Direct phasing algorithm for protein crystals with high solvent content using low-resolution diffraction data
In this study, a novel phase-retrieval workflow is proposed that eliminates the need for a reference density distribution by utilizing low-resolution diffraction data in phasing algorithms. The approach involves randomly assigning one out of 12 possible phases at 30 ° intervals (or two for centric reflections) to produce an initial envelope, which is then refined through density modification after each run of phase retrieval. To evaluate the success of the phase-retrieval procedure, information entropy is introduced as a new metric. This approach was validated using ten protein structures with high solvent content, demons...
Source: Acta Crystallographica Section D - June 14, 2023 Category: Biochemistry Authors: Jiang, Y.-M. Miao, H. Pan, X.-Y. Wang, Q. Dong, Z. Geng, Z. Dong, Y.-H. Tags: low-resolution envelopes iterative projection algorithms phasing phase determination research papers Source Type: research
Structural basis of regioselective tryptophan dibromination by the single-component flavin-dependent halogenase AetF
The flavin-dependent halogenase (FDH) AetF successively brominates tryptophan at C5 and C7 to generate 5,7-dibromotryptophan. In contrast to the well studied two-component tryptophan halogenases, AetF is a single-component flavoprotein monooxygenase. Here, crystal structures of AetF alone and in complex with various substrates are presented, representing the first experimental structures of a single-component FDH. Rotational pseudosymmetry and pseudomerohedral twinning complicated the phasing of one structure. AetF is structurally related to flavin-dependent monooxygenases. It contains two dinucleotide-binding domains for ...
Source: Acta Crystallographica Section D - June 14, 2023 Category: Biochemistry Authors: G ä fe, S. Niemann, H.H. Tags: aetokthonotoxin biocatalysis bromination enzymes Rossmann fold site selectivity AetF substrate binding research papers Source Type: research
Structural insights into the substrate specificity and activity of a novel mannose 2-epimerase from Runella slithyformis
In this study, structures of Runella slithyformis ME (RsME) and its D254A mutant [RsME(D254A)] were determined in their apo forms and as intermediate-analog complexes [RsME – d-glucitol and RsME(D254A) – d-glucitol]. RsME possesses the ( α / α )6-barrel of the AGE superfamily members but has a unique pocket-covering long loop (loop α 7 – α 8). The RsME – d-glucitol structure showed that loop α 7 – α 8 moves towards d-glucitol and closes the active pocket. Trp251 and Asp254 in loop α 7 – α 8 are only conserved in MEs and interact with d-glucitol. Kinetic analyses of the mutants confirmed the importanc...
Source: Acta Crystallographica Section D - June 14, 2023 Category: Biochemistry Authors: Wang, H. Sun, X. Saburi, W. Hashiguchi, S. Yu, J. Ose, T. Mori, H. Yao, M. Tags: mannose 2-epimerase Runella slithyformis crystal structure substrate specificity enzyme mechanism research papers Source Type: research
Sequence-assignment validation in protein crystal structure models with checkMySequence
Sequence-register shifts remain one of the most elusive errors in experimental macromolecular models. They may affect model interpretation and propagate to newly built models from older structures. In a recent publication, it was shown that register shifts in cryo-EM models of proteins can be detected using a systematic reassignment of short model fragments to the target sequence. Here, it is shown that the same approach can be used to detect register shifts in crystal structure models using standard, model-bias-corrected electron-density maps (2mFo − DFc). Five register-shift errors in models deposited in the PDB detect...
Source: Acta Crystallographica Section D - June 14, 2023 Category: Biochemistry Authors: Chojnowski, G. Tags: macromolecular crystallography register shifts findMySequence model validation checkMySequence sequence validation research papers Source Type: research
Structural and binding studies of a new chitin-active AA10 lytic polysaccharide monooxygenase from the marine bacterium Vibrio campbellii
In this study, the first crystal structures of a complete four-domain chitin-active AA10 lytic polysaccharide monooxygenase from the chitinolytic bacterium Vibrio campbellii type strain ATCC BAA-1116 are reported. The crystal structures of apo and copper-bound VhLPMO10A were resolved as homodimers with four distinct domains: an N-terminal AA10 catalytic (CatD) domain connected to a GlcNAc-binding (GbpA_2) domain, followed by a module X domain and a C-terminal carbohydrate-binding module (CBM73). Size-exclusion chromatography and small-angle X-ray scattering analysis confirmed that VhLPMO10A exists as a monomer in solution....
Source: Acta Crystallographica Section D - May 30, 2023 Category: Biochemistry Authors: Zhou, Y. Wannapaiboon, S. Prongjit, M. Pornsuwan, S. Sucharitakul, J. Kamonsutthipaijit, N. Robinson, R.C. Suginta, W. Tags: chitin oxidation copper-dependent enzymes Vibrio spp. lytic polysaccharide monooxygenases research papers Source Type: research
The CCP4 suite: integrative software for macromolecular crystallography
This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world. (Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - May 30, 2023 Category: Biochemistry Authors: Agirre, J. Atanasova, M. Bagdonas, H. Ballard, C.B. Basl é , A. Beilsten-Edmands, J. Borges, R.J. Brown, D.G. Burgos-M á rmol, J.J. Berrisford, J.M. Bond, P.S. Caballero, I. Catapano, L. Chojnowski, G. Cook, A.G. Cowtan, K.D. Croll, T.I. Debreczeni, J. Tags: Collaborative Computational Project No. 4 CCP4 crystallography software macromolecular crystallography research papers Source Type: research
Continuous development in macromolecular crystallography with CCP4
(Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - May 30, 2023 Category: Biochemistry Authors: Martinez-Ripoll, M. Albert, A. Tags: Collaborative Computational Project No. 4 CCP4 X-ray crystallography software macromolecular crystallography scientific commentaries Source Type: research
Unravelling the secrets of multi-domain lytic polysaccharide monooxygenases (LPMOs)
(Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - May 30, 2023 Category: Biochemistry Authors: Vaaje-Kolstad, G. Eijsink, V.G.H. Tags: multi-domain lytic polysaccharide monooxygenases copper-dependent enzymes marine bacteria Vibrio spp. chitin recycling scientific commentaries Source Type: research
Structural and functional investigation of a fungal member of carbohydrate esterase family 15 with potential specificity for rare xylans
In plant cell walls, covalent bonds between polysaccharides and lignin increase recalcitrance to degradation. Ester bonds are known to exist between glucuronic acid moieties on glucuronoxylan and lignin, and these can be cleaved by glucuronoyl esterases (GEs) from carbohydrate esterase family 15 (CE15). GEs are found in both bacteria and fungi, and some microorganisms also encode multiple GEs, although the reason for this is still not fully clear. The fungus Lentithecium fluviatile encodes three CE15 enzymes, of which two have previously been heterologously produced, although neither was active on the tested model substrat...
Source: Acta Crystallographica Section D - May 25, 2023 Category: Biochemistry Authors: Mazurkewich, S. Scholzen, K.C. Brusch, R.H. Poulsen, J.-C.N. Theibich, Y. H ü ttner, S. Olsson, L. Larsbrink, J. Lo Leggio, L. Tags: lignocellulose degradation glucuronyl esterases hemicellulose α / β hydrolases biomass conversion rare xylans Lentithecium fluviatile research papers Source Type: research
Near-atomic resolution reconstructions from in situ revitrified cryo samples
A microsecond time-resolved version of cryo-electron microscopy (cryo-EM) has recently been introduced to enable observation of the fast conformational motions of proteins. The technique involves locally melting a cryo sample with a laser beam to allow the proteins to undergo dynamics in the liquid phase. When the laser is switched off, the sample cools within just a few microseconds and revitrifies, trapping particles in their transient configurations, in which they can subsequently be imaged. Two alternative implementations of the technique have previously been described, using either an optical microscope or performing ...
Source: Acta Crystallographica Section D - May 23, 2023 Category: Biochemistry Authors: Bongiovanni, G. Harder, O.F. Voss, J.M. Drabbels, M. Lorenz, U.J. Tags: microsecond melting and revitrification microsecond time-resolved cryo-EM protein dynamics time-resolved electron microscopy preferential orientation research papers Source Type: research
Analysis and validation of overall N-glycan conformation in Privateer
The oligosaccharides in N-glycosylation provide key structural and functional contributions to a glycoprotein. These contributions are dependent on the composition and overall conformation of the glycans. The Privateer software allows structural biologists to evaluate and improve the atomic structures of carbohydrates, including N-glycans; this software has recently been extended to check glycan composition through the use of glycomics data. Here, a broadening of the scope of the software to analyse and validate the overall conformation of N-glycans is presented, focusing on a newly compiled set of glycosidic linkage torsi...
Source: Acta Crystallographica Section D - May 23, 2023 Category: Biochemistry Authors: Dialpuri, J.S. Bagdonas, H. Atanasova, M. Schofield, L.C. Hekkelman, M.L. Joosten, R.P. Agirre, J. Tags: glycobiology validation Privateer N-glycans torsion angles research papers Source Type: research
Structure-based discovery of an antipsychotic drug, paliperidone, as a modulator of human superoxide dismutase 1: a potential therapeutic target in amyotrophic lateral sclerosis
Aggregates of the antioxidant superoxide dismutase 1 (SOD1) are one of the major contributors to the pathogenesis of amyotrophic lateral sclerosis (ALS). Mutations in SOD1 lead to an unstable structure and aggregation that perturbs the balance of reactive oxygen species in cells. Oxidation damage to the solvent-exposed Trp32 also causes aggregation of SOD1. Here, the FDA-approved antipsychotic drug paliperidone is identified to interact with Trp32 of SOD1 by structure-based pharmacophore mapping and crystallographic studies. Paliperidone is used for the treatment of schizophrenia. The crystal structure of the complex with ...
Source: Acta Crystallographica Section D - May 19, 2023 Category: Biochemistry Authors: Aouti, S. Padavattan, S. Padmanabhan, B. Tags: ALS SOD1 superoxide dismutase tryptophan oxidation modulators antipsychotic drugs paliperidone pharmacophore mapping crystal structure binding assays research papers Source Type: research
Cysteine synthase: multiple structures of a key enzyme in cysteine synthesis and a potential drug target for Chagas disease and leishmaniasis
Chagas disease is a neglected tropical disease (NTD) caused by Trypanosoma cruzi, whilst leishmaniasis, which is caused by over 20 species of Leishmania, represents a group of NTDs endemic to most countries in the tropical and subtropical belt of the planet. These diseases remain a significant health problem both in endemic countries and globally. These parasites and other trypanosomatids, including T. theileri, a bovine pathogen, rely on cysteine biosynthesis for the production of trypanothione, which is essential for parasite survival in hosts. The de novo pathway of cysteine biosynthesis requires the conversion of O-ace...
Source: Acta Crystallographica Section D - May 19, 2023 Category: Biochemistry Authors: Sowerby, K. Freitag-Pohl, S. Murillo, A.M. Silber, A.M. Pohl, E. Tags: amino-acid metabolism cysteine synthase PLP-dependent enzymes X-ray crystallography Chagas disease leishmaniasis Trypanosoma theileri Trypanosoma cruzi Leishmania infantum research papers Source Type: research
The type III secretion chaperone SctY may shield the hydrophobic export gate-binding C-terminus of its substrate SctX
Gram-negative bacteria such as Aeromonas and Yersinia spp. have developed mechanisms to inhibit the immune defense of their host. Effector proteins are directly injected into the host cytoplasm from the bacterial cytosol via type III secretion systems (T3SSs), where they modulate the cytoskeleton and signaling of the cell. Assembly of, and secretion via, T3SSs is tightly regulated by a number of bacterial proteins, including SctX (AscX in Aeromonas), the secretion of which is essential for T3SS function. Here, crystal structures of AscX in complex with SctY chaperones from Yersinia or Photorhabdus spp. carrying homologous ...
Source: Acta Crystallographica Section D - May 19, 2023 Category: Biochemistry Authors: Gilzer, D. Kowal, J.L. Flottmann, F. Niemann, H.H. Tags: helix bending protein – protein interactions type III secretion systems YscX YscY AscX Aeromonas hydrophila Yersinia enterocolitica type III secretion chaperone SctY research papers Source Type: research
Structure of reverse gyrase with a minimal latch that supports ATP-dependent positive supercoiling without specific interactions with the topoisomerase domain
Reverse gyrase is the only topoisomerase that introduces positive supercoils into DNA in an ATP-dependent reaction. Positive DNA supercoiling becomes possible through the functional cooperation of the N-terminal helicase domain of reverse gyrase with its C-terminal type IA topoisomerase domain. This cooperation is mediated by a reverse-gyrase-specific insertion into the helicase domain termed the `latch'. The latch consists of a globular domain inserted at the top of a β -bulge loop that connects this globular part to the helicase domain. While the globular domain shows little conservation in sequence and length and is...
Source: Acta Crystallographica Section D - May 19, 2023 Category: Biochemistry Authors: Mhaindarkar, V.P. Rasche, R. K ü mmel, D. Rudolph, M.G. Klostermeier, D. Tags: reverse gyrases helicases topoisomerases latch positive DNA supercoiling extremophiles inter-domain communication research papers Source Type: research
