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PDBsum entry 2fgy

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protein metals Protein-protein interface(s) links
Lyase PDB id
2fgy
Jmol
Contents
Protein chains
471 a.a. *
Metals
_ZN ×4
Waters ×557
* Residue conservation analysis
PDB id:
2fgy
Name: Lyase
Title: Beta carbonic anhydrase from the carboxysomal shell of halothiobacillus neapolitanus (csosca)
Structure: Carboxysome shell polypeptide. Chain: a, b. Engineered: yes. Mutation: yes
Source: Halothiobacillus neapolitanus. Organism_taxid: 927. Gene: csosca. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: gene name is previously known as csos3
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.171     R-free:   0.217
Authors: M.R.Sawaya
Key ref:
M.R.Sawaya et al. (2006). The structure of beta-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two. J Biol Chem, 281, 7546-7555. PubMed id: 16407248 DOI: 10.1074/jbc.M510464200
Date:
22-Dec-05     Release date:   17-Jan-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O85042  (O85042_THINE) -  Carboxysome shell polypeptide
Seq:
Struc:
514 a.a.
471 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     metal ion binding     1 term  

 

 
DOI no: 10.1074/jbc.M510464200 J Biol Chem 281:7546-7555 (2006)
PubMed id: 16407248  
 
 
The structure of beta-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two.
M.R.Sawaya, G.C.Cannon, S.Heinhorst, S.Tanaka, E.B.Williams, T.O.Yeates, C.A.Kerfeld.
 
  ABSTRACT  
 
CsoSCA (formerly CsoS3) is a bacterial carbonic anhydrase localized in the shell of a cellular microcompartment called the carboxysome, where it converts HCO(3)(-) to CO(2) for use in carbon fixation by ribulose-bisphosphate carboxylase/oxygenase (RuBisCO). CsoSCA lacks significant sequence similarity to any of the four known classes of carbonic anhydrase (alpha, beta, gamma, or delta), and so it was initially classified as belonging to a new class, epsilon. The crystal structure of CsoSCA from Halothiobacillus neapolitanus reveals that it is actually a representative member of a new subclass of beta-carbonic anhydrases, distinguished by a lack of active site pairing. Whereas a typical beta-carbonic anhydrase maintains a pair of active sites organized within a two-fold symmetric homodimer or pair of fused, homologous domains, the two domains in CsoSCA have diverged to the point that only one domain in the pair retains a viable active site. We suggest that this defunct and somewhat diminished domain has evolved a new function, specific to its carboxysomal environment. Despite the level of sequence divergence that separates CsoSCA from the other two subclasses of beta-carbonic anhydrases, there is a remarkable level of structural similarity among active site regions, which suggests a common catalytic mechanism for the interconversion of HCO(3)(-) and CO(2). Crystal packing analysis suggests that CsoSCA exists within the carboxysome shell either as a homodimer or as extended filaments.
 
  Selected figure(s)  
 
Figure 3.
FIGURE 3. The loss of active site pairing in carboxysomal -carbonic anhydrases. In P. sativum (A, upper panel), active site pairing is accomplished through homodimerization. Molecule A of the dimer is shown in yellow; molecule B is shown in red. Green spheres mark the location of the two identical active site zinc ions. An ellipse marks the location of a two-fold symmetry axis. Superimposed molecules A and B are shown in C, lower panel. Only the very C-terminal (C-term) tails are not superimposable (colored gray). In P. purpureum (B, upper panel), the same pairing is accomplished by a single polypeptide, not a dimer. The N-terminal (N-term) domain is shown in yellow; the C-terminal domain is shown in red. Pseudo-two-fold symmetry is still evident but is not exact (B, lower panel). Non-superimposable regions are shown in gray. Presumably, the P. purpureum carbonic anhydrase arose from gene duplication and fusion. Divergence appears minimal (70% sequence identity between domains). In A, upper panel, CsoSCA, like the P. purpureum enzyme appears to be the result of gene duplication and fusion. However, divergence between the two internal domains has progressed to the extent that the C-terminal domain has lost all active site residues that it presumably once contained. Superimposed catalytic and C-terminal domains (C, lower panel) show much larger areas of structural nonequivalence (gray).
Figure 4.
FIGURE 4. Conservation of active site structure and mechanism. A, currently available structures of -carbonic anhydrases can be divided into two groups: those in which the conserved aspartate and arginine residues are hydrogen-bonded to each other (CsoSCA, P. sativum, M. thermoautotrophicum, and Rv1284) and those in which the hydrogen bonds are broken (P. purpureum, E. coli, and Rv3588c). These are represented in dark gray and light gray, respectively. In the former group, a water molecule serves as the fourth ligand to the zinc ion. In the latter group, the aspartate plays this role. The duality of conformations suggests a conformational flexibility that might play a role in catalysis. Residue numbering corresponds to CsoSCA. B, a stereo figure showing a superpositioning of CsoSCA (light gray) and P. sativum (dark gray) enzymes. A ion was modeled into the active site, based on similarities with the position of the acetate ion found in the P. sativum structure. Small changes in orientation of the allowed hydrogen bonds to form between the and zinc, His-397, Asp-175, and backbone nitrogens of Ala-254 and Ala-255.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 7546-7555) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20865174 C.Mura, C.M.McCrimmon, J.Vertrees, and M.R.Sawaya (2010).
An introduction to biomolecular graphics.
  PLoS Comput Biol, 6, 0.  
19925807 C.V.Iancu, D.M.Morris, Z.Dou, S.Heinhorst, G.C.Cannon, and G.J.Jensen (2010).
Organization, structure, and assembly of alpha-carboxysomes determined by electron cryotomography of intact cells.
  J Mol Biol, 396, 105-117.  
20400567 K.P.Dobrinski, A.J.Boller, and K.M.Scott (2010).
Expression and function of four carbonic anhydrase homologs in the deep-sea chemolithoautotroph Thiomicrospira crunogena.
  Appl Environ Microbiol, 76, 3561-3567.  
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.  
19487728 D.J.Scanlan, M.Ostrowski, S.Mazard, A.Dufresne, L.Garczarek, W.R.Hess, A.F.Post, M.Hagemann, I.Paulsen, and F.Partensky (2009).
Ecological genomics of marine picocyanobacteria.
  Microbiol Mol Biol Rev, 73, 249-299.  
19844578 F.Cai, B.B.Menon, G.C.Cannon, K.J.Curry, J.M.Shively, and S.Heinhorst (2009).
The pentameric vertex proteins are necessary for the icosahedral carboxysome shell to function as a CO2 leakage barrier.
  PLoS One, 4, e7521.  
19742174 M.Dimou, A.Paunescu, G.Aivalakis, E.Flemetakis, and P.Katinakis (2009).
Co-localization of Carbonic Anhydrase and Phosphoenol-pyruvate Carboxylase and Localization of Pyruvate Kinase in Roots and Hypocotyls of Etiolated Glycine max Seedlings.
  Int J Mol Sci, 10, 2896-2910.  
19296112 S.Elleuche, and S.Pöggeler (2009).
Evolution of carbonic anhydrases in fungi.
  Curr Genet, 55, 211-222.  
18355161 D.M.Morris, and G.J.Jensen (2008).
Toward a biomechanical understanding of whole bacterial cells.
  Annu Rev Biochem, 77, 583-613.  
17899012 F.Cai, S.Heinhorst, J.M.Shively, and G.C.Cannon (2008).
Transcript analysis of the Halothiobacillus neapolitanus cso operon.
  Arch Microbiol, 189, 141-150.  
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
18937343 S.Cheng, Y.Liu, C.S.Crowley, T.O.Yeates, and T.A.Bobik (2008).
Bacterial microcompartments: their properties and paradoxes.
  Bioessays, 30, 1084-1095.  
17993516 S.S.Cot, A.K.So, and G.S.Espie (2008).
A multiprotein bicarbonate dehydration complex essential to carboxysome function in cyanobacteria.
  J Bacteriol, 190, 936-945.  
18679172 T.O.Yeates, C.A.Kerfeld, S.Heinhorst, G.C.Cannon, and J.M.Shively (2008).
Protein-based organelles in bacteria: carboxysomes and related microcompartments.
  Nat Rev Microbiol, 6, 681-691.  
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
17510781 A.Rizzello, M.A.Ciardiello, R.Acierno, V.Carratore, T.Verri, G.di Prisco, C.Storelli, and M.Maffia (2007).
Biochemical characterization of a S-glutathionylated carbonic anhydrase isolated from gills of the Antarctic icefish Chionodraco hamatus.
  Protein J, 26, 335-348.  
17669419 C.V.Iancu, H.J.Ding, D.M.Morris, D.P.Dias, A.D.Gonzales, A.Martino, and G.J.Jensen (2007).
The structure of isolated Synechococcus strain WH8102 carboxysomes as revealed by electron cryotomography.
  J Mol Biol, 372, 764-773.  
17407539 N.Fabre, I.M.Reiter, N.Becuwe-Linka, B.Genty, and D.Rumeau (2007).
Characterization and expression analysis of genes encoding alpha and beta carbonic anhydrases in Arabidopsis.
  Plant Cell Environ, 30, 617-629.  
17573429 S.Marino, K.Hayakawa, K.Hatada, M.Benfatto, A.Rizzello, M.Maffia, and L.Bubacco (2007).
Structural features that govern enzymatic activity in carbonic anhydrase from a low-temperature adapted fish, Chionodraco hamatus.
  Biophys J, 93, 2781-2790.  
17518518 Y.Tsai, M.R.Sawaya, G.C.Cannon, F.Cai, E.B.Williams, S.Heinhorst, C.A.Kerfeld, and T.O.Yeates (2007).
Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome.
  PLoS Biol, 5, e144.
PDB codes: 2ewh 2g13
17105352 K.M.Scott, S.M.Sievert, F.N.Abril, L.A.Ball, C.J.Barrett, R.A.Blake, A.J.Boller, P.S.Chain, J.A.Clark, C.R.Davis, C.Detter, K.F.Do, K.P.Dobrinski, B.I.Faza, K.A.Fitzpatrick, S.K.Freyermuth, T.L.Harmer, L.J.Hauser, M.Hügler, C.A.Kerfeld, M.G.Klotz, W.W.Kong, M.Land, A.Lapidus, F.W.Larimer, D.L.Longo, S.Lucas, S.A.Malfatti, S.E.Massey, D.D.Martin, Z.McCuddin, F.Meyer, J.L.Moore, L.H.Ocampo, J.H.Paul, I.T.Paulsen, D.K.Reep, Q.Ren, R.L.Ross, P.Y.Sato, P.Thomas, L.E.Tinkham, and G.T.Zeruth (2006).
The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2.
  PLoS Biol, 4, e383.  
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.  
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.