Crystallization and X-ray analysis of Borrelia burgdorferi β -barrel assembly machinery A
Mitochondria, chloroplasts and several species of bacteria have outer membrane proteins (OMPs) that perform many essential biological functions. The β -barrel assembly machinery (BAM) complex is one of the OMPs of Borrelia burgdorferi, the pathogenic spirochete that causes Lyme disease, and its BamA component (BbBamA) includes a C-terminal β -barrel domain and five N-terminal periplasmic polypeptide-transport-associated (POTRA) domains, which together perform a central transport function. In the current work, the production, crystallization and X-ray analysis of the three N-terminal POTRA domains of BbBamA (BbBamA-POTRA ...
Source: Acta Crystallographica Section F - May 28, 2020 Category: Biochemistry Authors: Dong, S. Chu, H. Wen, K. Yu, Q. Li, H. Wang, C. Qin, X. Tags: Borrelia burgdorferi BbBamA-POTRA P1 – P3 crystallization research communications Source Type: research
Crystal structure of gluconate 5-dehydrogenase from Lentibacter algarum
Gluconate 5-dehydrogenase (Ga5DH; EC 1.1.1.69) from Lentibacter algarum (LaGa5DH) was recombinantly expressed in Escherichia coli and purified to homogeneity. The protein was crystallized and the crystal structure was solved at 2.1 Å resolution. The crystal belonged to the monoclinic system, with space group P1 and unit-cell parameters a = 55.42, b = 55.48, c = 79.16 Å , α = 100.51, β = 105.66, γ = 97.99 ° . The structure revealed LaGaDH to be a tetramer, with each subunit consisting of six α -helices and three antiparallel β -hairpins. LaGa5DH has high structural similarity to other Ga5DH...
Source: Acta Crystallographica Section F - April 28, 2020 Category: Biochemistry Authors: Tian, D. Fu, X. Cao, W. Yuan, H. Tags: crystal structure gluconate 5-dehydrogenase Lentibacter algarum research communications Source Type: research
Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport
The transmembrane intracellular lectin ER – Golgi intermediate compartment protein 53 (ERGIC-53) and the soluble EF-hand multiple coagulation factor deficiency protein 2 (MCFD2) form a complex that functions as a cargo receptor, trafficking various glycoproteins between the endoplasmic reticulum (ER) and the Golgi apparatus. It has been demonstrated that the carbohydrate-recognition domain (CRD) of ERGIC-53 (ERGIC-53CRD) interacts with N-linked glycans on cargo glycoproteins, whereas MCFD2 recognizes polypeptide segments of cargo glycoproteins. Crystal structures of ERGIC-53CRD complexed with MCFD2 and mannosyl oligosacc...
Source: Acta Crystallographica Section F - April 28, 2020 Category: Biochemistry Authors: Satoh, T. Nishio, M. Suzuki, K. Yagi-Utsumi, M. Kamiya, Y. Mizushima, T. Kato, K. Tags: cargo receptor conformational polymorphism crystal packing glycoprotein transport intracellular lectin MCFD2 ERGIC-53 research communications Source Type: research
Crystal structure of the nucleoid-associated protein Fis (PA4853) from Pseudomonas aeruginosa
Factor for inversion stimulation (Fis) is a versatile bacterial nucleoid-associated protein that can directly bind and bend DNA to influence DNA topology. It also plays crucial roles in regulating bacterial virulence factors and in optimizing bacterial adaptation to various environments. Fis from Pseudomonas aeruginosa (PA4853, referred to as PaFis) has recently been found to be required for virulence by regulating the expression of type III secretion system (T3SS) genes. PaFis can specifically bind to the promoter region of exsA, which functions as a T3SS master regulator, to regulate its expression and plays an essential...
Source: Acta Crystallographica Section F - April 28, 2020 Category: Biochemistry Authors: Zhou, J. Gao, Z. Zhang, H. Dong, Y. Tags: nucleoid-associated protein Fis DNA-binding protein crystal structure helix – turn helix motif Pseudomonas aeruginosa factor for inversion stimulation research communications Source Type: research
Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway
The enzyme 4-hydroxy-tetrahydrodipicolinate synthase (DapA) is involved in the production of lysine and precursor molecules for peptidoglycan synthesis. In a multistep reaction, DapA converts pyruvate and l-aspartate-4-semialdehyde to 4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid. In many organisms, lysine binds allosterically to DapA, causing negative feedback, thus making the enzyme an important regulatory component of the pathway. Here, the 2.1 Å resolution crystal structure of DapA from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV is reported. The enzyme crystallized as a contaminant of a ...
Source: Acta Crystallographica Section F - April 27, 2020 Category: Biochemistry Authors: Schmitz, R.A. Dietl, A. M ü ller, M. Berben, T. Op den Camp, H.J.M. Barends, T.R.M. Tags: 4-hydroxy-tetrahydrodipicolinate synthase Methylacidiphilum fumariolicum SolV methanotroph aminotransferase pathway research communications Source Type: research
Characterization of the Pseudomonas aeruginosa T6SS PldB immunity proteins PA5086, PA5087 and PA5088 explains a novel stockpiling mechanism
The bacterial type VI secretion system (T6SS) secretes many toxic effectors to gain advantage in interbacterial competition and for eukaryotic host infection. The cognate immunity proteins of these effectors protect bacteria from their own effectors. PldB is a T6SS trans-kingdom effector in Pseudomonas aeruginosa that can infect both prokaryotic and eukaryotic cells. Three proteins, PA5086, PA5087 and PA5088, are employed to suppress the toxicity of PldB-family proteins. The structures of PA5087 and PA5088 have previously been reported, but the identification of further distinctions between these immunity proteins is neede...
Source: Acta Crystallographica Section F - April 27, 2020 Category: Biochemistry Authors: Wen, H. Geng, Z. Gao, Z. She, Z. Dong, Y. Tags: X-ray crystallography T6SS immunity proteins stockpiling mechanism electrostatic potential surface PA5086 Pseudomonas aeruginosa type VI secretion system research communications Source Type: research
Structure of a single-chain H2A/H2B dimer
Chromatin is the complex assembly of nucleic acids and proteins that makes up the physiological form of the eukaryotic genome. The nucleosome is the fundamental repeating unit of chromatin, and is composed of ∼ 147 bp of DNA wrapped around a histone octamer formed by two copies of each core histone: H2A, H2B, H3 and H4. Prior to nucleosome assembly, and during histone eviction, histones are typically assembled into soluble H2A/H2B dimers and H3/H4 dimers and tetramers. A multitude of factors interact with soluble histone dimers and tetramers, including chaperones, importins, histone-modifying enzymes and chromatin-re...
Source: Acta Crystallographica Section F - April 27, 2020 Category: Biochemistry Authors: Warren, C. Bonanno, J.B. Almo, S.C. Shechter, D. Tags: histones chromatin H2A/H2B dimer Xenopus laevis crystallography research communications Source Type: research
Crystal structure of Arabidopsis thaliana casein kinase 2 α 1
Casein kinase 2 (CK2) is a ubiquitous pleiotropic enzyme that is highly conserved across eukaryotic kingdoms. CK2 is singular amongst kinases as it is highly rigid and constitutively active. Arabidopsis thaliana is widely used as a model system in molecular plant research; the biological functions of A. thaliana CK2 are well studied in vivo and many of its substrates have been identified. Here, crystal structures of the α subunit of A. thaliana CK2 in three crystal forms and of its complex with the nonhydrolyzable ATP analog AMppNHp are presented. While the C-lobe of the enzyme is highly rigid, structural plasticity is...
Source: Acta Crystallographica Section F - April 5, 2020 Category: Biochemistry Authors: Demulder, M. De Veylder, L. Loris, R. Tags: casein kinase CK2 structural flexibility ATP binding Arabidopsis thaliana research communications Source Type: research
Structure of the Mycobacterium smegmatis α -maltose-1-phosphate synthase GlgM
Mycobacterium tuberculosis produces glycogen (also known as α -glucan) to help evade human immunity. This pathogen uses the GlgE pathway to generate glycogen rather than the more well known glycogen synthase GlgA pathway, which is absent in this bacterium. Thus, the building block for this glucose polymer is α -maltose-1-phosphate rather than an NDP-glucose donor. One of the routes to α -maltose-1-phosphate is now known to involve the GlgA homologue GlgM, which uses ADP-glucose as a donor and α -glucose-1-phosphate as an acceptor. To help compare GlgA (a GT5 family member) with GlgM enzymes (GT4 family members), the X-...
Source: Acta Crystallographica Section F - April 2, 2020 Category: Biochemistry Authors: Syson, K. Stevenson, C.E.M. Lawson, D.M. Bornemann, S. Tags: GlgM α -maltose-1-phosphate synthase glycosyltransferase glycogen -glucan research communications Source Type: research
Rv0100, a proposed acyl carrier protein in Mycobacterium tuberculosis: expression, purification and crystallization. Corrigendum
The true identity of the protein found in the crystals reported by Bondoc et al. [(2019), Acta Cryst. F75, 646 – 651] is given. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 1, 2020 Category: Biochemistry Authors: Bondoc, J.M.G. Gutka, H.J. Almutairi, M.M. Patwell, R. Rutter, M.W. Wolf, N.M. Samudrala, R. Mehboob, S. Dementiev, A. Abad-Zapatero, C. Movahedzadeh, F. Tags: acyl carrier protein Mycobacterium tuberculosis Mycobacterium smegmatis Rv0100 corrigendum addenda and errata Source Type: research
Visualizing an unseen enemy; mobilizing structural biology to counter COVID-19
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 31, 2020 Category: Biochemistry Authors: Baker, E.N. Tags: COVID-19 coronaviruses SARS-CoV-2 editorial Source Type: research
Crystal structure of monomeric Amuc_1100 from Akkermansia muciniphila
This study provides a structural basis for the elucidation of the molecular mechanism of Amuc_1100. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 31, 2020 Category: Biochemistry Authors: Mou, L. Peng, X. Chen, Y. Xiao, Q. Liao, H. Liu, M. Guo, L. Liu, Y. Zhang, X. Deng, D. Tags: Akkermansia muciniphila type IV pili Amuc_1100 gut microbes crystal structure research communications Source Type: research
Structural characterization of human O-phosphoethanolamine phospho-lyase
Human O-phosphoethanolamine phospho-lyase (hEtnppl; EC 4.2.3.2) is a pyridoxal 5 ′ -phosphate-dependent enzyme that catalyzes the degradation of O-phosphoethanolamine (PEA) into acetaldehyde, phosphate and ammonia. Physiologically, the enzyme is involved in phospholipid metabolism, as PEA is the precursor of phosphatidylethanolamine in the CDP-ethanolamine (Kennedy) pathway. Here, the crystal structure of hEtnppl in complex with pyridoxamine 5 ′ -phosphate was determined at 2.05 Å resolution by molecular replacement using the structure of A1RDF1 from Arthrobacter aurescens TC1 (PDB entry 5g4i) as the search model....
Source: Acta Crystallographica Section F - March 31, 2020 Category: Biochemistry Authors: Vettraino, C. Peracchi, A. Donini, S. Parisini, E. Tags: O-phosphoethanolamine phospho-lyase lyases PMP crystal structure research communications Source Type: research
Crystal structure of Arabidopsis thaliana neutral invertase 2
The metabolism of sucrose is of crucial importance for life on Earth. In plants, enzymes called invertases split sucrose into glucose and fructose, contributing to the regulation of metabolic fluxes. Invertases differ in their localization and pH optimum. Acidic invertases present in plant cell walls and vacuoles belong to glycoside hydrolase family 32 (GH32) and have an all- β structure. In contrast, neutral invertases are located in the cytosol and organelles such as chloroplasts and mitochondria. These poorly understood enzymes are classified into a separate GH100 family. Recent crystal structures of the closely relate...
Source: Acta Crystallographica Section F - March 2, 2020 Category: Biochemistry Authors: Tarkowski, Ł .P. Tsirkone, V.G. Osipov, E.M. Beelen, S. Lammens, W. Vergauwen, R. Van den Ende, W. Strelkov, S.V. Tags: GH100 neutral invertase Arabidopsis thaliana crystal structure research communications Source Type: research
Structural insights into the catalytic mechanism of Bacillus subtilis BacF
The nonribosomal biosynthesis of the dipeptide antibiotic bacilysin is achieved by the concerted action of multiple enzymes in the Bacillus subtilis bac operon. BacF (YwfG), encoded by the bacF gene, is a fold type I pyridoxal 5-phosphate (PLP)-dependent stereospecific transaminase. Activity assays with l-phenylalanine and 4-hydroxyphenylpyruvic acid (4HPP), a chemical analogue of tetrahydrohydroxyphenylpyruvic acid (H4HPP), revealed stereospecific substrate preferences, a finding that was consistent with previous reports on the role of this enzyme in bacilysin synthesis. The crystal structure of this dimeric enzyme was de...
Source: Acta Crystallographica Section F - March 2, 2020 Category: Biochemistry Authors: Deshmukh, A. Gopal, B. Tags: transaminases external aldimine stereospecificity enzyme catalysis bacilysin synthesis research communications Source Type: research
