PDBsum entry 1ddz

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Lyase PDB id
Protein chains
481 a.a. *
_ZN ×4
Waters ×612
* Residue conservation analysis

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Key reference
Title X-Ray structure of beta-Carbonic anhydrase from the red alga, Porphyridium purpureum, Reveals a novel catalytic site for co(2) hydration.
Authors S.Mitsuhashi, T.Mizushima, E.Yamashita, M.Yamamoto, T.Kumasaka, H.Moriyama, T.Ueki, S.Miyachi, T.Tsukihara.
Ref. J Biol Chem, 2000, 275, 5521-5526. [DOI no: 10.1074/jbc.275.8.5521]
PubMed id 10681531
The carbonic anhydrases (CAs) fall into three evolutionarily distinct families designated alpha-, beta-, and gamma-CAs based on their primary structure. beta-CAs are present in higher plants, algae, and prokaryotes, and are involved in inorganic carbon utilization. Here, we describe the novel x-ray structure of beta-CA from the red alga, Porphyridium purpureum, at 2.2-A resolution using intrinsic zinc multiwavelength anomalous diffraction phasing. The CA monomer is composed of two internally repeating structures, being folded as a pair of fundamentally equivalent motifs of an alpha/beta domain and three projecting alpha-helices. The motif is obviously distinct from that of either alpha- or gamma-CAs. This homodimeric CA appears like a tetramer with a pseudo 222 symmetry. The active site zinc is coordinated by a Cys-Asp-His-Cys tetrad that is strictly conserved among the beta-CAs. No water molecule is found in a zinc-liganding radius, indicating that the zinc-hydroxide mechanism in alpha-CAs, and possibly in gamma-CAs, is not directly applicable to the case in beta-CAs. Zinc coordination environments of the CAs provide an interesting example of the convergent evolution of distinct catalytic sites required for the same CO(2) hydration reaction.
Figure 1.
Fig. 1. Schematic drawings illustrating the structure of P. purpureum CA. A, stereo view of ribbon diagram of a monomer along pseudo 2-fold axis of a monomer. The N- and C-terminal halves and the other parts are colored blue, green, and gray, respectively. -Helices and -strands are shown as ribbons and arrows, respectively. The positions of zinc are shown as red spheres. N and C termini are marked. B, a C trace of the dimer. One monomer is shown in blue, the other in red. The positions of zinc are shown as green spheres. Left, a view looking down along pseudo 2-fold axis of a dimer. Right, a view looking down along 2-fold axis of a dimer. Note that a long turn segment (residues 310-339) connecting the N- and C-terminal halves protrudes out from one monomer to the surface of the counter monomer and has no symmetrical counterpart. Closed circles, black open circles, and red open circles represent 2-fold axis between the dimer, pseudo 2-fold axis between the dimer, and pseudo 2-fold axis within a monomer, respectively.
Figure 4.
Fig. 4. Proposed CO[2] hydration mechanism based on the x-ray structure of P. purpureum CA. See text for the explanation of each step.
The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 5521-5526) copyright 2000.
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