Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures

Luo, Zhipu

doi:10.1038/srep37123

Cited by 24 publications

(21 citation statements)

References 30 publications

(27 reference statements)

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“…The crystal structure of Mt SHMT3 was solved by SAD using the recently developed method of soaking crystals with selenourea ( Luo, 2016 ). For phasing, data from two crystals were merged.…”

Section: Methodsmentioning

confidence: 99%

Chloroplastic Serine Hydroxymethyltransferase From Medicago truncatula: A Structural Characterization

et al. 2018

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Serine hydroxymethyltransferase (SHMT, EC 2.1.2.1) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme which catalyzes the reversible serine-to-glycine conversion in either a tetrahydrofolate-dependent or -independent manner. The enzyme is also responsible for the tetrahydrofolate-independent cleavage of other β-hydroxy amino acids. In addition to being an essential player in the serine homeostasis, SHMT action is the main source of activated one-carbon units, which links SHMT activity with the control of cell proliferation. In plants, studies of SHMT enzymes are more complicated than of those of, e.g., bacterial or mammalian origins because plant genomes encode multiple SHMT isozymes that are targeted to different subcellular compartments: cytosol, mitochondria, plastids, and nucleus. Here we report crystal structures of chloroplast-targeted SHMT from Medicago truncatula (MtSHMT3). MtSHMT3 is a tetramer in solution, composed of two tight and obligate dimers. Our complexes with PLP internal aldimine, PLP-serine and PLP-glycine external aldimines, and PLP internal aldimine with a free glycine reveal structural details of the MtSHMT3-catalyzed reaction. Capturing the enzyme in different stages along the course of the slow tetrahydrofolate-independent serine-to-glycine conversion allowed to observe a unique conformation of the PLP-serine γ-hydroxyl group, and a concerted movement of two tyrosine residues in the active site.

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“…The crystal structure of Mt SHMT3 was solved by SAD using the recently developed method of soaking crystals with selenourea ( Luo, 2016 ). For phasing, data from two crystals were merged.…”

Section: Methodsmentioning

confidence: 99%

Chloroplastic Serine Hydroxymethyltransferase From Medicago truncatula: A Structural Characterization

et al. 2018

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“…Forexample,formate can only be used by Shewanella species as the electron donor and the electrons generated from formate oxidation are passed to the electrode.Inthis process, bacterial cells are not growing,b ut are simply respiring. [16,17] Then, we investigated the morphology of PPy-coated S. oneidensis MR-1 by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Unlike the smooth surface of native S. oneidensis MR-1 (Figure 1d), the PPycoated S. oneidensis MR-1 possessed ar ough surface (Figure 1c).…”

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confidence: 99%

Living and Conducting: Coating Individual Bacterial Cells with In Situ Formed Polypyrrole

et al. 2017

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Coating individual bacterial cells with conjugated polymers to endow them with more functionalities is highly desirable. Here, we developed an in situ polymerization method to coat polypyrrole on the surface of individual Shewanella oneidensis MR-1, Escherichia coli, Ochrobacterium anthropic or Streptococcus thermophilus. All of these as-coated cells from different bacterial species displayed enhanced conductivities without affecting viability, suggesting the generality of our coating method. Because of their excellent conductivity, we employed polypyrrole-coated Shewanella oneidensis MR-1 as an anode in microbial fuel cells (MFCs) and found that not only direct contact-based extracellular electron transfer is dramatically enhanced, but also the viability of bacterial cells in MFCs is improved. Our results indicate that coating individual bacteria with conjugated polymers could be a promising strategy to enhance their performance or enrich them with more functionalities.

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“…This approach enables the use of SeUrea quantitatively and can be adapted for phasing other structures. As previously discussed, SeUrea does not form a stable aqueous solution, so a reducing agent like sodium sulfite (Na 2 SO 3 ) or TCEP is added to slow down the oxidation of SeUrea 34 . The stability of SeUrea was improved by using a higher concentration of Na 2 SO 3 to prepare the 1 M SeUrea/Na 2 SO 3 solution, allowing the stock solution to be stored at −20 °C for several months.…”

Section: Discussionmentioning

confidence: 99%

“…MpPR-1i has less than 25% sequence identity with any of the structures in the protein data bank, which hampered efforts at solving the structure using molecular replacement. The crystal structure of MpPR-1i was determined using selenourea (SeUrea) soaking method to solve the phase problem 34 . This is the first de novo structure determined by SeUrea phasing.…”

Section: Introductionmentioning

confidence: 99%

Crystal Structure of MpPR-1i, a SCP/TAPS protein from Moniliophthora perniciosa, the fungus that causes Witches’ Broom Disease of Cacao

Baroni

Luo

Darwiche

et al. 2017

Sci Rep

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The pathogenic fungi Moniliophthora perniciosa causes Witches’ Broom Disease (WBD) of cacao. The structure of MpPR-1i, a protein expressed by M. perniciosa when it infects cacao, are presented. This is the first reported de novo structure determined by single-wavelength anomalous dispersion phasing upon soaking with selenourea. Each monomer has flexible loop regions linking the core alpha-beta-alpha sandwich topology that comprise ~50% of the structure, making it difficult to generate an accurate homology model of the protein. MpPR-1i is monomeric in solution but is packed as a high ~70% solvent content, crystallographic heptamer. The greatest conformational flexibility between monomers is found in loops exposed to the solvent channel that connect the two longest strands. MpPR-1i lacks the conserved CAP tetrad and is incapable of binding divalent cations. MpPR-1i has the ability to bind lipids, which may have roles in its infection of cacao. These lipids likely bind in the palmitate binding cavity as observed in tablysin-15, since MpPR-1i binds palmitate with comparable affinity as tablysin-15. Further studies are required to clarify the possible roles and underlying mechanisms of neutral lipid binding, as well as their effects on the pathogenesis of M. perniciosa so as to develop new interventions for WBD.

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Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures

Cited by 24 publications

References 30 publications

Chloroplastic Serine Hydroxymethyltransferase From Medicago truncatula: A Structural Characterization

Chloroplastic Serine Hydroxymethyltransferase From Medicago truncatula: A Structural Characterization

Living and Conducting: Coating Individual Bacterial Cells with In Situ Formed Polypyrrole

Crystal Structure of MpPR-1i, a SCP/TAPS protein from Moniliophthora perniciosa, the fungus that causes Witches’ Broom Disease of Cacao

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