Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the program<i>Zanuda</i>

Лебедев, А. А.; Isupov, Michail N.

doi:10.1107/s1399004714014795

Cited by 91 publications

(84 citation statements)

References 46 publications

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“…Analysis of the data with PHENIX Xtriage and POINTLESS do not suggest contributions from twinning or translational noncrystallographic symmetry. Furthermore, analysis with ZANUDA in CCP4 is consistent with the P3 2 21 space group used in this study . Thus, we hypothesize that the high R free value may be due a small but significant amount of degradation that is observed during the purification process.…”

Section: Resultssupporting

confidence: 81%

Crystal structure of lipoate-bound lipoate ligase 1, LipL1, from Plasmodium falciparum

2017

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Plasmodium falciparum lipoate protein ligase 1 (PfLipL1) is an ATP-dependent ligase that belongs to the biotin/lipoate A/B protein ligase family (PFAM PF03099). PfLipL1 is the only known canonical lipoate ligase in Pf and functions as a redox switch between two lipoylation routes in the parasite mitochondrion. Here, we report the crystal structure of a deletion construct of PfLipL1 (PfLipL1Δ243–279) bound to lipoate, and validate the lipoylation activity of this construct in both an in vitro lipoylation assay and a cell based lipoylation assay. This characterization represents the first step in understanding the redox dependence of the lipoylation mechanism in malaria parasites.

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Section: Resultssupporting

confidence: 81%

Crystal structure of lipoate-bound lipoate ligase 1, LipL1, from Plasmodium falciparum

2017

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“…The structure of FasR Δ33 -C 20 The orthorhombic C222 1 space group of the FasR-DNA crystals was confirmed by several standard procedures (23,35), notably including integration in the corresponding triclinic group and using molecular replacement as a means of deducing real symmetry. However, the DNA molecule (one double-stranded oligonucleotide per ASU) was found sitting with its long axis approximately perpendicular to one of the orthorhombic 2-fold axes, revealing both alternative 5' 3' orientations to be present in different unit cells of the crystal.…”

Section: Structure Determination and Refinementmentioning

confidence: 92%

Mycobacterium tuberculosisFasR senses long fatty acyl-CoA through a tunnel, inducing DNA-dissociation via a transmission spine

Lara

Diacovich

Trajtenberg

et al. 2020

Preprint

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Mycobacterium tuberculosis is a pathogen with a unique cell envelope including very long fatty acids, implicated in bacterial resistance and host immune modulation. FasR is a two-domain transcriptional activator that belongs to the TetR family of regulators, and plays a central role in mycobacterial longchain fatty acyl-CoA sensing and lipid biosynthesis regulation. We now disclose crystal structures of M. tuberculosis FasR in complex with acyl effector ligands and with DNA, uncovering its sensory and switching mechanisms. A long tunnel traverses the entire effector-binding domain, enabling long fatty acyl effectors to bind. Only when the tunnel is entirely occupied, the protein dimer adopts a rigid configuration, with its DNA-binding domains in an open state that leads to DNA dissociation.Structure-guided point-mutations further support this effector-dependent mechanism. The proteinfolding hydrophobic core, connecting the two domains, is completed by the effector ligand into a continuous spine, explaining the allosteric flexible-to-ordered transition. The transmission spine is conserved in all TetR-like transcription factors, offering new opportunities for anti-tuberculosis drug discovery.2 act as major effector molecules that interact with the host, playing key roles in pathogenicity and also providing a barrier against environmental stress, antibiotics, and the host's immune response (1).Understanding the biogenesis of the mycobacterial cell wall will thus provide with relevant insights into the biology of this pathogen, also identifying potential targets for the development of new antimycobacterial compounds.The outer membrane of Mtb comprises very long-chain fatty acids (mycolic acids), found in the inner leaflet covalently bonded to the arabinogalactan-peptidoglycan layer, and also in the outer leaflet as non-covalently associated lipids in the form of trehalose-mono-and di-mycolate (2). Mycolic acids, a hallmark of Mycobacterium, are synthesized by way of two fatty acid synthase systems, FAS I and FAS II. The multidomain single protein FAS I catalyses de novo biosynthesis of acyl-CoAs in a bimodal fashion rendering C 16-18 and C 24-26 derivatives (3). Long chain acyl-CoAs are used as primers by the FAS II multiprotein system, and iteratively condensed with malonyl-acyl carrier protein (malonyl-ACP) leading to very long-chain meromycolyl-ACPs (up to C 56 ). The latter are eventually condensed to FAS I-synthesized C 24-26 fatty acids (previously activated by the acyl-CoA carboxylase 4 complex (4)) to produce mycolic acids. The long-chain acyl-CoAs generated by FAS I are not only used as precursors of mycolic acids, but also for the biosynthesis of phospholipids, triacylglycerides, diverse polyketides and other complex lipids, relevant for Mtb pathogenicity (5,6). A complex regulatory network integrating all these pathways must exist in order to maintain lipid homeostasis. However, and despite the biological relevance of lipid-derived molecules in Mtb's lifecycle, little is known about the environmental signa...

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“…The original MR solution had a wrong choice of origin and did not refine. ZANUDA [35] was used to find a true origin out of four possible ones.…”

Section: Data Collection and Structure Determinationmentioning

confidence: 99%

Discovery and characterization of thermophilic limonene‐1,2‐epoxide hydrolases from hot spring metagenomic libraries

et al. 2015

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The epoxide hydrolases (EHs) represent an attractive option for the synthesis of chiral epoxides and 1,2-diols which are valuable building blocks for the synthesis of several pharmaceutical compounds. A metagenomic approach has been used to identify two new members of the atypical EH limonene-1,2-epoxide hydrolase (LEH) family of enzymes. These two LEHs (Tomsk-LEH and CH55-LEH) show EH activities towards different epoxide substrates, differing in most cases from those previously identified for Rhodococcus erythropolis (Re-LEH) in terms of stereoselectivity. Tomsk-LEH and CH55-LEH, both from thermophilic sources, have higher optimal temperatures and apparent melting temperatures than Re-LEH. The new LEH enzymes have been crystallized and their structures solved to high resolution in the native form and in complex with the inhibitor valpromide for Tomsk-LEH and poly(ethylene glycol) for CH55-LEH. The structural analysis has provided insights into the LEH mechanism, substrate specificity and stereoselectivity of these new LEH enzymes, which has been supported by mutagenesis studies. DatabaseThe atomic coordinates and structure factors of the crystal structures have been deposited in the Protein Data Bank with the codes 5AIF (Tomsk-LEH native structure), 5AIG (Tomsk-LEH valpromide complex), 5AIH (CH55-LEH native structure) and 5AII (CH55-LEH PEG complex). Nucleotide sequence data are available in the GenBank databases under the accession numbers KP765711 (Tomsk-LEH) and KP765710 (CH55-LEH).Abbreviations CH55-LEH, limonene-1,2-epoxide hydrolase from the metagenomic DNA from the Chinese sample; de, diastereomeric excess; ee, enantiomeric excess; EH, epoxide hydrolase; LEH, limonene-1,2-epoxide hydrolase; Mt-LEH, Mycobacterium tuberculosis limonene-1,2-epoxide hydrolase; PEG, poly(ethylene glycol); Re-LEH, Rhodococcus erythropolis limonene-1,2-epoxide hydrolase; Tomsk-LEH, limonene-1,2-epoxide hydrolase from the metagenomic DNA from the Tomsk sample.

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Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the programZanuda

Cited by 91 publications

References 46 publications

Crystal structure of lipoate-bound lipoate ligase 1, LipL1, from Plasmodium falciparum

Crystal structure of lipoate-bound lipoate ligase 1, LipL1, from Plasmodium falciparum

Mycobacterium tuberculosisFasR senses long fatty acyl-CoA through a tunnel, inducing DNA-dissociation via a transmission spine

Discovery and characterization of thermophilic limonene‐1,2‐epoxide hydrolases from hot spring metagenomic libraries

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