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Chirgadze YN, Boshkova EA, Kargatov AM, Chirgadze NY. Functional identification of 'hypothetical protein' structures with unknown function. J Biomol Struct Dyn 2022:1-5. [PMID: 35694832 DOI: 10.1080/07391102.2022.2085806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Y N Chirgadze
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - E A Boshkova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - A M Kargatov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - N Y Chirgadze
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada.,X-CHIP Technologies Inc, Toronto, Ontario, Canada
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Park JM, Trevor Sewell B, Benedik MJ. Cyanide bioremediation: the potential of engineered nitrilases. Appl Microbiol Biotechnol 2017; 101:3029-3042. [PMID: 28265723 DOI: 10.1007/s00253-017-8204-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 11/29/2022]
Abstract
The cyanide-degrading nitrilases are of notable interest for their potential to remediate cyanide contaminated waste streams, especially as generated in the gold mining, pharmaceutical, and electroplating industries. This review provides a brief overview of cyanide remediation in general but with a particular focus on the cyanide-degrading nitrilases. These are of special interest as the hydrolysis reaction does not require secondary substrates or cofactors, making these enzymes particularly good candidates for industrial remediation processes. The genetic approaches that have been used to date for engineering improved enzymes are described; however, recent structural insights provide a promising new approach.
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Affiliation(s)
- Jason M Park
- Department of Biology, Texas A&M University, College Station, TX, 77843-3258, USA
| | - B Trevor Sewell
- Structural Biology Research Unit, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
| | - Michael J Benedik
- Department of Biology, Texas A&M University, College Station, TX, 77843-3258, USA.
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Chirgadze YN, Clarke TE, Romanov V, Kisselman G, Wu-Brown J, Soloveychik M, Chan TSY, Gordon RD, Battaile KP, Pai EF, Chirgadze NY. The structure of SAV1646 from Staphylococcus aureus belonging to a new `ribosome-associated' subfamily of bacterial proteins. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:332-7. [PMID: 25664743 DOI: 10.1107/s1399004714025619] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 11/23/2014] [Indexed: 11/10/2022]
Abstract
The crystal structure of the SAV1646 protein from the pathogenic microorganism Staphylococcus aureus has been determined at 1.7 Å resolution. The 106-amino-acid protein forms a two-layer sandwich with α/β topology. The protein molecules associate as dimers in the crystal and in solution, with the monomers related by a pseudo-twofold rotation axis. A sequence-homology search identified the protein as a member of a new subfamily of yet uncharacterized bacterial `ribosome-associated' proteins with at least 13 members to date. A detailed analysis of the crystal protein structure along with the genomic structure of the operon containing the sav1646 gene allowed a tentative functional model of this protein to be proposed. The SAV1646 dimer is assumed to form a complex with ribosomal proteins L21 and L27 which could help to complete the assembly of the large subunit of the ribosome.
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Affiliation(s)
- Yuri N Chirgadze
- Institute of Protein Research, Russian Academy of Sciences, Puschino 142290, Moscow Region, Russian Federation
| | - Teresa E Clarke
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Vladimir Romanov
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Gera Kisselman
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Jean Wu-Brown
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Maria Soloveychik
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Tiffany S Y Chan
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Roni D Gordon
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Kevin P Battaile
- Hauptman-Woodward Medical Research Institute, IMCA-CAT, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Emil F Pai
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Nickolay Y Chirgadze
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
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