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Observation of a calcium-binding site in the gamma-class carbonic anhydrase from Pyrococcus horikoshii.

Jeyakanthan J, Rangarajan S, Mridula P, Kanaujia SP, Shiro Y, Kuramitsu S, Yokoyama S, Sekar K
Acta Crystallogr D Biol Crystallogr 64 1012-9 (2008)
Related entries: 1v3w, 1v67

Cited: 25 times
EuropePMC logo PMID: 18931408

Abstract

Carbonic anhydrases are zinc-containing metalloenzymes that catalyze the interconversion of carbon dioxide and bicarbonate. Three crystal structures of gamma-class carbonic anhydrase (one of which is bound to a bicarbonate molecule) from the aerobic OT3 strain of the hyperthermophilic archeon Pyrococcus horikoshii have been solved by molecular replacement in space group F4(1)32. The asymmetric unit contains a monomer of 173 amino acids and a catalytic Zn2+ ion. The protein fold is a regular prism formed by a left-handed beta-helix, similar to previously reported structures. The active-site Zn2+ ion located at the interface between the two monomers is bound to three histidyl residues and a water molecule in a tetrahedral fashion. In addition to the 20 beta-strands comprising the beta-helix, there is also a long C-terminal alpha-helix. For the first time, Ca2+ ions have been observed in addition to the catalytic Zn2+ ion. It is hypothesized that Tyr159 (which corresponds to the catalytically important Asn202 in previously reported structures) utilizes C-H...pi interactions to fulfill its functions. This study may shed light on the catalytic mechanism of the enzyme and throw open new questions on the mechanism of product removal in carbonic anhydrases.

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  5. Biochemical, structural, and computational studies of a γ-carbonic anhydrase from the pathogenic bacterium Burkholderia pseudomallei. Di Fiore A, De Luca V, Langella E, Nocentini A, Buonanno M, Monti SM, Supuran CT, Capasso C, De Simone G. Comput Struct Biotechnol J 20 4185-4194 (2022)
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  7. The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. Timofeeva TA, Sadykova GK, Lomakina NF, Gambaryan AS, Rudneva IA, Timofeeva EB, Shilov AA, Boravleva EY, Zhuravleva MM, Ivanov PA, Ryazanova EL, Prilipov AG. Mol Biol 54 861-869 (2020)


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  4. Folding and Stability of Ankyrin Repeats Control Biological Protein Function. Kumar A, Balbach J. Biomolecules 11 840 (2021)

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  2. Atomic structure of a mitochondrial complex I intermediate from vascular plants. Maldonado M, Padavannil A, Zhou L, Guo F, Letts JA. Elife 9 e56664 (2020)
  3. Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA). Grötzinger SW, Alam I, Ba Alawi W, Bajic VB, Stingl U, Eppinger J. Front Microbiol 5 134 (2014)
  4. Structures of the γ-class carbonic anhydrase homologue YrdA suggest a possible allosteric switch. Park HM, Park JH, Choi JW, Lee J, Kim BY, Jung CH, Kim JS. Acta Crystallogr D Biol Crystallogr 68 920-926 (2012)
  5. Insights on the regulation of the phenylacetate degradation pathway from Escherichia coli. Fernández C, Díaz E, García JL. Environ Microbiol Rep 6 239-250 (2014)
  6. Crystal Structure and Active Site Engineering of a Halophilic γ-Carbonic Anhydrase. Vogler M, Karan R, Renn D, Vancea A, Vielberg MT, Grötzinger SW, DasSarma P, DasSarma S, Eppinger J, Groll M, Rueping M. Front Microbiol 11 742 (2020)
  7. The three-dimensional Structure of a mycobacterial DapD provides insights into DapD diversity and reveals unexpected particulars about the enzymatic mechanism. Schuldt L, Weyand S, Kefala G, Weiss MS. J Mol Biol 389 863-879 (2009)
  8. Ancillary contributions of heterologous biotin protein ligase and carbonic anhydrase for CO2 incorporation into 3-hydroxypropionate by metabolically engineered Pyrococcus furiosus. Lian H, Zeldes BM, Lipscomb GL, Hawkins AB, Han Y, Loder AJ, Nishiyama D, Adams MW, Kelly RM. Biotechnol Bioeng 113 2652-2660 (2016)
  9. Cryo-EM structure of the respiratory I + III2 supercomplex from Arabidopsis thaliana at 2 Å resolution. Klusch N, Dreimann M, Senkler J, Rugen N, Kühlbrandt W, Braun HP. Nat Plants 9 142-156 (2023)
  10. Role of Trp19 and Tyr200 in catalysis by the γ-class carbonic anhydrase from Methanosarcina thermophila. Zimmerman S, Domsic JF, Tu C, Robbins AH, McKenna R, Silverman DN, Ferry JG. Arch Biochem Biophys 529 11-17 (2013)
  11. Crystal Structure of a Highly Thermostable α-Carbonic Anhydrase from Persephonella marina EX-H1. Kim S, Sung J, Yeon J, Choi SH, Jin MS. Mol Cells 42 460-469 (2019)
  12. In Silico Investigation of Potential Applications of Gamma Carbonic Anhydrases as Catalysts of CO2 Biomineralization Processes: A Visit to the Thermophilic Bacteria Persephonella hydrogeniphila, Persephonella marina, Thermosulfidibacter takaii, and Thermus thermophilus. Manyumwa CV, Bishop ÖT. Int J Mol Sci 22 2861 (2021)
  13. Carbonic anhydrase modification for carbon management. Giri A, Pant D. Environ Sci Pollut Res Int 27 1294-1318 (2020)


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