PDBsum entry 2fgy

Lyase

PDB id: 2fgy

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

Protein chains

O85042  (CSOCA_HALNC) -  Carboxysome shell carbonic anhydrase from Halothiobacillus neapolitanus (strain ATCC 23641 / c2)

Seq: 514 a.a.

Struc: 471 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

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: 10.1074/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.