PDBsum entry 1ddz

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Lyase PDB id
Protein chains
481 a.a.
_ZN ×4
Waters ×612
PDB id:
Name: Lyase
Title: X-ray structure of a beta-carbonic anhydrase from the red alga, porphyridium purpureum r-1
Structure: Carbonic anhydrase. Chain: a, b. Engineered: yes
Source: Porphyridium purpureum. Organism_taxid: 35688. Variant: r-1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.20Å     R-factor:   0.208     R-free:   0.274
Authors: S.Mitsuhashi,T.Mizushima,E.Yamashita,S.Miyachi,T.Tsukihara
Key ref:
S.Mitsuhashi et al. (2000). X-ray structure of beta-carbonic anhydrase from the red alga, Porphyridium purpureum, reveals a novel catalytic site for CO(2) hydration. J Biol Chem, 275, 5521-5526. PubMed id: 10681531 DOI: 10.1074/jbc.275.8.5521
12-Nov-99     Release date:   08-Mar-00    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q43060  (Q43060_PORCR) -  Carbonic anhydrase
571 a.a.
481 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Carbonate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
= CO(2)
+ H(2)O
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbon utilization   1 term 
  Biochemical function     carbonate dehydratase activity     2 terms  


    Added reference    
DOI no: 10.1074/jbc.275.8.5521 J Biol Chem 275:5521-5526 (2000)
PubMed id: 10681531  
X-ray structure of beta-carbonic anhydrase from the red alga, Porphyridium purpureum, reveals a novel catalytic site for CO(2) hydration.
S.Mitsuhashi, T.Mizushima, E.Yamashita, M.Yamamoto, T.Kumasaka, H.Moriyama, T.Ueki, S.Miyachi, T.Tsukihara.
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.
  Selected figure(s)  
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.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19679198 J.F.Domsic, and R.McKenna (2010).
Sequestration of carbon dioxide by the hydrophobic pocket of the carbonic anhydrases.
  Biochim Biophys Acta, 1804, 326-331.  
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
19296112 S.Elleuche, and S.Pöggeler (2009).
Evolution of carbonic anhydrases in fungi.
  Curr Genet, 55, 211-222.  
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.  
19549309 X.Wang, U.Gowik, H.Tang, J.E.Bowers, P.Westhoff, and A.H.Paterson (2009).
Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses.
  Genome Biol, 10, R68.  
19852838 Y.B.Teng, Y.L.Jiang, Y.X.He, W.W.He, F.M.Lian, Y.Chen, and C.Z.Zhou (2009).
Structural insights into the substrate tunnel of Saccharomyces cerevisiae carbonic anhydrase Nce103.
  BMC Struct Biol, 9, 67.
PDB code: 3eyx
18931408 J.Jeyakanthan, S.Rangarajan, P.Mridula, S.P.Kanaujia, Y.Shiro, S.Kuramitsu, S.Yokoyama, and K.Sekar (2008).
Observation of a calcium-binding site in the gamma-class carbonic anhydrase from Pyrococcus horikoshii.
  Acta Crystallogr D Biol Crystallogr, 64, 1012-1019.
PDB codes: 1v3w 1v67 2fko
18405332 R.A.Ynalvez, Y.Xiao, A.S.Ward, K.Cunnusamy, and J.V.Moroney (2008).
Identification and characterization of two closely related beta-carbonic anhydrases from Chlamydomonas reinhardtii.
  Physiol Plant, 133, 15-26.  
19012038 S.Morishita, I.Nishimori, T.Minakuchi, S.Onishi, H.Takeuchi, T.Sugiura, D.Vullo, A.Scozzafava, and C.T.Supuran (2008).
Cloning, polymorphism, and inhibition of beta-carbonic anhydrase of Helicobacter pylori.
  J Gastroenterol, 43, 849-857.  
18335973 V.M.Krishnamurthy, G.K.Kaufman, A.R.Urbach, I.Gitlin, K.L.Gudiksen, D.B.Weibel, and G.M.Whitesides (2008).
Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding.
  Chem Rev, 108, 946.  
18322527 Y.Xu, L.Feng, P.D.Jeffrey, Y.Shi, and F.M.Morel (2008).
Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms.
  Nature, 452, 56-61.
PDB codes: 3bob 3boc 3boe 3boh 3boj
17623850 B.Tamames, S.F.Sousa, J.Tamames, P.A.Fernandes, and M.J.Ramos (2007).
Analysis of zinc-ligand bond lengths in metalloproteins: trends and patterns.
  Proteins, 69, 466-475.  
17222138 H.Park, B.Song, and F.M.Morel (2007).
Diversity of the cadmium-containing carbonic anhydrase in marine diatoms and natural waters.
  Environ Microbiol, 9, 403-413.  
16863473 B.W.Clare, and C.T.Supuran (2006).
A perspective on quantitative structure-activity relationships and carbonic anhydrase inhibitors.
  Expert Opin Drug Metab Toxicol, 2, 113-137.  
16400172 E.G.Mogensen, G.Janbon, J.Chaloupka, C.Steegborn, M.S.Fu, F.Moyrand, T.Klengel, D.S.Pearson, M.A.Geeves, J.Buck, L.R.Levin, and F.A.Mühlschlegel (2006).
Cryptococcus neoformans senses CO2 through the carbonic anhydrase Can2 and the adenylyl cyclase Cac1.
  Eukaryot Cell, 5, 103-111.  
16821039 K.N.Sas, L.Kovács, O.Zsíros, Z.Gombos, G.Garab, L.Hemmingsen, and E.Danielsen (2006).
Fast cadmium inhibition of photosynthesis in cyanobacteria in vivo and in vitro studies using perturbed angular correlation of gamma-rays.
  J Biol Inorg Chem, 11, 725-734.  
17012396 S.Heinhorst, E.B.Williams, F.Cai, C.D.Murin, J.M.Shively, and G.C.Cannon (2006).
Characterization of the carboxysomal carbonic anhydrase CsoSCA from Halothiobacillus neapolitanus.
  J Bacteriol, 188, 8087-8094.  
12500287 C.T.Supuran, A.Scozzafava, and A.Casini (2003).
Carbonic anhydrase inhibitors.
  Med Res Rev, 23, 146-189.  
12193617 B.Kusian, D.Sültemeyer, and B.Bowien (2002).
Carbonic anhydrase is essential for growth of Ralstonia eutropha at ambient CO(2) concentrations.
  J Bacteriol, 184, 5018-5026.  
12107142 K.S.Smith, C.Ingram-Smith, and J.G.Ferry (2002).
Roles of the conserved aspartate and arginine in the catalytic mechanism of an archaeal beta-class carbonic anhydrase.
  J Bacteriol, 184, 4240-4245.  
12220492 T.Kumasaka, M.Yamamoto, E.Yamashita, H.Moriyama, and T.Ueki (2002).
Trichromatic concept optimizes MAD experiments in synchrotron X-ray crystallography.
  Structure, 10, 1205-1210.  
11241598 H.Strasdeit (2001).
The First Cadmium-Specific Enzyme.
  Angew Chem Int Ed Engl, 40, 707-709.  
11316870 J.D.Cronk, J.A.Endrizzi, M.R.Cronk, J.W.O'neill, and K.Y.Zhang (2001).
Crystal structure of E. coli beta-carbonic anhydrase, an enzyme with an unusual pH-dependent activity.
  Protein Sci, 10, 911-922.
PDB codes: 1i6o 1i6p
11256616 A.Liljas, and M.Laurberg (2000).
A wheel invented three times. The molecular structures of the three carbonic anhydrases.
  EMBO Rep, 1, 16-17.  
11015190 E.H.Cox, G.L.McLendon, F.M.Morel, T.W.Lane, R.C.Prince, I.J.Pickering, and G.N.George (2000).
The active site structure of Thalassiosira weissflogii carbonic anhydrase 1.
  Biochemistry, 39, 12128-12130.  
10957638 J.D.Cronk, J.W.O'Neill, M.R.Cronk, J.A.Endrizzi, and K.Y.Zhang (2000).
Cloning, crystallization and preliminary characterization of a beta-carbonic anhydrase from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 56, 1176-1179.  
11073902 K.S.Smith, N.J.Cosper, C.Stalhandske, R.A.Scott, and J.G.Ferry (2000).
Structural and kinetic characterization of an archaeal beta-class carbonic anhydrase.
  J Bacteriol, 182, 6605-6613.  
10924115 T.M.Iverson, B.E.Alber, C.Kisker, J.G.Ferry, and D.C.Rees (2000).
A closer look at the active site of gamma-class carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila.
  Biochemistry, 39, 9222-9231.
PDB codes: 1qq0 1qre 1qrf 1qrg 1qrl 1qrm
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.