Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser
Riboswitches are conformationally dynamic RNAs that regulate gene expression by binding specific small molecules. ZTP riboswitches bind the purine-biosynthetic intermediate 5-aminoimidazole-4-carboxamide riboside 5 ′ -monophosphate (ZMP) and its triphosphorylated form (ZTP). Ligand binding to this riboswitch ultimately upregulates genes involved in folate and purine metabolism. Using an X-ray free-electron laser (XFEL), the room-temperature structure of the Fusobacterium ulcerans ZTP riboswitch bound to ZMP has now been determined at 4.1   Å resolution. This model, which was refined against a data set from &s...
Source: Acta Crystallographica Section F - June 28, 2019 Category: Biochemistry Authors: Jones, C. Tran, B. Conrad, C. Stagno, J. Trachman, R. Fischer, P. Meents, A. Ferr é -D'Amar é , A. Tags: RNA structure riboswitches ZTP X-ray free-electron lasers research communications Source Type: research

Structural characterization of Treponema pallidum Tp0225 reveals an unexpected leucine-rich repeat architecture
The phylogenetically divergent spirochete bacterium Treponema pallidum subsp. pallidum is the causative agent of syphilis. Central to the capacity of T.   pallidum to establish infection is the ability of the pathogen to attach to a diversity of host cells. Many pathogenic bacteria employ leucine-rich repeat (LRR) domain-containing proteins to mediate protein – protein interactions, including attachment to host components and establishment of infection. Intriguingly, T. pallidum expresses only one putative LRR domain-containing protein (Tp0225) with an unknown function. In an effort to ascribe a function to Tp02...
Source: Acta Crystallographica Section F - June 26, 2019 Category: Biochemistry Authors: Ramaswamy, R. Houston, S. Loveless, B. Cameron, C.E. Boulanger, M.J. Tags: syphilis Treponema pallidum X-ray crystallography leucine rich-repeat domain research communications Source Type: research

Crystal structure of an iron superoxide dismutase from the pathogenic amoeba Acanthamoeba castellanii
The iron superoxide dismutase found in the pathogenic amoeba Acanthamoeba castellanii (AcFeSOD) may play essential roles in the survival of the parasite, not only by protecting it from endogenous oxidative stress but also by detoxifying oxidative killing of the parasite by host immune effector cells. The AcFeSOD protein was expressed in a stable form using an Escherichia coli expression system and was crystallized by the microbatch and hanging-drop vapour-diffusion methods. The structure was determined to 2.33   Å resolution from a single AcFeSOD crystal. The crystal belonged to the hexagonal space group P61 and co...
Source: Acta Crystallographica Section F - June 26, 2019 Category: Biochemistry Authors: Dao, O. Asaithambi, K. Na, B.K. Lee, K.H. Tags: iron superoxide dismutase Acanthamoeba castellanii research communications Source Type: research

Crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase from Thermoplasma acidophilum in complex with the substrate sn-glycerol 1-phosphate
In this study, the crystal structure of the archaeal group II GGGPS from Thermoplasma acidophilum (TaGGGPS) was determined at 2.35   Å resolution. The structure of TaGGGPS showed that it has a TIM-barrel fold, the third helix of which is disordered ( α 3*), and that it forms a homodimer, although a pre-existing structure of an archaeal group II GGGPS (from Methanothermobacter thermautotrophicus) showed a hexameric form. The structure of TaGGGPS showed the precise G1P-recognition mechanism of an archaeal group II GGGPS. The structure of TaGGGPS and molecular-dynamics simulation analysis showed fluctuation of t...
Source: Acta Crystallographica Section F - June 26, 2019 Category: Biochemistry Authors: Nemoto, N. Miyazono, K. Tanokura, M. Yamagishi, A. Tags: geranylgeranylglyceryl phosphate synthase TIM barrel archaea prenyltransferases ether lipid biosynthesis research communications Source Type: research

Changes in the allosteric site of human liver pyruvate kinase upon activator binding include the breakage of an intersubunit cation – π bond
In this study, the X-ray crystal structures of four hLPYK variants were solved to make structural correlations with existing functional data. The variants are D499N, W527H, Δ 529/S531G (called GGG here) and S531E. The results revealed a conformational toggle between the open and closed positions of the allosteric loop. In the absence of Fru-1,6-BP the open position is stabilized, in part, by a cation – π bond between Trp527 and Arg538 ′ (from an adjacent monomer). In the S531E variant glutamate binds in place of the 6 ′ -phosphate of Fru-1,6-BP in the allosteric site, leading to partial allosteri...
Source: Acta Crystallographica Section F - June 10, 2019 Category: Biochemistry Authors: McFarlane, J.S. Ronnebaum, T.A. Meneely, K.M. Chilton, A. Fenton, A.W. Lamb, A.L. Tags: pyruvate kinase allosterism human liver isozyme research communications Source Type: research

Structural analysis of the HIN1 domain of interferon-inducible protein 204
Interferon-inducible protein 204 (p204) binds to microbial DNA to elicit inflammatory responses and induce interferon production. p204 also modulates cell proliferation and differentiation by regulating various transcription factors. The C-terminal HIN domains in p204 are believed to be responsible for DNA binding, but the binding mode is not fully understood. The DNA-binding affinity of the p204 HIN1 domain has been characterized and its crystal structure has been determined, providing insight into its interaction with DNA. Surface-charge distribution together with sequence alignment suggests that the p204 HIN domain uses...
Source: Acta Crystallographica Section F - June 10, 2019 Category: Biochemistry Authors: Tian, Y. Yin, Q. Tags: interferon-inducible protein 204 p204 HIN domain DNA binding research communications Source Type: research

Crystal structure of the flavin-dependent thymidylate synthase Thy1 from Thermus thermophilus with an extra C-terminal domain
The thymidylate synthases ThyA and Thy1 are enzymes that catalyse the formation of thymidine monophosphate from 2 ′ -deoxyuridine monophosphate. Thy1 (or ThyX) requires flavin for catalytic reactions, while ThyA does not. In the present study, the crystal structure of the flavin-dependent thymidylate synthase Thy1 from Thermus thermophilus HB8 (TtThy1, TTHA1096) was determined in complex with FAD and phosphate at 2.5   Å resolution. TtThy1 is a tetrameric molecule like other Thy1 proteins, to which four FAD molecules are bound. In the crystal of TtThy1, two phosphate ions were bound to each dUMP-binding site....
Source: Acta Crystallographica Section F - June 6, 2019 Category: Biochemistry Authors: Ogawa, A. Sampei, G. Kawai, G. Tags: flavin-dependent thymidylate synthase pyrimidine nucleotide biosynthetic pathway C-terminal domain research communications Source Type: research

A new crystal structure and small-angle X-ray scattering analysis of the homodimer of human SFPQ
Splicing factor proline/glutamine-rich (SFPQ) is an essential RNA-binding protein that is implicated in many aspects of nuclear function. The structures of SFPQ and two paralogs, non-POU domain-containing octamer-binding protein and paraspeckle component 1, from the Drosophila behavior human splicing protein family have previously been characterized. The unusual arrangement of the four domains, two RNA-recognition motifs (RRMs), a conserved region termed the NonA/paraspeckle (NOPS) domain and a C-terminal coiled coil, in   the intertwined dimer provides a potentially unique RNA-binding surface. However, the molecular ...
Source: Acta Crystallographica Section F - May 21, 2019 Category: Biochemistry Authors: Hewage, T.W. Caria, S. Lee, M. Tags: SFPQ DBHS protein family nuclear protein RNA-recognition motif PSPC1 NONO dimerization crystal structure solution scattering Drosophila behavior human splicing research communications Source Type: research

Crystallization of a potassium ion channel and X-ray and neutron data collection
The mechanism by which potassium ions are transported through ion channels is currently being investigated by several groups using many different techniques. Clarification of the location of water molecules during transport is central to understanding how these integral membrane proteins function. Neutrons have a unique sensitivity to both hydrogen and potassium, rendering neutron crystallography capable of distinguishing waters from K+ ions. Here, the collection of a complete neutron data set from a potassium ion channel to a resolution of 3.55   Å using the Macromolecular Neutron Diffractometer (MaNDi) is reporte...
Source: Acta Crystallographica Section F - May 21, 2019 Category: Biochemistry Authors: Langan, P.S. Vandavasi, V.G. Sullivan, B. Harp, J. Weiss, K. Coates, L. Tags: neutron diffraction X-ray diffraction membrane proteins ion channels research communications Source Type: research

Structure of the Prx6-subfamily 1-Cys peroxiredoxin from Sulfolobus islandicus
Aerobic thermoacidophilic archaea belonging to the genus Sulfolobus harbor peroxiredoxins, thiol-dependent peroxidases that assist in protecting the cells from oxidative damage. Here, the crystal structure of the 1-Cys peroxiredoxin from Sulfolobus islandicus, named 1-Cys SiPrx, is presented. A 2.75   Å resolution data set was collected from a crystal belonging to space group P212121, with unit-cell parameters a = 86.8, b = 159.1, c = 189.3   Å , α = β = γ = 90 ° . The structure was solved by molecular replacement using the homologous Aeropyrum pernix peroxiredoxin (ApPrx) structure as ...
Source: Acta Crystallographica Section F - May 13, 2019 Category: Biochemistry Authors: Stroobants, S. Van Molle, I. Saidi, Q. Jonckheere, K. Maes, D. Peeters, E. Tags: peroxiredoxins archaea Sulfolobus islandicus Prx6 chaperones research communications Source Type: research

Cruzain structures: apocruzain and cruzain bound to S-methyl thiomethanesulfonate and implications for drug design
Chagas disease, which is caused by Trypanosoma cruzi, affects more than six million people worldwide. Cruzain is the major cysteine protease involved in the survival of this parasite. Here, the expression, purification and crystallization of this enzyme are reported. The cruzain crystals diffracted to 1.2   Å resolution, yielding two novel cruzain structures: apocruzain and cruzain bound to the reversible covalent inhibitor S-methyl thiomethanesulfonate. Mass-spectrometric experiments confirmed the presence of a methylthiol group attached to the catalytic cysteine. Comparison of these structures with previously pub...
Source: Acta Crystallographica Section F - May 13, 2019 Category: Biochemistry Authors: Barbosa da Silva, E. Dall, E. Briza, P. Brandstetter, H. Ferreira, R.S. Tags: cruzain Chagas disease MMTS Trypanosoma cruzi research communications Source Type: research

Crystal structure of the SPRY domain of human SPSB2 in the apo state
The SPRY domain-containing SOCS box protein 2 (SPSB2) is one of four mammalian SPSB proteins that are characterized by a C-terminal SOCS box and a central SPRY/B30.2 domain. SPSB2 interacts with inducible nitric oxide synthase (iNOS) via the SPRY domain and polyubiquitinates iNOS, resulting in its proteasomal degradation. Inhibitors that can disrupt SPSB2 – iNOS interaction and augment NO production may serve as novel anti-infective and anticancer agents. The previously determined murine SPSB2 structure may not reflect the true apo conformation of the iNOS-binding site. Here, the crystal structure of human SPSB2 SPRY...
Source: Acta Crystallographica Section F - May 10, 2019 Category: Biochemistry Authors: Luo, Y. Li, K. Yang, J. Zhang, D. Zhou, Y. Kuang, Z. Tags: SPRY domain of SPRY domain-containing human SOCS box protein 2 SPSB2 SPRY/B30.2 domain iNOS apo structure His6 tag research communications Source Type: research

Crystal structure of the SPRY domain of human SOCS box protein 2 in the apo state
The SPRY domain-containing SOCS box protein 2 (SPSB2) is one of four mammalian SPSB proteins that are characterized by a C-terminal SOCS box and a central SPRY/B30.2 domain. SPSB2 interacts with inducible nitric oxide synthase (iNOS) via the SPRY domain and polyubiquitinates iNOS, resulting in its proteasomal degradation. Inhibitors that can disrupt SPSB2 – iNOS interaction and augment NO production may serve as novel anti-infective and anticancer agents. The previously determined murine SPSB2 structure may not reflect the true apo conformation of the iNOS-binding site. Here, the crystal structure of human SPSB2 SPRY...
Source: Acta Crystallographica Section F - May 10, 2019 Category: Biochemistry Authors: Luo, Y. Li, K. Yang, J. Zhang, D. Zhou, Y. Kuang, Z. Tags: SPRY domain of SPRY domain-containing human SOCS box protein 2 SPSB2 SPRY/B30.2 domain iNOS apo structure His6 tag research communications Source Type: research

Structures of soluble rabbit neprilysin complexed with phosphoramidon or thiorphan
Neutral endopeptidase (neprilysin; NEP) is a proteinase that cleaves a wide variety of peptides and has been implicated in Alzheimer's disease, cardiovascular conditions, arthritis and other inflammatory diseases. The structure of the soluble extracellular domain (residues 55 – 750) of rabbit neprilysin was solved both in its native form at 2.1   Å resolution, and bound to the inhibitors phosphoramidon and thiorphan at 2.8 and 3.0   Å resolution, respectively. Consistent with the extracellular domain of human neprilysin, the structure reveals a large central cavity which contains the active site and t...
Source: Acta Crystallographica Section F - May 10, 2019 Category: Biochemistry Authors: Labiuk, S.L. Sygusch, J. Grochulski, P. Tags: neutral endopeptidase neprilysin phosphoramidon thiorphan research communications Source Type: research

Structure of Aspergillus aculeatus β -1,4-galactanase in complex with galactobiose
β -1,4-Galactanases are glycoside hydrolases that are involved in the degradation of pectin and belong to family 53 in the classification of glycoside hydrolases. Previous studies have elucidated the structures of several fungal and two bacterial galactanases, while biochemical studies have indicated differences in the product profiles of different members of the family. Structural studies of ligand complexes have to date been limited to the bacterial members of the family. Here, the first structure of a fungal galactanase in complex with a disaccharide is presented. Galactobiose binds to subsites − 1 and &minus...
Source: Acta Crystallographica Section F - May 10, 2019 Category: Biochemistry Authors: Torpenholt, S. Poulsen, J.-C.N. Muderspach, S.J. De Maria, L. Lo Leggio, L. Tags: glycoside hydrolases specificity pectin oligosaccharides Aspergillus aculeatus β -1,4-galactanases research communications Source Type: research

Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 30, 2019 Category: Biochemistry Authors: Helliwell, J.R. Minor, W. Weiss, M.S. Garman, E.F. Read, R.J. Newman, J. van Raaij, M.J. Hajdu, J. Baker, E.N. Tags: FAIR diffraction data IUCr policy editorial Source Type: research

Comparative structure analysis of the ETSi domain of ERG3 and its complex with the E74 promoter DNA sequence. Corrigendum
The article by Sharma et al. [(2018), Acta Cryst. F74, 656 – 663] is corrected. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 29, 2019 Category: Biochemistry Authors: Sharma, R. Gangwar, S.P. Saxena, A.K. Tags: prostate cancer ETS transcription factor ERG3 E74 promoter DNA corrigendum addenda and errata Source Type: research

High-resolution crystal structure of the reduced Grx1 from Saccharomyces cerevisiae
Grx1, a cytosolic thiol – disulfide oxidoreductase, actively maintains cellular redox homeostasis using glutathione substrates (reduced, GSH, and oxidized, GSSG). Here, the crystallization of reduced Grx1 from the yeast Saccharomyces cerevisiae (yGrx1) in space group P212121 and its structure solution and refinement to 1.22   Å resolution are reported. To study the structure – function relationship of yeast Grx1, the crystal structure of reduced yGrx1 was compared with the existing structures of the oxidized and glutathionylated forms. These comparisons revealed structural differences in the conformatio...
Source: Acta Crystallographica Section F - April 26, 2019 Category: Biochemistry Authors: Maghool, S. La Fontaine, S. Maher, M.J. Tags: glutaredoxin Saccharomyces cerevisiae Grx1 reduced form research communications Source Type: research

Evaluation of a crystallographic surrogate for kallikrein 5 in the discovery of novel inhibitors for Netherton syndrome
The inhibition of kallikrein 5 (KLK5) has been identified as a potential strategy for treatment of the genetic skin disorder Netherton syndrome, in which loss-of-function mutations in the SPINK5 gene lead to down-regulation of the endogenous inhibitor LEKTI-1 and profound skin-barrier defects with severe allergic manifestations. To aid in the development of a medicine for this target, an X-ray crystallographic system was developed to facilitate fragment-guided chemistry and knowledge-based drug-discovery approaches. Here, the development of a surrogate crystallographic system in place of KLK5, which proved to be challengin...
Source: Acta Crystallographica Section F - April 26, 2019 Category: Biochemistry Authors: Thorpe, J.H. Edgar, E.V. Smith, K.J. Lewell, X.Q. Rella, M. White, G.V. Polyakova, O. Nassau, P. Walker, A.L. Holmes, D.S. Pearce, A.C. Wang, Y. Liddle, J. Hovnanian, A. Tags: Netherton syndrome kallikrein GSK144 structure-guided design medicinal chemistry research communications Source Type: research

Phasing with calcium at home
With better tools for data processing and with synchrotron beamlines that are capable of collecting data at longer wavelengths, sulfur-based native single-wavelength anomalous dispersion (SAD) phasing has become the `first-choice' method for de novo protein structure determination. However, for many proteins native SAD phasing can be simplified by taking advantage of their interactions with natural metal cofactors that are stronger anomalous scatterers than sulfur. This is demonstrated here for four unique domains of a 1.5   MDa calcium-dependent adhesion protein using the anomalous diffraction of the chelated calcium io...
Source: Acta Crystallographica Section F - April 26, 2019 Category: Biochemistry Authors: Guo, S. Campbell, R. Davies, P.L. Allingham, J.S. Tags: calcium phasing chromium rotating anode single-wavelength anomalous diffraction calcium-binding proteins research communications Source Type: research

Crystal structures of the amino-terminal domain of LpoA from Escherichia coli and Haemophilus influenzae
The bacterial periplasmic protein LpoA is an outer membrane lipoprotein and an activator for the cross-linking activity of PBP1A, a bifunctional peptidoglycan synthase. Previous structures of the amino-terminal (N) domain of LpoA showed it to consist entirely of helices and loops, with at least four tetratricopeptide-like repeats. Although the previously determined orthorhombic crystal structure of the N domain of Haemophilus influenzae LpoA showed a typical curved structure with a concave groove, an NMR structure of the same domain from Escherichia coli was relatively flat. Here, a crystal structure of the N domain of E. ...
Source: Acta Crystallographica Section F - April 26, 2019 Category: Biochemistry Authors: Kelley, A. Vijayalakshmi, J. Saper, M.A. Tags: outer membrane lipoprotein peptidoglycans TPR domain conformational differences LpoA N-terminal domains research communications Source Type: research

Novel T9 loop conformation of filamenting temperature-sensitive mutant Z from Mycobacterium tuberculosis
As of 2017, tuberculosis had infected 1.7 billion people (23% of the population of the world) and caused ten million deaths. Mycobacterium tuberculosis (Mtb) is quickly evolving, and new strains are classified as multidrug resistant. Thus, the identification of novel druggable targets is essential to combat the proliferation of these drug-resistant strains. Filamenting temperature-sensitive mutant Z (FtsZ) is a key protein involved in cytokinesis, an important process for Mtb proliferation and viability. FtsZ is required for bacterial cell division because it polymerizes into a structure called the Z-ring, which recruits a...
Source: Acta Crystallographica Section F - April 24, 2019 Category: Biochemistry Authors: Lazo, E.O. Jakoncic, J. RoyChowdhury, S. Awasthi, D. Ojima, I. Tags: tuberculosis Mycobacterium tuberculosis FtsZ T9 loop filamenting temperature-sensitive mutant Z research communications Source Type: research

Structural basis for oligomerization of the prokaryotic peptide transporter PepTSo2
This study provides valuable insights into the oligomerization mechanism of this MFS-type transporter, which will further pave the way for understanding other oligomeric membrane proteins. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 24, 2019 Category: Biochemistry Authors: Nagamura, R. Fukuda, M. Kawamoto, A. Matoba, K. Dohmae, N. Ishitani, R. Takagi, J. Nureki, O. Tags: peptide transporter major facilitator superfamily lipidic cubic phase single-particle cryo-electron microscopy membrane transporter oligomerization cryo-EM X-ray crystallography research communications Source Type: research

Cryo-EM structure of the Ebola virus nucleoprotein – RNA complex
Ebola virus is an emerging virus that is capable of causing a deadly disease in humans. Replication, transcription and packaging of the viral genome are carried out by the viral nucleocapsid. The nucleocapsid is a complex of the viral nucleoprotein, RNA and several other viral proteins. The nucleoprotein forms large, RNA-bound, helical filaments and acts as a scaffold for additional viral proteins. The 3.1   Å resolution single-particle cryo-electron microscopy structure of the nucleoprotein – RNA helical filament presented here resembles previous structures determined at lower resolution, while providing imp...
Source: Acta Crystallographica Section F - April 24, 2019 Category: Biochemistry Authors: Kirchdoerfer, R.N. Saphire, E.O. Ward, A.B. Tags: Ebola virus nucleoprotein NP helix cryo-electron microscopy research communications Source Type: research

Noncovalent structure of SENP1 in complex with SUMO2
SUMOylation is a post-translational modification in which a small ubiquitin-like molecule (SUMO) is appended to substrate proteins and is known to influence myriads of biological processes. A delicate interplay between several families of SUMOylation proteins and their substrates ensures the proper level of SUMOylation required for normal cell function. Among the SUMO proteins, SUMO2 is known to form mono-SUMOylated proteins and engage in poly-SUMO chain formation, while sentrin-specific protease 1 (SENP1) is a key enzyme in regulating both events. Determination of the SENP1 – SUMO2 interaction is therefore necessary...
Source: Acta Crystallographica Section F - April 24, 2019 Category: Biochemistry Authors: Ambaye, N.D. Tags: SENP1 SUMO2 protease SUMOylation X-ray diffraction cancer research communications Source Type: research

Crystal structure of the cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5
Haloalkane dehalogenases (HLDs) convert halogenated aliphatic pollutants to less toxic compounds by a hydrolytic mechanism. Owing to their broad substrate specificity and high enantioselectivity, haloalkane dehalogenases can function as biosensors to detect toxic compounds in the environment or can be used for the production of optically pure compounds. Here, the structural analysis of the haloalkane dehalogenase DpcA isolated from the psychrophilic bacterium Psychrobacter cryohalolentis K5 is presented at the atomic resolution of 1.05   Å . This enzyme exhibits a low temperature optimum, making it attractive for e...
Source: Acta Crystallographica Section F - April 24, 2019 Category: Biochemistry Authors: Tratsiak, K. Prudnikova, T. Drienovska, I. Damborsky, J. Brynda, J. Pachl, P. Kuty, M. Chaloupkova, R. Rezacova, P. Kuta Smatanova, I. Tags: haloalkane dehalogenase α / β -hydrolase X-ray diffraction psychrophiles structural analysis Psychrobacter cryohalolentis research communications Source Type: research

The putative polysaccharide deacetylase Ba0331: cloning, expression, crystallization and structure determination
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 conserv...
Source: Acta Crystallographica Section F - April 3, 2019 Category: Biochemistry Authors: Andreou, A. Giastas, P. Arnaouteli, S. Tzanodaskalaki, M. Tzartos, S.J. Bethanis, K. Bouriotis, V. Eliopoulos, E.E. Tags: Bacillus anthracis Ba0331 X-ray crystal structure metalloenzymes CE4 family lipoprotein polysaccharide deacetylase research communications Source Type: research

Igni18, a novel metallo-hydrolase from the hyperthermophilic archaeon Ignicoccus hospitalis KIN4/I: cloning, expression, purification and X-ray analysis
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 = 67.42, c   =   253.77   Å , α = β = 90.0, &ga...
Source: Acta Crystallographica Section F - April 2, 2019 Category: Biochemistry Authors: Kobus, S. Perez-Garcia, P. Hoeppner, A. Holzscheck, N. Kovacic, F. Streit, W.R. Jaeger, K.-E. Chow, J. Smits, S.H.J. Tags: Ignicoccus hospitalis α / β -hydrolases metallo- -lactamases research communications Source Type: research

Functional and structural characterization of IdnL7, an adenylation enzyme involved in incednine biosynthesis
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 2.1   Å resolution. The structure of IdnL7 explains t...
Source: Acta Crystallographica Section F - April 2, 2019 Category: Biochemistry Authors: Cie ś lak, J. Miyanaga, A. Takaishi, M. Kudo, F. Eguchi, T. Tags: macrolactam antibiotics polyketides crystal structure adenylation enzyme natural product biosynthesis research communications Source Type: research

Structure of a critical metabolic enzyme: S-adenosylmethionine synthetase from Cryptosporidium parvum
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. Here, the structure of an AdoMet synthetase from th...
Source: Acta Crystallographica Section F - April 2, 2019 Category: Biochemistry Authors: Ohren, J. Parungao, G.F. Viola, R.E. Tags: enzyme structure S-adenosylmethionine synthetase antiparasitic drugs subunit interface Cryptosporidium parvum research communications Source Type: research

Crystal structure of phosphoribulokinase from Synechococcus sp. strain PCC 6301
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. A second disulfide bond appears to...
Source: Acta Crystallographica Section F - April 2, 2019 Category: Biochemistry Authors: Wilson, R.H. Hayer-Hartl, M. Bracher, A. Tags: phosphoribulokinase Calvin – Benson Bassham cycle photosynthesis dark reaction redox regulation transferases research communications Source Type: research

Pseudomonas aeruginosa esterase PA2949, a bacterial homolog of the human membrane esterase ABHD6: expression, purification and crystallization
This study provides hints on the functional similarity of ABHD6-like proteins in prokaryotes and eukaryotes, and might guide the structural study of these difficult-to-crystallize proteins. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 2, 2019 Category: Biochemistry Authors: Bleffert, F. Granzin, J. Gohlke, H. Batra-Safferling, R. Jaeger, K.-E. Kovacic, F. Tags: Pseudomonas aeruginosa PA2949 esterases ABHD6 endocannabinoid signalling pathway Parkinson's disease Alzheimer's disease research communications Source Type: research

Perdeuteration, large crystal growth and neutron data collection of Leishmania mexicana triose-phosphate isomerase E65Q variant
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. To resolve these questions, it is necessary to determine the hydrogen positions using neutron crystallography. N...
Source: Acta Crystallographica Section F - April 2, 2019 Category: Biochemistry Authors: Kelp š as, V. Lafumat, B. Blakeley, M.P. Coquelle, N. Oksanen, E. von Wachenfeldt, C. Tags: triose-phosphate isomerase neutron diffraction Laue method large crystals perdeuteration research communications Source Type: research

Crystallization of the human tetraspanin protein CD9
In this study, attempts were made to crystallize human CD9, a representative member of the tetraspanin family, and it was demonstrated that the truncation of a variable region in the second long extracellular loop significantly improved crystal growth. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 2, 2019 Category: Biochemistry Authors: Umeda, R. Nishizawa, T. Nureki, O. Tags: crystallization LCP membrane proteins CD9 tetraspanins research communications Source Type: research

Crystal structure of the putative peptide-binding protein AppA from Clostridium difficile
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. Peptide binding to either protein c...
Source: Acta Crystallographica Section F - March 13, 2019 Category: Biochemistry Authors: Hughes, A. Wilson, S. Dodson, E.J. Turkenburg, J.P. Wilkinson, A.J. Tags: Clostridium difficile peptide transport OppA AppA sporulation research communications Source Type: research

BacMam production and crystal structure of nonglycosylated apo human furin at 1.89   Å resolution
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 repor...
Source: Acta Crystallographica Section F - March 13, 2019 Category: Biochemistry Authors: Pearce, K.H. Overton, L.K. Gampe, R.T. Barrett, G.B. Taylor, J.D. McKee, D.D. Campobasso, N. Nolte, R.T. Reid, R.A. Tags: furin nonglycosylated apo serine proteinase hydrolase BacMam research communications Source Type: research

Crystal structure of protein tyrosine phosphatase-2 from Cydia pomonella granulovirus
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 ...
Source: Acta Crystallographica Section F - March 13, 2019 Category: Biochemistry Authors: Huang, G. Oliver, M.R. Keown, J.R. Goldstone, D.C. Metcalf, P. Tags: Cydia pomonella granulovirus PTP-2 protein tyrosine phosphatase-2 phosphatases research communications Source Type: research

The structure of lipopolysaccharide transport protein B (LptB) from Burkholderia pseudomallei
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 LptB2FG protein complex extracts lipid A from the outer leaflet of the inner membrane. This process requires energy, and upon hydrolysis of ATP one component of the heteromeric ...
Source: Acta Crystallographica Section F - March 13, 2019 Category: Biochemistry Authors: Pankov, G. Dawson, A. Hunter, W.N. Tags: ABC transporters ATPases lipopolysaccharide transport complex protein – protein interactions research communications Source Type: research

The structure of an iron-containing alcohol dehydrogenase from a hyperthermophilic archaeon in two chemical states
An iron-containing alcohol dehydrogenase (FeADH) from the hyperthermophilic archaeon Thermococcus thioreducens was crystallized in unit cells belonging to space groups P21, P212121 and P43212, 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. In the mo...
Source: Acta Crystallographica Section F - March 13, 2019 Category: Biochemistry Authors: Larson, S.B. Jones, J.A. McPherson, A. Tags: NADP oxidation – reduction thermophile active site dimers alcohol dehydrogenase Thermococcus thioreducens research communications Source Type: research

Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase
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 isop...
Source: Acta Crystallographica Section F - March 13, 2019 Category: Biochemistry Authors: Ko, T.-P. Xiao, X. Guo, R.-T. Huang, J.-W. Liu, W. Chen, C.-C. Tags: Rv2361c cis-prenyltransferase catalytic mechanism thiodiphosphate inhibitor cell-wall biosynthesis Mycobacterium tuberculosis decaprenyl diphosphate synthase research communications Source Type: research

Welcoming Janet Newman with a BLAST on crystallization strategy
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 1, 2019 Category: Biochemistry Authors: van Raaij, M.J. Tags: editorial crystallization Source Type: research

The structure of CgnJ, a domain of unknown function protein from the crocagin gene cluster
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. Here, the first crystal structure of a protein from the crocagin-biosynthetic ...
Source: Acta Crystallographica Section F - February 21, 2019 Category: Biochemistry Authors: Adam, S. Klein, A. Surup, F. Koehnke, J. Tags: crocagin RiPPs CgnJ domains of unknown function research communications Source Type: research

Crystal structure of the legume lectin-like domain of an ERGIC-53-like protein from Entamoeba histolytica
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 ...
Source: Acta Crystallographica Section F - February 21, 2019 Category: Biochemistry Authors: Khan, F. Suguna, K. Tags: ERGIC-53-like proteins legume lectin-like domains Entamoeba histolytica membrane proteins intracellular cargo receptors research communications Source Type: research

Neutron crystallographic study of heterotrimeric glutamine amidotransferase CAB
This study represented a challenge in current neutron diffraction technology. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 21, 2019 Category: Biochemistry Authors: Li, L. Adachi, M. Yu, J. Kato, K. Shinoda, A. Ostermann, A. Schrader, T.E. Ose, T. Yao, M. Tags: glutamine amidotransferase CAB GatCAB ammonia-self-sufficient mechanism ammonia channel neutron diffraction research communications Source Type: research

BLASTing away preconceptions in crystallization trials
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. This research investigates whether, given current information, one can detect any co...
Source: Acta Crystallographica Section F - February 21, 2019 Category: Biochemistry Authors: Abrahams, G.J. Newman, J. Tags: PDB Protein Data Bank REMARK 280 crystallization sequences BLAST research communications Source Type: research

Structure of glycerol dehydrogenase (GldA) from Escherichia coli
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 = 65.6 ° C). Sitting-drop sparse-matrix screens were used for protein crystalli...
Source: Acta Crystallographica Section F - February 21, 2019 Category: Biochemistry Authors: Zhang, J. Nanjaraj Urs, A.N. Lin, L. Zhou, Y. Hu, Y. Hua, G. Gao, Q. Yuchi, Z. Zhang, Y. Tags: glycerol dehydrogenase thermal stability crystal structure glycerol metabolism research communications Source Type: research

Neutron and X-ray analysis of the Fenna – Matthews – Olson photosynthetic antenna complex from Prosthecochloris aestuarii
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 ...
Source: Acta Crystallographica Section F - February 20, 2019 Category: Biochemistry Authors: Lu, X. Selvaraj, B. Ghimire-Rijal, S. Orf, G.S. Meilleur, F. Blankenship, R.E. Cuneo, M.J. Myles, D.A.A. Tags: neutron crystallography photosynthesis hydrogen site energy neutron diffraction Fenna – Matthews Olson protein Prosthecochloris aestuarii research communications Source Type: research

Carbonic anhydrase II in complex with carboxylic acid-based inhibitors
This study examines an important class of alternative, non-sulfonamide-based CA inhibitors and provides insight to facilitate the structure-guided design of CA isoform-specific inhibitors. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 20, 2019 Category: Biochemistry Authors: Lomelino, C.L. McKenna, R. Tags: carbonic anhydrase II carboxylic acids structure-guided drug design research communications Source Type: research

Preparation of stable recombinant Osm1 noncovalently bound with flavin adenosine dinucleotide cofactor for structural study
In this study, monomeric and stable recombinant Osm1 was successfully prepared for structural study. During purification, it was realized that the majority of recombinant Osm1 expressed in Escherichia coli lacked the flavin adenosine dinucleotide (FAD) cofactor. However, exogenously introduced FAD could be incorporated into recombinant Osm1, generating stable and homogenous holo Osm1. Moreover, after removing a flexible fragment by limited proteolysis, holo Osm1 formed isotropic crystals that retained catalytic activity. X-ray diffraction data were successfully collected from the Osm1 crystals to a resolution of 1.75   &...
Source: Acta Crystallographica Section F - February 20, 2019 Category: Biochemistry Authors: Kim, S.H. Park, H.H. Tags: soluble fumarate reductase anaerobiosis Osm1 limited proteolysis stabilization crystallization research communications Source Type: research

Crystal structure of the type VI immunity protein Tdi1 (Atu4351) from Agrobacterium tumefaciens
The type VI secretion system (T6SS) is a novel multiprotein needle-like apparatus that is distributed widely in Gram-negative bacteria. Bacteria harboring T6SSs inject various effectors into both eukaryotic and prokaryotic cells for interspecies competition or virulence-related processes. The toxicities of the effectors can be neutralized by their cognate immunity proteins. Tde1 (Atu4350) – Tdi1 (Atu4351) has recently been characterized as a T6SS effector – immunity pair in the soil bacterium Agrobacterium tumefaciens and the neutralization mechanism remains unknown. Here, the crystal structure of the immunity ...
Source: Acta Crystallographica Section F - February 20, 2019 Category: Biochemistry Authors: Shi, L. Gao, Z. Zhang, T. Zhang, H. Dong, Y. Tags: type VI secretion system effector – immunity pair Tdi1 GAD-like domain DUF1851 domain bacterial nanomachines research communications Source Type: research