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Bhatia I, Yadav S, Biswal BK. Identification, structure determination and analysis of Mycobacterium smegmatis acyl-carrier protein synthase (AcpS) crystallized serendipitously. Acta Crystallogr F Struct Biol Commun 2022; 78:252-264. [DOI: 10.1107/s2053230x22005738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/26/2022] [Indexed: 11/11/2022] Open
Abstract
The unintended crystallization of proteins which generally originate from the expression host instead of the target recombinant proteins is periodically reported. Despite the massive technological advances in the field, assigning a structural model to the corresponding diffraction data is not a trivial task. Here, the structure of acyl-carrier protein synthase (AcpS) from Mycobacterium smegmatis (msAcpS), which crystallized inadvertently in an experimental setup to grow crystals of a Mycobacterium tuberculosis protein using M. smegmatis as an expression system, is reported. After numerous unsuccessful attempts to solve the structure of the target protein by the molecular-replacement method no convincing solutions were obtained, indicating that the diffraction data may correspond to a crystal of an artifactual protein, which was finally identified by the Sequence-Independent Molecular replacement Based on Available Databases (SIMBAD) server. The msAcpS structure was solved at 2.27 Å resolution and structural analysis showed an overall conserved fold. msAcpS formed a trimeric structure similar to those of other reported structures of AcpS from various organisms; however, the residues involved in trimer formation are not strictly conserved. An unrelated metal ion (Ni2+), which was possibly incorporated during protein purification, was observed in the proximity of His49 and His116. Structural and sequence differences were observed in the loop connecting the α3 and α4 helices that is responsible for the open and closed conformations of the enzyme. Moreover, the structural analysis of msAcpS augments the current understanding of this enzyme, which plays a crucial role in the functional activation of acyl-carrier proteins in the fatty-acid biosynthesis pathway.
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Mao X, Chen J, van Oosterhout C, Zhang H, Liu G, Zhuang Y, Mock T. Diversity, prevalence, and expression of cyanase genes (cynS) in planktonic marine microorganisms. THE ISME JOURNAL 2022; 16:602-605. [PMID: 34408267 PMCID: PMC8776842 DOI: 10.1038/s41396-021-01081-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023]
Abstract
Cyanate is utilized by many microbes as an organic nitrogen source. The key enzyme for cyanate metabolism is cyanase, converting cyanate to ammonium and carbon dioxide. Although the cyanase gene cynS has been identified in many species, the diversity, prevalence, and expression of cynS in marine microbial communities remains poorly understood. Here, based on the full-length cDNA sequence of a dinoflagellate cynS and 260 homologs across the tree of life, we extend the conserved nature of cyanases by the identification of additional ultra-conserved residues as part of the modeled holoenzyme structure. Our phylogenetic analysis showed that horizontal gene transfer of cynS appears to be more prominent than previously reported for bacteria, archaea, chlorophytes, and metazoans. Quantitative analyses of marine planktonic metagenomes revealed that cynS is as prevalent as ureC (urease subunit alpha), suggesting that cyanate plays an important role in nitrogen metabolism of marine microbes. Highly abundant cynS transcripts from phytoplankton and nitrite-oxidizing bacteria identified in global ocean metatranscriptomes indicate that cyanases potentially occupy a key position in the marine nitrogen cycle by facilitating photosynthetic assimilation of organic N and its remineralisation to NO3 by the activity of nitrifying bacteria.
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Affiliation(s)
- Xuewei Mao
- grid.4422.00000 0001 2152 3263Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100 China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China ,grid.8273.e0000 0001 1092 7967School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
| | - Jianwei Chen
- grid.21155.320000 0001 2034 1839BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China ,grid.21155.320000 0001 2034 1839Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555 China
| | - Cock van Oosterhout
- grid.8273.e0000 0001 1092 7967School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
| | - Huan Zhang
- grid.63054.340000 0001 0860 4915Department of Marine Sciences, University of Connecticut, Groton, CT 06340 USA
| | - Guangxing Liu
- grid.4422.00000 0001 2152 3263Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100 China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Yunyun Zhuang
- grid.4422.00000 0001 2152 3263Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100 China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Thomas Mock
- grid.8273.e0000 0001 1092 7967School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
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Newman J, van Raaij MJ. Contamination or serendipity - doing the wrong thing by chance. Acta Crystallogr F Struct Biol Commun 2020; 76:391. [PMID: 32880585 PMCID: PMC7470042 DOI: 10.1107/s2053230x20012029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The Editors consider contaminant proteins.
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Affiliation(s)
- Janet Newman
- Collaborative Crystallisation Centre (C3), CSIRO, 343 Royal Parade, Parkville, VIC 3052 Australia
| | - Mark J. van Raaij
- Department of Molecular Structure, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, E-28049, Spain
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