strategies of Bacillus anthracis that promote a fatal disease.
  Drug Discov Today Dis Mech, 4, 253-258.  
17942116 J.T.Warren, Q.Guo, and W.J.Tang (2007).
A 1.3-A structure of zinc-bound N-terminal domain of calmodulin elucidates potential early ion-binding step.
  J Mol Biol, 374, 517-527.
PDB code: 2pq3
  17095744 K.Sherer, Y.Li, X.Cui, and P.Q.Eichacker (2007).
Lethal and edema toxins in the pathogenesis of Bacillus anthracis septic shock: implications for therapy.
  Am J Respir Crit Care Med, 175, 211-221.  
17555370 Y.Li, K.Sherer, X.Cui, and P.Q.Eichacker (2007).
New insights into the pathogenesis and treatment of anthrax toxin-induced shock.
  Expert Opin Biol Ther, 7, 843-854.  
17082768 F.Dal Molin, F.Tonello, D.Ladant, I.Zornetta, I.Zamparo, G.Di Benedetto, M.Zaccolo, and C.Montecucco (2006).
Cell entry and cAMP imaging of anthrax edema toxin.
  EMBO J, 25, 5405-5413.  
16672596 P.Keim, M.Mock, J.Young, and T.M.Koehler (2006).
The International Bacillus anthracis, B. cereus, and B. thuringiensis Conference, "Bacillus-ACT05".
  J Bacteriol, 188, 3433-3441.  
16251269 D.B.Lacy, H.C.Lin, R.A.Melnyk, O.Schueler-Furman, L.Reither, K.Cunningham, D.Baker, and R.J.Collier (2005).
A model of anthrax toxin lethal factor bound to protective antigen.
  Proc Natl Acad Sci U S A, 102, 16409-16414.  
16138079 Q.Guo, Y.Shen, Y.S.Lee, C.S.Gibbs, M.Mrksich, and W.J.Tang (2005).
Structural basis for the interaction of Bordetella pertussis adenylyl cyclase toxin with calmodulin.
  EMBO J, 24, 3190-3201.
PDB codes: 1yrt 1yru 1zot 2col
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.

 

spacer
spacer