PDBsum entry 3bob

Lyase

PDB id: 3bob

Contents

Protein chain

209 a.a.

Metals

_CD

Waters ×250

PDB id:

3bob

Name:

Lyase

Title:

Carbonic anhydrase from marine diatom thalassiosira weissflogii- cadmium bound domain 2

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

Resolution:

1.45Å R-factor: 0.167 R-free: 0.194

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

Date:

17-Dec-07 Release date: 22-Jan-08

Protein chain

Q50EL4  (Q50EL4_THAWE) -  Cadmium-specific carbonic anhydrase (Fragment) from Thalassiosira weissflogii

Seq: 616 a.a.

Struc: 209 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.1.1 - carbonic anhydrase.
• Reaction: hydrogencarbonate + H⁺ = CO2 + H2O
• Cofactor: Zn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

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.

ABSTRACT

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.