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Acta Crystallographica. Section F, Structural Biology Communications

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https://read.qxmd.com/read/30950833/the-putative-polysaccharide-deacetylase-ba0331-cloning-expression-crystallization-and-structure-determination
#1
Athena Andreou, Petros Giastas, Sofia Arnaouteli, Mary Tzanodaskalaki, Socrates J Tzartos, Kostas Bethanis, Vassilis Bouriotis, Elias E Eliopoulos
Ba0331 is a putative polysaccharide deacetylase from Bacillus anthracis, the etiological agent of the disease anthrax, that contributes to adaptation of the bacterium under extreme conditions and to maintenance of the cell shape. In the present study, the crystal structure of Ba0331 was determined at 2.6 Å resolution. The structure consists of two domains: a fibronectin type 3-like (Fn3-like) domain and a NodB catalytic domain. The latter is present in all carbohydrate esterase family 4 enzymes, while a comparative analysis of the Fn3-like domain revealed structural plasticity despite the retention of the conserved Fn3-like domain characteristics...
April 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30950832/igni18-a-novel-metallo-hydrolase-from-the-hyperthermophilic-archaeon-ignicoccus-hospitalis-kin4-i-cloning-expression-purification-and-x-ray-analysis
#2
Stefanie Kobus, Pablo Perez-Garcia, Astrid Hoeppner, Nicholas Holzscheck, Filip Kovacic, Wolfgang R Streit, Karl Erich Jaeger, Jennifer Chow, Sander H J Smits
The hyperthermophilic crenarchaeon Ignicoccus hospitalis KIN4/I possesses at least 35 putative genes encoding enzymes that belong to the α/β-hydrolase superfamily. One of those genes, the metallo-hydrolase-encoding igni18, was cloned and heterologously expressed in Pichia pastoris. The enzyme produced was purified in its catalytically active form. The recombinant enzyme was successfully crystallized and the crystal diffracted to a resolution of 2.3 Å. The crystal belonged to space group R32, with unit-cell parameters a = b = 67...
April 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30950831/functional-and-structural-characterization-of-idnl7-an-adenylation-enzyme-involved-in-incednine-biosynthesis
#3
Jolanta Cieślak, Akimasa Miyanaga, Makoto Takaishi, Fumitaka Kudo, Tadashi Eguchi
Adenylation enzymes play an important role in the selective incorporation of the cognate carboxylate substrates in natural product biosynthesis. Here, the biochemical and structural characterization of the adenylation enzyme IdnL7, which is involved in the biosynthesis of the macrolactam polyketide antibiotic incednine, is reported. Biochemical analysis showed that IdnL7 selects and activates several small amino acids. The structure of IdnL7 in complex with an L-alanyl-adenylate intermediate mimic, 5'-O-[N-(L-alanyl)sulfamoyl]adenosine, was determined at 2...
April 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30950830/structure-of-a-critical-metabolic-enzyme-s-adenosylmethionine-synthetase-from-cryptosporidium-parvum
#4
Jeffrey Ohren, Gwenn G Parungao, Ronald E Viola
S-Adenosyl-L-methionine (AdoMet), the primary methyl donor in most biological methylation reactions, is produced from ATP and methionine in a multistep reaction catalyzed by AdoMet synthetase. The diversity of group-transfer reactions that involve AdoMet places this compound at a key crossroads in amino-acid, nucleic acid and lipid metabolism, and disruption of its synthesis has adverse consequences for all forms of life. The family of AdoMet synthetases is highly conserved, and structures of this enzyme have been determined from organisms ranging from bacteria to humans...
April 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30950829/crystal-structure-of-phosphoribulokinase-from-synechococcus-sp-strain-pcc-6301
#5
Robert H Wilson, Manajit Hayer-Hartl, Andreas Bracher
Phosphoribulokinase (PRK) catalyses the ATP-dependent phosphorylation of ribulose 5-phosphate to give ribulose 1,5-bisphosphate. Regulation of this reaction in response to light controls carbon fixation during photosynthesis. Here, the crystal structure of PRK from the cyanobacterium Synechococcus sp. strain PCC 6301 is presented. The enzyme is dimeric and has an α/β-fold with an 18-stranded β-sheet at its core. Interestingly, a disulfide bond is found between Cys40 and the P-loop residue Cys18, revealing the structural basis for the redox inactivation of PRK activity...
April 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30950828/pseudomonas-aeruginosa-esterase-pa2949-a-bacterial-homolog-of-the-human-membrane-esterase-abhd6-expression-purification-and-crystallization
#6
Florian Bleffert, Joachim Granzin, Holger Gohlke, Renu Batra-Safferling, Karl Erich Jaeger, Filip Kovacic
The human membrane-bound α/β-hydrolase domain 6 (ABHD6) protein modulates endocannabinoid signaling, which controls appetite, pain and learning, as well as being linked to Alzheimer's and Parkinson's diseases, through the degradation of the key lipid messenger 2-arachidonylglycerol (2-AG). This makes ABHD6 an attractive therapeutic target that lacks structural information. In order to better understand the molecular mechanism of 2-AG-hydrolyzing enzymes, the PA2949 protein from Pseudomonas aeruginosa, which has 49% sequence similarity to the ABHD6 protein, was cloned, overexpressed, purified and crystallized...
April 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30950827/perdeuteration-large-crystal-growth-and-neutron-data-collection-of-leishmania-mexicana-triose-phosphate-isomerase-e65q-variant
#7
Vinardas Kelpšas, Bénédicte Lafumat, Matthew P Blakeley, Nicolas Coquelle, Esko Oksanen, Claes von Wachenfeldt
Triose-phosphate isomerase (TIM) catalyses the interconversion of dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. Two catalytic mechanisms have been proposed based on two reaction-intermediate analogues, 2-phosphoglycolate (2PG) and phosphoglycolohydroxamate (PGH), that have been used as mimics of the cis-enediol(ate) intermediate in several studies of TIM. The protonation states that are critical for the mechanistic interpretation of these structures are generally not visible in the X-ray structures...
April 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30950826/crystallization-of-the-human-tetraspanin-protein-cd9
#8
Rie Umeda, Tomohiro Nishizawa, Osamu Nureki
The tetraspanin family of proteins with four membrane-spanning proteins function in a wide range of physiological processes in higher organisms, including cell migration and proliferation, cell fusion, fertilization and virus infection. Although the recently reported structure of CD81 unveiled the basic architecture of this family for the first time, further structural and functional studies are required in order to understand the mechanistic details of the complicated functions of the tetraspanin-family proteins...
April 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30950825/crystal-structure-of-the-putative-peptide-binding-protein-appa-from-clostridium-difficile
#9
Adam Hughes, Samuel Wilson, Eleanor J Dodson, Johan P Turkenburg, Anthony J Wilkinson
Peptides play an important signalling role in Bacillus subtilis, where their uptake by one of two ABC-type oligopeptide transporters, Opp and App, is required for efficient sporulation. Homologues of these transporters in Clostridium difficile have been characterized, but their role, and hence that of peptides, in regulating sporulation in this organism is less clear. Here, the oligopeptide-binding receptor proteins for these transporters, CdAppA and CdOppA, have been purified and partially characterized, and the crystal structure of CdAppA has been determined in an open unliganded form...
April 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30950824/bacmam-production-and-crystal-structure-of-nonglycosylated-apo-human-furin-at-1-89-%C3%A3-resolution
#10
Kenneth H Pearce, Laurie K Overton, Robert T Gampe, George B Barrett, J David Taylor, David D McKee, Nino Campobasso, Robert T Nolte, Robert A Reid
Furin, also called proprotein convertase subtilisin/kexin 3 (PCSK3), is a calcium-dependent serine endoprotease that processes a wide variety of proproteins involved in cell function and homeostasis. Dysregulation of furin has been implicated in numerous disease states, including cancer and fibrosis. Mammalian cell expression of the furin ectodomain typically produces a highly glycosylated, heterogeneous protein, which can make crystallographic studies difficult. Here, the expression and purification of nonglycosylated human furin using the BacMam technology and site-directed mutagenesis of the glycosylation sites is reported...
April 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30950823/crystal-structure-of-protein-tyrosine-phosphatase-2-from-cydia-pomonella-granulovirus
#11
Guangmei Huang, Michael R Oliver, Jeremy R Keown, David C Goldstone, Peter Metcalf
Many viral genomes encode kinase and phosphatase enzymes to manipulate pathways that are controlled by phosphorylation events. The majority of viral phosphatase genes occur in the Baculoviridae and Poxviridae families of large DNA viruses. The corresponding protein sequences belong to four major homology groups, and structures are currently available for only two of these. Here, the first structure from the third group, the protein tyrosine phosphatase-2 (PTP-2) class of viral phosphatases, is described. It is shown that Cydia pomonella granulovirus PTP-2 has the same general fold and active-site architecture as described previously for other phosphatases, in the absence of significant sequence homology...
April 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30950822/the-structure-of-lipopolysaccharide-transport-protein-b-lptb-from-burkholderia-pseudomallei
#12
Genady Pankov, Alice Dawson, William N Hunter
The thick outer membrane (OM) of Gram-negative bacteria performs an important protective role against hostile environments, supports cell integrity, and contributes to surface adhesion and in some cases also to virulence. A major component of the OM is lipopolysaccharide (LPS), a complex glycolipid attached to a core containing fatty-acyl chains. The assembly and transport of lipid A, the membrane anchor for LPS, to the OM begins when a heteromeric LptB2 FG protein complex extracts lipid A from the outer leaflet of the inner membrane...
April 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30950821/the-structure-of-an-iron-containing-alcohol-dehydrogenase-from-a-hyperthermophilic-archaeon-in-two-chemical-states
#13
Steven B Larson, Jesse A Jones, Alexander McPherson
An iron-containing alcohol dehydrogenase (FeADH) from the hyperthermophilic archaeon Thermococcus thioreducens was crystallized in unit cells belonging to space groups P21 , P21 21 21 and P43 21 2, and the crystal structures were solved at 2.4, 2.1 and 1.9 Å resolution, respectively, by molecular replacement using the FeADH from Thermotoga maritima (Schwarzenbacher et al., 2004) as a model. In the monoclinic and orthorhombic crystals the dehydrogenase (molecular mass 41.5 kDa) existed as a dimer containing a twofold noncrystallographic symmetry axis, which was crystallographic in the tetragonal crystals...
April 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30950820/substrate-analogue-complex-structure-of-mycobacterium-tuberculosis-decaprenyl-diphosphate-synthase
#14
Tzu Ping Ko, Xiansha Xiao, Rey Ting Guo, Jian Wen Huang, Weidong Liu, Chun Chi Chen
Decaprenyl diphosphate synthase from Mycobacterium tuberculosis (MtDPPS, also known as Rv2361c) catalyzes the consecutive elongation of ω,E,Z-farnesyl diphosphate (EZ-FPP) by seven isoprene units by forming new cis double bonds. The protein folds into a butterfly-like homodimer like most other cis-type prenyltransferases. The starting allylic substrate EZ-FPP is bound to the S1 site and the homoallylic substrate to be incorporated, isopentenyl diphosphate, is bound to the S2 site. Here, a 1.55 Å resolution structure of MtDPPS in complex with the substrate analogues geranyl S-thiodiphosphate (GSPP) and isopentenyl S-thiodiphosphate bound to their respective sites in one subunit clearly shows the active-site configuration and the magnesium-coordinated geometry for catalysis...
April 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30839296/the-structure-of-cgnj-a-domain-of-unknown-function-protein-from-the-crocagin-gene-cluster
#15
Sebastian Adam, Andreas Klein, Frank Surup, Jesko Koehnke
Natural products often contain interesting new chemical entities that are introduced into the structure of a compound by the enzymatic machinery of the producing organism. The recently described crocagins are novel polycyclic peptides which belong to the class of ribosomally synthesized and post-translationally modified peptide natural products. They have been shown to bind to the conserved prokaryotic carbon-storage regulator A in vitro. In efforts to understand crocagin biosynthesis, the putative biosynthetic genes were expressed and purified...
March 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30839295/crystal-structure-of-the-legume-lectin-like-domain-of-an-ergic-53-like-protein-from-entamoeba-histolytica
#16
Farha Khan, Kaza Suguna
ERGIC-53-like proteins are type I membrane proteins that belong to the class of intracellular cargo receptors and are known to be indispensable for the intracellular transport of glycoproteins. They are implicated in transporting glycoproteins between the endoplasmic reticulum and the Golgi body. The crystal structure of the legume lectin-like domain of an ERGIC-53-like protein from Entamoeba histolytica has been determined at 2.4 Å resolution. Although the overall structure of the domain resembles those of its mammalian and yeast orthologs (ERGIC-53 and Emp46, respectively), there are significant changes in the carbohydrate-binding site...
March 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30839294/neutron-crystallographic-study-of-heterotrimeric-glutamine-amidotransferase-cab
#17
Long Li, Motoyasu Adachi, Jian Yu, Koji Kato, Akira Shinoda, Andreas Ostermann, Tobias E Schrader, Toyoyuki Ose, Min Yao
Heterotrimeric glutamine amidotransferase CAB (GatCAB) possesses an ammonia-self-sufficient mechanism in which ammonia is produced and used in the inner complex by GatA and GatB, respectively. The X-ray structure of GatCAB revealed that the two identified active sites of GatA and GatB are markedly distant, but are connected in the complex by a channel of 30 Å in length. In order to clarify whether ammonia is transferred through this channel in GatCAB by visualizing ammonia, neutron diffraction studies are indispensable...
March 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30839293/blasting-away-preconceptions-in-crystallization-trials
#18
Gabriel Jan Abrahams, Janet Newman
Crystallization is in many cases a critical step for solving the three-dimensional structure of a protein molecule. Determining which set of chemicals to use in the initial screen is typically agnostic of the protein under investigation; however, crystallization efficiency could potentially be improved if this were not the case. Previous work has assumed that sequence similarity may provide useful information about appropriate crystallization cocktails; however, the authors are not aware of any quantitative verification of this assumption...
March 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30839292/structure-of-glycerol-dehydrogenase-glda-from-escherichia-coli
#19
Jun Zhang, Ankanahalli N Nanjaraj Urs, Lianyun Lin, Yan Zhou, Yiling Hu, Gaoqun Hua, Qiang Gao, Zhiguang Yuchi, Yan Zhang
Escherichia coli (strain K-12, substrain MG1655) glycerol dehydrogenase (GldA) is required to catalyze the first step in fermentative glycerol metabolism. The protein was expressed and purified to homogeneity using a simple combination of heat-shock and chromatographic methods. The high yield of the protein (∼250 mg per litre of culture) allows large-scale production for potential industrial applications. Purified GldA exhibited a homogeneous tetrameric state (∼161 kDa) in solution and relatively high thermostability (Tm = 65...
March 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://read.qxmd.com/read/30839291/neutron-and-x-ray-analysis-of-the-fenna-matthews-olson-photosynthetic-antenna-complex-from-prosthecochloris-aestuarii
#20
Xun Lu, Brinda Selvaraj, Sudipa Ghimire-Rijal, Gregory S Orf, Flora Meilleur, Robert E Blankenship, Matthew J Cuneo, Dean A A Myles
The Fenna-Matthews-Olson protein from Prosthecochloris aestuarii (PaFMO) has been crystallized in a new form that is amenable to high-resolution X-ray and neutron analysis. The crystals belonged to space group H3, with unit-cell parameters a = b = 83.64, c = 294.78 Å, and diffracted X-rays to ∼1.7 Å resolution at room temperature. Large PaFMO crystals grown to volumes of 0.3-0.5 mm3 diffracted neutrons to 2.2 Å resolution on the MaNDi neutron diffractometer at the Spallation Neutron Source. The resolution of the neutron data will allow direct determination of the positions of H atoms in the structure, which are believed to be fundamentally important in tuning the individual excitation energies of bacteriochlorophylls in this archetypal photosynthetic antenna complex...
March 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
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