PDBsum entry 3boe

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Lyase PDB id
Protein chain
209 a.a.
Waters ×247
PDB id:
Name: Lyase
Title: Carbonic anhydrase from marine diatom thalassiosira weissflo cadmium bound domain 2 with acetate (cdca1-r2)
Structure: Cadmium-specific carbonic anhydrase. Chain: a. Fragment: domain 2, cdca1-r2. Engineered: yes
Source: Thalassiosira weissflogii. Organism_taxid: 67004. Gene: cdca1. Expressed in: escherichia coli. Expression_system_taxid: 562
1.40Å     R-factor:   0.166     R-free:   0.186
Authors: Y.Xu,L.Feng,P.D.Jeffrey,Y.Shi,F.M.M.Morel
Key ref:
Y.Xu et al. (2008). Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms. Nature, 452, 56-61. PubMed id: 18322527 DOI: 10.1038/nature06636
17-Dec-07     Release date:   22-Jan-08    
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Protein chain
Pfam   ArchSchema ?
Q50EL4  (Q50EL4_THAWE) -  Cadmium-specific carbonic anhydrase (Fragment)
616 a.a.
209 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1038/nature06636 Nature 452:56-61 (2008)
PubMed id: 18322527  
Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms.
Y.Xu, L.Feng, P.D.Jeffrey, Y.Shi, F.M.Morel.
Carbonic anhydrase, a zinc enzyme found in organisms from all kingdoms, catalyses the reversible hydration of carbon dioxide and is used for inorganic carbon acquisition by phytoplankton. In the oceans, where zinc is nearly depleted, diatoms use cadmium as a catalytic metal atom in cadmium carbonic anhydrase (CDCA). Here we report the crystal structures of CDCA in four distinct forms: cadmium-bound, zinc-bound, metal-free and acetate-bound. Despite lack of sequence homology, CDCA is a structural mimic of a functional beta-carbonic anhydrase dimer, with striking similarity in the spatial organization of the active site residues. CDCA readily exchanges cadmium and zinc at its active site--an apparently unique adaptation to oceanic life that is explained by a stable opening of the metal coordinating site in the absence of metal. Given the central role of diatoms in exporting carbon to the deep sea, their use of cadmium in an enzyme critical for carbon acquisition establishes a remarkable link between the global cycles of cadmium and carbon.
  Selected figure(s)  
Figure 1.
Figure 1: Structure of the second CA repeat of CDCA1 (CDCA1-R2). a, Overall structure of the Cd-bound CDCA1-R2. Two lobes of the structure are coloured blue and green. Cd is highlighted in red, and Cd-coordinating residues are coloured yellow. b, Comparison of the active site conformation between CDCA-R2 (green) and -CA (blue). The active site residues in CDCA-R2 and -CA are coloured yellow and orange, respectively. Hydrogen bonds are represented by red dashed lines. Cd and the water ligand are shown in large and small red spheres, respectively. (A stereo view is shown in Supplementary Fig. 1b.) c, Comparison of Cd- and Zn-coordination in CDCA1-R2. Metal coordination and hydrogen bonds are indicated by red and green dashed lines, respectively; numbers indicate bond lengths in Å. W1–W3, water molecules. Structural images were prepared using MOLSCRIPT^44 and GRASP^45.
Figure 3.
Figure 3: Structure of CDCA1-R2 bound to substrate analogue acetate. a, A close-up view of the region around acetate. The F[o] - F[c] electron density map surrounding acetate was calculated using simulated annealing with the omission of acetate and was contoured at 5 . b, A close-up view of the active site conformation. Metal coordination and hydrogen bonds are indicated by red and green dashed lines, respectively. Relevant distances are indicated (Å). c, A hydrophobic channel traverses through CDCA1-R2. Cd is highlighted in red. Acetate is shown in yellow. The conserved hydrophobic residues that line the channel are shown in magenta. (Stereo views of a and b are shown in Supplementary Fig.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 452, 56-61) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21321195 B.M.Hopkinson, C.L.Dupont, A.E.Allen, and F.M.Morel (2011).
Efficiency of the CO2-concentrating mechanism of diatoms.
  Proc Natl Acad Sci U S A, 108, 3830-3837.  
20803169 C.T.Supuran (2011).
Carbonic anhydrase inhibition with natural products: novel chemotypes and inhibition mechanisms.
  Mol Divers, 15, 305-316.  
21402476 F.Carta, A.Innocenti, R.A.Hall, F.A.Mühlschlegel, A.Scozzafava, and C.T.Supuran (2011).
Carbonic anhydrase inhibitors. Inhibition of the β-class enzymes from the fungal pathogens Candida albicans and Cryptococcus neoformans with branched aliphatic/aromatic carboxylates and their derivatives.
  Bioorg Med Chem Lett, 21, 2521-2526.  
21298147 F.Pannetier, G.Ohanessian, and G.Frison (2011).
Comparison between α- and β-carbonic anhydrases: can Zn(His)3(H2O) and Zn(His)(Cys)2(H2O) sites lead to equivalent enzymes?
  Dalton Trans, 40, 2696-2698.  
21377464 J.A.Cuesta-Seijo, M.S.Borchert, J.C.Navarro-Poulsen, K.M.Schnorr, S.B.Mortensen, and L.Lo Leggio (2011).
Structure of a dimeric fungal α-type carbonic anhydrase.
  FEBS Lett, 585, 1042-1048.  
20490881 J.A.Tamames, and M.J.Ramos (2011).
Metals in proteins: cluster analysis studies.
  J Mol Model, 17, 429-442.  
  21329207 J.R.Reinfelder (2011).
Carbon concentrating mechanisms in eukaryotic marine phytoplankton.
  Ann Rev Mar Sci, 3, 291-315.  
21212893 O.Amata, T.Marino, N.Russo, and M.Toscano (2011).
Catalytic activity of a ζ-class zinc and cadmium containing carbonic anhydrase. Compared work mechanisms.
  Phys Chem Chem Phys, 13, 3468-3477.  
20019664 C.A.Ohlin, E.M.Villa, J.R.Rustad, and W.H.Casey (2010).
Dissolution of insulating oxide materials at the molecular scale.
  Nat Mater, 9, 11-19.  
19747990 J.G.Ferry (2010).
The gamma class of carbonic anhydrases.
  Biochim Biophys Acta, 1804, 374-381.  
20659325 L.Syrjänen, M.Tolvanen, M.Hilvo, A.Olatubosun, A.Innocenti, A.Scozzafava, J.Leppiniemi, B.Niederhauser, V.P.Hytönen, T.A.Gorr, S.Parkkila, and C.T.Supuran (2010).
Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates.
  BMC Biochem, 11, 28.  
20512401 M.Smiri, A.Chaoui, N.Rouhier, C.Kamel, E.Gelhaye, J.P.Jacquot, and E.El Ferjani (2010).
Cadmium induced mitochondrial redox changes in germinating pea seed.
  Biometals, 23, 973-984.  
19675642 K.J.Waldron, J.C.Rutherford, D.Ford, and N.J.Robinson (2009).
Metalloproteins and metal sensing.
  Nature, 460, 823-830.  
19079350 K.J.Waldron, and N.J.Robinson (2009).
How do bacterial cells ensure that metalloproteins get the correct metal?
  Nat Rev Microbiol, 7, 25-35.  
19459702 R.S.Rowlett, C.Tu, J.Lee, A.G.Herman, D.A.Chapnick, S.H.Shah, and P.C.Gareiss (2009).
Allosteric site variants of Haemophilus influenzae beta-carbonic anhydrase.
  Biochemistry, 48, 6146-6156.
PDB codes: 3e1v 3e1w 3e24 3e28 3e2a 3e2w
19365544 S.Elleuche, and S.Pöggeler (2009).
Beta-carbonic anhydrases play a role in fruiting body development and ascospore germination in the filamentous fungus Sordaria macrospora.
  PLoS ONE, 4, e5177.  
18617510 A.Moya, S.Tambutté, A.Bertucci, E.Tambutté, S.Lotto, D.Vullo, C.T.Supuran, D.Allemand, and D.Zoccola (2008).
Carbonic anhydrase in the scleractinian coral Stylophora pistillata: characterization, localization, and role in biomineralization.
  J Biol Chem, 283, 25475-25484.  
18498530 F.M.Morel (2008).
The co-evolution of phytoplankton and trace element cycles in the oceans.
  Geobiology, 6, 318-324.  
18768466 J.F.Domsic, B.S.Avvaru, C.U.Kim, S.M.Gruner, M.Agbandje-McKenna, D.N.Silverman, and R.McKenna (2008).
Entrapment of Carbon Dioxide in the Active Site of Carbonic Anhydrase II.
  J Biol Chem, 283, 30766-30771.
PDB codes: 3d92 3d93
18535849 R.E.Mirams, S.J.Smith, K.S.Hadler, D.L.Ollis, G.Schenk, and L.R.Gahan (2008).
Cadmium(II) complexes of the glycerophosphodiester-degrading enzyme GpdQ and a biomimetic N,O ligand.
  J Biol Inorg Chem, 13, 1065-1072.  
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.