X-ray structure of cyanide-bound bovine heart cytochrome c oxidase in the fully oxidized state at 2.0 Å resolution
The X-ray structure of cyanide-bound bovine heart cytochrome c oxidase in the fully oxidized state was determined at 2.0 Å resolution. The structure reveals that the peroxide that bridges the two metals in the fully oxidized state is replaced by a cyanide ion bound in a nearly symmetric end-on fashion without significantly changing the protein conformation outside the two metal sites. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - May 22, 2015 Category: Biochemistry Authors: Yano, N.Muramoto, K.Mochizuki, M.Shinzawa-Itoh, K.Yamashita, E.Yoshikawa, S.Tsukihara, T. Tags: membrane protein cytochrome c oxidase research communications Source Type: research

Structure of Chlamydomonas reinhardtii THB1, a group 1 truncated hemoglobin with a rare histidine–lysine heme ligation
THB1 is one of several group 1 truncated hemoglobins (TrHb1s) encoded in the genome of the unicellular green alga Chlamydomonas reinhardtii. THB1 expression is under the control of NIT2, the master regulator of nitrate assimilation, which also controls the expression of the only nitrate reductase in the cell, NIT1. In vitro and physiological evidence suggests that THB1 converts the nitric oxide generated by NIT1 into nitrate. To aid in the elucidation of the function and mechanism of THB1, the structure of the protein was solved in the ferric state. THB1 resembles other TrHb1s, but also exhibits distinct features associate...
Source: Acta Crystallographica Section F - May 20, 2015 Category: Biochemistry Authors: Rice, S.L.Boucher, L.E.Schlessman, J.L.Preimesberger, M.R.Bosch, J.Lecomte, J.T.J. Tags: 2/2 hemoglobin distal ligand nitric oxide dioxygenase nitrogen metabolism lysine coordination research communications Source Type: research

Crystallization of interleukin-18 for structure-based inhibitor design
In this study, surface-entropy reduction (SER) and rational protein design were employed to facilitate the crystallization of hIL-18. The results provide an excellent platform for structure-based drug design. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - May 20, 2015 Category: Biochemistry Authors: Krumm, B.Meng, X.Xiang, Y.Deng, J. Tags: cytokines interleukin-18 immune defense surface-entropy reduction research communications Source Type: research

The structure of a contact-dependent growth-inhibition (CDI) immunity protein from Neisseria meningitidis MC58
Contact-dependent growth inhibition (CDI) is an important mechanism of intercellular competition between neighboring Gram-negative bacteria. CDI systems encode large surface-exposed CdiA effector proteins that carry a variety of C-terminal toxin domains (CdiA-CTs). All CDI+ bacteria also produce CdiI immunity proteins that specifically bind to the cognate CdiA-CT and neutralize its toxin activity to prevent auto-inhibition. Here, the X-ray crystal structure of a CdiI immunity protein from Neisseria meningitidis MC58 is presented at 1.45 Å resolution. The CdiI protein has structural homology to the Whirly family of ...
Source: Acta Crystallographica Section F - May 20, 2015 Category: Biochemistry Authors: Tan, K.Johnson, P.M.Stols, L.Boubion, B.Eschenfeldt, W.Babnigg, G.Hayes, C.S.Joachimiak, A.Goulding, C.W. Tags: contact-dependent growth inhibition CdiA-CT toxin domain CdiI immunity protein – immunity protein complex Neisseria meningitidis docking studies research communications Source Type: research

Expression, crystallization and X-ray diffraction analysis of a complex between B7-H6, a tumor cell ligand for the natural cytotoxicity receptor NKp30, and an inhibitory antibody
Natural killer (NK) cells are essential components of the innate immune response to tumors and viral infections. In humans, the activating natural cytotoxicity receptor NKp30 plays a major role in NK cell-mediated tumor cell lysis. NKp30 recognizes the cell-surface protein B7-H6, which is expressed on tumor, but not healthy, cells. A mouse monoclonal antibody (17B1.3) against human B7-H6 has been developed (Kd = 0.2 µM) to investigate NKp30-mediated NK cell activation and to target tumors expressing B7-H6. Surprisingly, 17B1.3 blocks NK cell activation without interfering with the binding of B7-H6 to NKp30. Underst...
Source: Acta Crystallographica Section F - May 20, 2015 Category: Biochemistry Authors: Xu, X.Li, Y.Gauthier, L.Chen, Q.Vivier, E.Mariuzza, R.A. Tags: NK cell NKp30 B7-H6 antibody research communications Source Type: research

Functional characterization of heat-shock protein 90 from Oryza sativa and crystal structure of its N-terminal domain
In this study, biochemical characterization of an Hsp90 protein from rice (Oryza sativa; OsHsp90) has been performed and the crystal structure of its N-terminal domain (OsHsp90-NTD) was determined. The binding of OsHsp90 to its substrate ATP and the inhibitor 17-AAG was studied by fluorescence spectroscopy. The protein also exhibited a weak ATPase activity. The crystal structure of OsHsp90-NTD was solved in complex with the nonhydrolyzable ATP analogue AMPPCP at 3.1 Å resolution. The domain was crystallized by cross-seeding with crystals of the N-terminal domain of Hsp90 from Dictyostelium discoideum, which shares ...
Source: Acta Crystallographica Section F - May 20, 2015 Category: Biochemistry Authors: Raman, S.Suguna, K. Tags: Hsp90 Oryza sativa 17-AAG ATPase activity cross-seeding research communications Source Type: research

High-resolution crystal structure of the leucine-rich repeat domain of the human tumour suppressor PP32A (ANP32A)
Acidic leucine-rich nuclear phosphoprotein 32A (PP32A) is a tumour suppressor whose expression is altered in many cancers. It is an apoptotic enhancer that stimulates apoptosome-mediated caspase activation and also forms part of a complex involved in caspase-independent apoptosis (the SET complex). Crystals of a fragment of human PP32A corresponding to the leucine-rich repeat domain, a widespread motif suitable for protein–protein interactions, have been obtained. The structure has been refined to 1.56 Å resolution. This domain was previously solved at 2.4 and 2.69 Å resolution (PDB entries 2je0 and 2...
Source: Acta Crystallographica Section F - May 20, 2015 Category: Biochemistry Authors: Zamora-Caballero, S.Šiaučiunaite-Gaubard, L.Bravo, J. Tags: PP32A LRR domain structure tumour suppressor SET complex research communications Source Type: research

Expression, purification and crystallization of a family 55 β-1,3-glucanase from Chaetomium thermophilum
A β-1,3-glucanase from the thermophilic fungus Chaetomium thermophilum was overexpressed in Pichia pastoris, purified and crystallized in the presence of 1.8 M sodium/potassium phosphate pH 6.8 as a precipitant. Data to 2.0 Å resolution were collected in-house at 293 K from a single crystal. The crystal was found to belong to space group P21, with unit-cell parameters a = 64.1, b = 85.8, c = 68.5 Å, β = 93.1° and one molecule in the asymmetric unit. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - May 20, 2015 Category: Biochemistry Authors: Papageorgiou, A.C.Li, D. Tags: cellulose glucanase in situ diffraction seeding thermophilic fungus research communications Source Type: research

Purification, crystallization and preliminary X-ray diffraction analysis of the Escherichia coli common pilus chaperone EcpB
Pili are key cell-surface components that allow the attachment of bacteria to both biological and abiotic solid surfaces, whilst also mediating interactions between themselves. In Escherichia coli, the common pilus (Ecp) belongs to an alternative chaperone–usher (CU) pathway that plays a major role in both early biofilm formation and host-cell adhesion. The chaperone EcpB is involved in the biogenesis of the filament, which is composed of EcpA and EcpD. Initial attempts at crystallizing EcpB using natively purified protein from the bacterial periplasm were not successful; however, after the isolation of EcpB under de...
Source: Acta Crystallographica Section F - May 20, 2015 Category: Biochemistry Authors: Garnett, J.A.Diallo, M.Matthews, S.J. Tags: pili Ecp Escherichia coli research communications Source Type: research

Overexpression, purification, crystallization and preliminary X-ray diffraction of the nisin resistance protein from Streptococcus agalactiae
Nisin is a 34-amino-acid antimicrobial peptide produced by Lactococcus lactis belonging to the class of lantibiotics. Nisin displays a high bactericidal activity against various Gram-positive bacteria, including some human-pathogenic strains. However, there are some nisin-non-producing strains that are naturally resistant owing to the presence of the nsr gene within their genome. The encoded protein, NSR, cleaves off the last six amino acids of nisin, thereby reducing its bactericidal efficacy. An expression and purification protocol has been established for the NSR protein from Streptococcus agalactiae COH1. The protein w...
Source: Acta Crystallographica Section F - May 20, 2015 Category: Biochemistry Authors: Khosa, S.Hoeppner, A.Kleinschrodt, D.Smits, S.H.J. Tags: lantibiotic nisin resistance immunity lipoprotein Lactococcus lactis research communications Source Type: research

Crystallographic study of a novel DNA-binding domain of human HLTF involved in the template-switching pathway to avoid the replication arrest caused by DNA damage
In this study, the HIRAN domain of human HLTF was successfully crystallized. The crystals belonged to space group P41212 or P43212, with unit-cell parameters a = b = 130.0, c = 150.1 Å. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - May 20, 2015 Category: Biochemistry Authors: Ikegaya, Y.Hara, K.Hishiki, A.Yokoyama, H.Hashimoto, H. Tags: HIRAN domain HLTF template switching DNA-binding domain research communications Source Type: research

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of CofB, the minor pilin subunit of CFA/III from human enterotoxigenic Escherichia coli
In this study, constructs of wild-type CofB with an N-terminal truncation and the corresponding SeMet derivative were cloned, expressed, purified and crystallized. The crystals belonged to the rhombohedral space group R32, with unit-cell parameters a = b = 103.97, c = 364.57 Å for the wild-type construct and a = b = 103.47, c = 362.08 Å for the SeMet-derivatized form. Although the diffraction quality of these crystals was initially very poor, dehydration of the crystals substantially improved the resolution limit from ∼4.0 to ∼2.0 Å. The initial phase was solved by the single-wavelength anom...
Source: Acta Crystallographica Section F - May 20, 2015 Category: Biochemistry Authors: Kawahara, K.Oki, H.Fukakusa, S.Maruno, T.Kobayashi, Y.Motooka, D.Taniguchi, T.Honda, T.Iida, T.Nakamura, S.Ohkubo, T. Tags: ETEC type IVb pili minor pilin CFA/III CofB research communications Source Type: research

Multiple crystal forms of N,N′-diacetylchitobiose deacetylase from Pyrococcus furiosus
Native N,N′-diacetylchitobiose deacetylase from Pyrococcus furiosus (Pf-Dac) and its selenomethionine derivative (Se-Pf-Dac) were crystallized and analyzed in the presence and absence of cadmium ion. The four crystal structures fell into three different crystal-packing groups, with the cadmium-free Pf-Dac and Se-Pf-Dac belonging to the same space group, with homologous unit-cell parameters. The crystal structures in the presence of cadmium contained distorted octahedral cadmium complexes coordinated by three chlorides, two O atoms and an S or Se atom from the N-terminal methionine or selenomethionine, respectively. T...
Source: Acta Crystallographica Section F - May 20, 2015 Category: Biochemistry Authors: Nakamura, T.Niiyama, M.Hashimoto, W.Ida, K.Abe, M.Morita, J.Uegaki, K. Tags: N,N ′ -diacetylchitobiose deacetylase crystal-packing interaction selenomethionine cadmium complex research communications Source Type: research

Structure of human dual-specificity phosphatase 7, a potential cancer drug target
Human dual-specificity phosphatase 7 (DUSP7/Pyst2) is a 320-residue protein that belongs to the mitogen-activated protein kinase phosphatase (MKP) subfamily of dual-specificity phosphatases. Although its precise biological function is still not fully understood, previous reports have demonstrated that DUSP7 is overexpressed in myeloid leukemia and other malignancies. Therefore, there is interest in developing DUSP7 inhibitors as potential therapeutic agents, especially for cancer. Here, the purification, crystallization and structure determination of the catalytic domain of DUSP7 (Ser141–Ser289/C232S) at 1.67 &Arin...
Source: Acta Crystallographica Section F - May 20, 2015 Category: Biochemistry Authors: Lountos, G.T.Austin, B.P.Tropea, J.E.Waugh, D.S. Tags: dual-specificity phosphatase DUSP DUSP7 MAP kinase phosphatase PTP research communications Source Type: research

The structure of hookworm platelet inhibitor (HPI), a CAP superfamily member from Ancylostoma caninum
Secreted protein components of hookworm species include a number of representatives of the cysteine-rich/antigen 5/pathogenesis-related 1 (CAP) protein family known as Ancylostoma-secreted proteins (ASPs). Some of these have been considered as candidate antigens for the development of vaccines against hookworms. The functions of most CAP superfamily members are poorly understood, but one form, the hookworm platelet inhibitor (HPI), has been isolated as a putative antagonist of the platelet integrins αIIbβ3 and α2β1. Here, the crystal structure of HPI is described and its structural features are examin...
Source: Acta Crystallographica Section F - May 20, 2015 Category: Biochemistry Authors: Ma, D.Francischetti, I.M.B.Ribeiro, J.M.C.Andersen, J.F. Tags: antigen V hemostasis parasitism research communications Source Type: research

Iron superoxide dismutases in eukaryotic pathogens: new insights from Apicomplexa and Trypanosoma structures
This report presents the structures of three iron-dependent superoxide dismutases (FeSODs) from Trypanosoma cruzi, Leishmania major and Babesia bovis. Comparison with existing structures from Plasmodium and other trypanosome isoforms shows a very conserved overall fold with subtle differences. In particular, structural data suggest that B. bovis FeSOD may display similar resistance to peroxynitrite-mediated inactivation via an intramolecular electron-transfer pathway as previously described in T. cruzi FeSOD isoform B, thus providing valuable information for structure-based drug design. Furthermore, lysine-acetylation resu...
Source: Acta Crystallographica Section F - May 7, 2015 Category: Biochemistry Authors: Phan, I.Q.H.Davies, D.R.Moretti, N.S.Shanmugam, D.Cestari, I.Anupama, A.Fairman, J.W.Edwards, T.E.Stuart, K.Schenkman, S.Myler, P.J. Tags: iron superoxide dismutase Trypanosoma Apicomplexa research communications Source Type: research

Macromolecular crystallography and what it can contribute to antiparasite drug discovery
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 24, 2015 Category: Biochemistry Authors: Hunter, W.N.Weiss, M.S. Tags: molecular parasitology special issues editorial Source Type: research

Structures of prostaglandin F synthase from the protozoa Leishmania major and Trypanosoma cruzi with NADP
The crystal structures of prostaglandin F synthase (PGF) from both Leishmania major and Trypanosoma cruzi with and without their cofactor NADP have been determined to resolutions of 2.6 Å for T. cruzi PGF, 1.25 Å for T. cruzi PGF with NADP, 1.6 Å for L. major PGF and 1.8 Å for L. major PGF with NADP. These structures were determined by molecular replacement to a final R factor of less than 18.6% (Rfree of less than 22.9%). PGF in the infectious protozoa L. major and T. cruzi is a potential therapeutic target. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 21, 2015 Category: Biochemistry Authors: Moen, S.O.Fairman, J.W.Barnes, S.R.Sullivan, A.Nakazawa-Hewitt, S.Van Voorhis, W.C.Staker, B.L.Lorimer, D.D.Myler, P.J.Edwards, T.E. Tags: prostaglandin infectious diseases leishmaniasis Chagas disease SSGCID research communications Source Type: research

Structure of Plasmodium falciparum orotate phosphoribosyltransferase with autologous inhibitory protein–protein interactions
The most severe form of malaria is caused by the obligate parasite Plasmodium falciparum. Orotate phosphoribosyltransferase (OPRTase) is the fifth enzyme in the de novo pyrimidine-synthesis pathway in the parasite, which lacks salvage pathways. Among all of the malaria de novo pyrimidine-biosynthesis enzymes, the structure of P. falciparum OPRTase (PfOPRTase) was the only one unavailable until now. PfOPRTase that could be crystallized was obtained after some low-complexity sequences were removed. Four catalytic dimers were seen in the asymmetic unit (a total of eight polypeptides). In addition to revealing unique amino aci...
Source: Acta Crystallographica Section F - April 21, 2015 Category: Biochemistry Authors: Kumar, S.Krishnamoorthy, K.Mudeppa, D.G.Rathod, P.K. Tags: pyrimidine de novo salvage PRPP OMP prodrugs peptide inhibition research communications Source Type: research

Structure of an ADP-ribosylation factor, ARF1, from Entamoeba histolytica bound to Mg2+–GDP
Entamoeba histolytica is the etiological agent of amebiasis, a diarrheal disease which causes amoebic liver abscesses and amoebic colitis. Approximately 50 million people are infected worldwide with E. histolytica. With only 10% of infected people developing symptomatic amebiasis, there are still an estimated 100 000 deaths each year. Because of the emergence of resistant strains of the parasite, it is necessary to find a treatment which would be a proper response to this challenge. ADP-ribosylation factor (ARF) is a member of the ARF family of GTP-binding proteins. These proteins are ubiquitous in eukaryotic cells; they...
Source: Acta Crystallographica Section F - April 21, 2015 Category: Biochemistry Authors: Serbzhinskiy, D.A.Clifton, M.C.Sankaran, B.Staker, B.L.Edwards, T.E.Myler, P.J. Tags: GDP-ribosylation factor small GTPase ARFA1 structural genomics Seattle Structural Genomics Center for Infectious Disease SSGCID signaling protein research communications Source Type: research

Identification and structure solution of fragment hits against kinetoplastid N-myristoyltransferase
Trypanosoma brucei N-myristoyltransferase (TbNMT) is an attractive therapeutic target for the treatment of human African trypanosomiasis. Pyrazole sulfonamide (DDD85646), a potent inhibitor of TbNMT, has been identified in previous studies; however, poor central nervous system exposure restricts its use to the haemolymphatic form (stage 1) of the disease. In order to identify new chemical matter, a fragment screen was carried out by ligand-observed NMR spectroscopy, identifying hits that occupy the DDD85646 binding site. Crystal structures of hits from this assay have been obtained in complex with the closely related NMT f...
Source: Acta Crystallographica Section F - April 21, 2015 Category: Biochemistry Authors: Robinson, D.A.Wyatt, P.G. Tags: N-myristoyltransferase Trypanosoma brucei African trypanosomiasis research communications Source Type: research

Production, purification and crystallization of a trans-sialidase from Trypanosoma vivax
Sialidases and trans-sialidases play important roles in the life cycles of various microorganisms. These enzymes can serve nutritional purposes, act as virulence factors or mediate cellular interactions (cell evasion and invasion). In the case of the protozoan parasite Trypanosoma vivax, trans-sialidase activity has been suggested to be involved in infection-associated anaemia, which is the major pathology in the disease nagana. The physiological role of trypanosomal trans-sialidases in host–parasite interaction as well as their structures remain obscure. Here, the production, purification and crystallization of a re...
Source: Acta Crystallographica Section F - April 21, 2015 Category: Biochemistry Authors: Haynes, C.L.F.Ameloot, P.Remaut, H.Callewaert, N.Sterckx, Y.G.-J.Magez, S. Tags: trans-sialidase Trypanosoma vivax research communications Source Type: research

Structures of a histidine triad family protein from Entamoeba histolytica bound to sulfate, AMP and GMP
Three structures of the histidine triad family protein from Entamoeba histolytica, the causative agent of amoebic dysentery, were solved at high resolution within the Seattle Structural Genomics Center for Infectious Disease (SSGCID). The structures have sulfate (PDB entry 3oj7), AMP (PDB entry 3omf) or GMP (PDB entry 3oxk) bound in the active site, with sulfate occupying the same space as the α-phosphate of the two nucleotides. The Cα backbones of the three structures are nearly superimposable, with pairwise r.m.s.d.s ranging from 0.06 to 0.13 Å. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 21, 2015 Category: Biochemistry Authors: Lorimer, D.D.Choi, R.Abramov, A.Nakazawa Hewitt, S.Gardberg, A.S.Van Voorhis, W.C.Staker, B.L.Myler, P.J.Edwards, T.E. Tags: hydrolase structural genomics Seattle Structural Genomics Center for Infectious Disease SSGCID metal-binding protein research communications Source Type: research

Structures of aspartate aminotransferases from Trypanosoma brucei, Leishmania major and Giardia lamblia
The structures of three aspartate aminotransferases (AATs) from eukaryotic pathogens were solved within the Seattle Structural Genomics Center for Infectious Disease (SSGCID). Both the open and closed conformations of AAT were observed. Pyridoxal phosphate was bound to the active site via a Schiff base to a conserved lysine. An active-site mutant showed that Trypanosoma brucei AAT still binds pyridoxal phosphate even in the absence of the tethering lysine. The structures highlight the challenges for the structure-based design of inhibitors targeting the active site, while showing options for inhibitor design targeting the ...
Source: Acta Crystallographica Section F - April 21, 2015 Category: Biochemistry Authors: Abendroth, J.Choi, R.Wall, A.Clifton, M.C.Lukacs, C.M.Staker, B.L.Van Voorhis, W.Myler, P.Lorimer, D.D.Edwards, T.E. Tags: aspartate aminotransferase structural genomics Seattle Structural Genomics Center for Infectious Disease pyridoxalphosphate lysine Giardia lamblia Trypanosoma brucei Leishmania major research communications Source Type: research

Structure of uridine diphosphate N-acetylglucosamine pyrophosphorylase from Entamoeba histolytica
Uridine diphosphate N-acetylglucosamine pyrophosphorylase (UAP) catalyzes the final step in the synthesis of UDP-GlcNAc, which is involved in cell-wall biogenesis in plants and fungi and in protein glycosylation. Small-molecule inhibitors have been developed against UAP from Trypanosoma brucei that target an allosteric pocket to provide selectivity over the human enzyme. A 1.8 Å resolution crystal structure was determined of UAP from Entamoeba histolytica, an anaerobic parasitic protozoan that causes amoebic dysentery. Although E. histolytica UAP exhibits the same three-domain global architecture as other UAPs, it ...
Source: Acta Crystallographica Section F - April 21, 2015 Category: Biochemistry Authors: Edwards, T.E.Gardberg, A.S.Phan, I.Q.H.Zhang, Y.Staker, B.L.Myler, P.J.Lorimer, D.D. Tags: SSGCID Entamoeba histolytica amoebic dysentery parasitic protozoan allosteric regulation cell-wall biogenesis GlcNAc research communications Source Type: research

The X-ray structure of Plasmodium falciparum dihydroorotate dehydrogenase bound to a potent and selective N-phenylbenzamide inhibitor reveals novel binding-site interactions
Plasmodium species are protozoan parasites that are the causative agent of malaria. Malaria is a devastating disease, and its treatment and control have been hampered by the propensity of the parasite to become drug-resistant. Dihydroorotate dehydrogenase (DHODH) has been identified as a promising new target for the development of antimalarial agents. Here, the X-ray structure of P. falciparum DHODH bound to a potent and selective N-phenylbenzamide-based inhibitor (DSM59) is described at 2.3 Å resolution. The structure elucidates novel binding-site interactions and shows how conformational flexibility of the enzyme...
Source: Acta Crystallographica Section F - April 21, 2015 Category: Biochemistry Authors: Deng, X.Matthews, D.Rathod, P.K.Phillips, M.A. Tags: dihydroorotate dehydrogenase Plasmodium falciparum DSM59 research communications Source Type: research

Recombinant production, crystallization and crystal structure determination of dihydroorotate dehydrogenase from Leishmania (Viannia) braziliensis
In this study, a reproducible protocol for the heterologous expression of active dihydroorotate dehydrogenase from Leishmania (Viannia) braziliensis (LbDHODH) was developed and its crystal structure was determined at 2.12 Å resolution. L. (V.) braziliensis is the species responsible for the mucosal form of leishmaniasis, a neglected disease for which no cure or effective therapy is available. Analyses of sequence, structural and kinetic features classify LbDHODH as a member of the class 1A DHODHs and reveal a very high degree of structural conservation with the previously reported structures of orthologous trypanos...
Source: Acta Crystallographica Section F - April 21, 2015 Category: Biochemistry Authors: Reis, R.A.G.Lorenzato, E.Silva, V.C.Nonato, M.C. Tags: dihydroorotate dehydrogenase Leishmania (Viannia) braziliensis leishmaniasis research communications Source Type: research

The structure of tubulin-binding cofactor A from Leishmania major infers a mode of association during the early stages of microtubule assembly
This study provides a reagent and template to support further work in this area. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 21, 2015 Category: Biochemistry Authors: Barrack, K.L.Fyfe, P.K.Hunter, W.N. Tags: chaperone helical fold protein – protein interactions selenomethionine tubulin-binding protein research communications Source Type: research

Structure of Cryptosporidium IMP dehydrogenase bound to an inhibitor with in vivo antiparasitic activity
Inosine 5′-monophosphate dehydrogenase (IMPDH) is a promising target for the treatment of Cryptosporidium infections. Here, the structure of C. parvum IMPDH (CpIMPDH) in complex with inosine 5′-monophosphate (IMP) and P131, an inhibitor with in vivo anticryptosporidial activity, is reported. P131 contains two aromatic groups, one of which interacts with the hypoxanthine ring of IMP, while the second interacts with the aromatic ring of a tyrosine in the adjacent subunit. In addition, the amine and NO2 moieties bind in hydrated cavities, forming water-mediated hydrogen bonds to the protein. The design of compound...
Source: Acta Crystallographica Section F - April 21, 2015 Category: Biochemistry Authors: Kim, Y.Makowska-Grzyska, M.Gorla, S.K.Gollapalli, D.R.Cuny, G.D.Joachimiak, A.Hedstrom, L. Tags: Cryptosporidium inosine 5 ′ -monophosphate dehydrogenase P131 research communications Source Type: research

Structure of a CutA1 divalent-cation tolerance protein from Cryptosporidium parvum, the protozoal parasite responsible for cryptosporidiosis
Cryptosporidiosis is an infectious disease caused by protozoan parasites of the Cryptosporidium genus. Infection is associated with mild to severe diarrhea that usually resolves spontaneously in healthy human adults, but may lead to severe complications in young children and in immunocompromised patients. The genome of C. parvum contains a gene, CUTA_CRYPI, that may play a role in regulating the intracellular concentration of copper, which is a toxic element in excess. Here, the crystal structure of this CutA1 protein, Cp-CutA1, is reported at 2.0 Å resolution. As observed for other CutA1 structures, the 117-residu...
Source: Acta Crystallographica Section F - April 18, 2015 Category: Biochemistry Authors: Buchko, G.W.Abendroth, J.Clifton, M.C.Robinson, H.Zhang, Y.Hewitt, S.N.Staker, B.L.Edwards, T.E.Van Voorhis, W.C.Myler, P.J. Tags: Cryptosporidium parvum divalent-cation tolerance protein CutA1 cryptosporidiosis research communications Source Type: research

Solution-state NMR structure of the putative morphogene protein BolA (PFE0790c) from Plasmodium falciparum
Protozoa of the genus Plasmodium are responsible for malaria, which is perhaps the most important parasitic disease to infect mankind. The emergence of Plasmodium strains resistant to current therapeutics and prophylactics makes the development of new treatment strategies urgent. Among the potential targets for new antimalarial drugs is the BolA-like protein PFE0790c from Plasmodium falciparum (Pf-BolA). While the function of BolA is unknown, it has been linked to cell morphology by regulating transcription in response to stress. Using an NMR-based method, an ensemble of 20 structures of Pf-BolA was determined and deposite...
Source: Acta Crystallographica Section F - April 18, 2015 Category: Biochemistry Authors: Buchko, G.W.Yee, A.Semesi, A.Myler, P.J.Arrowsmith, C.H.Hui, R. Tags: Plasmodium falciparum BolA PFE0790c research communications Source Type: research

Towards a molecular understanding of the apicomplexan actin motor: on a road to novel targets for malaria remedies?
Apicomplexan parasites are the causative agents of notorious human and animal diseases that give rise to considerable human suffering and economic losses worldwide. The most prominent parasites of this phylum are the malaria-causing Plasmodium species, which are widespread in tropical and subtropical regions, and Toxoplasma gondii, which infects one third of the world's population. These parasites share a common form of gliding motility which relies on an actin–myosin motor. The components of this motor and the actin-regulatory proteins in Apicomplexa have unique features compared with all other eukaryotes. This, tog...
Source: Acta Crystallographica Section F - April 16, 2015 Category: Biochemistry Authors: Kumpula, E.-P.Kursula, I. Tags: malaria actin polymerization cytoskeleton regulation gliding motility drug design parasitology research communications Source Type: research

Three-dimensional structures in the design of therapeutics targeting parasitic protozoa: reflections on the past, present and future
Parasitic protozoa cause a range of diseases which threaten billions of human beings. They are responsible for tremendous mortality and morbidity in the least-developed areas of the world. Presented here is an overview of the evolution over the last three to four decades of structure-guided design of inhibitors, leads and drug candidates aiming at targets from parasitic protozoa. Target selection is a crucial and multi-faceted aspect of structure-guided drug design. The major impact of advances in molecular biology, genome sequencing and high-throughput screening is touched upon. The most advanced crystallographic techniqu...
Source: Acta Crystallographica Section F - April 16, 2015 Category: Biochemistry Authors: Hol, W.G.J. Tags: parasitic protozoa antiparasitic drug discovery research communications Source Type: research

Large-volume protein crystal growth for neutron macromolecular crystallography
Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large c...
Source: Acta Crystallographica Section F - March 30, 2015 Category: Biochemistry Authors: Ng, J.D.Baird, J.K.Coates, L.Garcia-Ruiz, J.M.Hodge, T.A.Huang, S. Tags: large-volume crystals neutron macromolecular crystallography research communications Source Type: research

Expression, purification, crystallization and preliminary X-ray diffraction analysis of a type II NADH:quinone oxidoreductase from the human pathogen Staphylococcus aureus
In recent years, type II NADH dehydrogenases (NDH-IIs) have emerged as potential drug targets for a wide range of human disease causative agents. In this work, the NDH-II enzyme from the Gram-positive human pathogen Staphylococcus aureus was recombinantly expressed in Escherichia coli, purified, crystallized and a crystallographic data set was collected at a wavelength of 0.873 Å. The crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 81.8, b = 86.0, c = 269.9 Å, contained four monomers per asymmetric unit and diffracted to a resolution of 3.32 Å. A molecular-re...
Source: Acta Crystallographica Section F - March 27, 2015 Category: Biochemistry Authors: Rosário, A.L.Sena, F.V.Batista, A.P.Oliveira, T.F.Athayde, D.Pereira, M.M.Brito, J.A.Archer, M. Tags: NDH-II NADH dehydrogenase respiratory chain Staphylococcus aureus research communications Source Type: research

Serendipitous crystallization and structure determination of cyanase (CynS) from Serratia proteamaculans
Cyanate hydratase (CynS) catalyzes the decomposition of cyanate and bicarbonate into ammonia and carbon dioxide. Here, the serendipitous crystallization of CynS from Serratia proteamaculans (SpCynS) is reported. SpCynS was crystallized as an impurity and its identity was determined using mass-spectrometric analysis. The crystals belonged to space group P1 and diffracted to 2.1 Å resolution. The overall structure of SpCynS is very similar to a previously determined structure of CynS from Escherichia coli. Density for a ligand bound to the SpCynS active site was observed, but could not be unambiguously identified. Ad...
Source: Acta Crystallographica Section F - March 21, 2015 Category: Biochemistry Authors: Butryn, A.Stoehr, G.Linke-Winnebeck, C.Hopfner, K.-P. Tags: CynS cyanase cyanate hydratase research communications Source Type: research

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AerF from Microcystis aeruginosa, a putative reductase participating in aeruginosin biosynthesis
This study reports the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AerF from Microcystis aeruginosa with a C-terminal His6 tag. The crystal diffracted to a maximum resolution of 1.38 Å and belonged to the tetragonal space group P4322, with unit-cell parameters a = b = 101.581, c = 116.094 Å. The calculated Matthews coefficient and solvent content of the crystal were 2.47 Å3 Da−1 and 50.32%, respectively. The initial model of the structure was obtained by the molecular-replacement method and refinement of the structure is in progress. (Sour...
Source: Acta Crystallographica Section F - March 21, 2015 Category: Biochemistry Authors: Ding, R.Xu, C.Chen, X.Bao, M.Qiu, X. Tags: Microcystis aeruginosa aeruginosin 2-carboxy-6-hydroxyoctahydroindole moiety AerF research communications Source Type: research

Complex assembly, crystallization and preliminary X-ray crystallographic analysis of the human Rod – Zwilch – ZW10 (RZZ) complex
The spindle-assembly checkpoint (SAC) monitors kinetochore – microtubule attachment during mitosis. In metazoans, the three-subunit Rod – Zwilch – ZW10 (RZZ) complex is a crucial SAC component that interacts with additional SAC-activating and SAC-silencing components, including the Mad1 – Mad2 complex and cytoplasmic dynein. The RZZ complex contains two copies of each subunit and has a predicted molecular mass of ∼ 800   kDa. Given the low abundance of the RZZ complex in natural sources, its recombinant reconstitution was attempted by co-expression of its subunits in insect cells. The RZZ comp...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Altenfeld, A. Wohlgemuth, S. Wehenkel, A. Vetter, I.R. Musacchio, A. Tags: spindle-assembly checkpoint cell division mitosis RZZ complex Rod Zwilch ZW10 kinetochore Ndc80 Mis12 Knl1 KMN network research communications Source Type: research

Expression, purification, crystallization and preliminary crystallographic analysis of a GH20 β -N-acetylglucosaminidase from the marine bacterium Vibrio harveyi
In this study, the crystallization and preliminary crystallographic data of wild-type VhGlcNAcase and its catalytically inactive mutant D437A in the absence and the presence of substrate are reported. Crystals of wild-type VhGlcNAcase were grown in 0.1   M sodium acetate pH 4.6, 1.4   M sodium malonate, while crystals of the D437A mutant were obtained in 0.1   M bis-tris pH 7.5, 0.1   M sodium acetate, 20% PEG 3350. X-ray data from the wild-type and the mutant crystals were collected at a synchrotron-radiation light source and were complete to a resolution of 2.5   Å . All crystals were composed of the same...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Meekrathok, P. B ü rger, M. Porfetye, A.T. Vetter, I.R. Suginta, W. Tags: β -N-acetylglucosaminidase Vibrio harveyi GH20 glycoside hydrolase family research communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of an endo-1,4- β -d-glucanase from Aspergillus aculeatus F-50
Cellulose is the most abundant renewable biomass on earth, and its decomposition has proven to be very useful in a wide variety of industries. Endo-1,4- β -d-glucanase (EC 3.2.1.4; endoglucanase), which can catalyze the random hydrolysis of β -1,4-glycosidic bonds to cleave cellulose into smaller fragments, is a key cellulolytic enzyme. An endoglucanase isolated from Aspergillus aculeatus F-50 (FI-CMCase) that was classified into glycoside hydrolase family 12 has been found to be effectively expressed in the industrial strain Pichia pastoris. Here, recombinant FI-CMCase was crystallized. Crystals belonging to the...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Chen, Y. Huang, J.-W. Chen, C.-C. Lai, H.-L. Jin, J. Guo, R.-T. Tags: cellulase endoglucanase Aspergillus industrial enzyme research communications Source Type: research

Crystallization and preliminary X-ray analysis of four cysteine proteases from Ficus carica latex
The latex of the common fig (Ficus carica) contains a mixture of at least five cysteine proteases commonly known as ficins (EC 3.4.22.3). Four of these proteases were purified to homogeneity and crystals were obtained in a variety of conditions. The four ficin (iso)forms appear in ten different crystal forms. All diffracted to better than 2.10 Å resolution and for each form at least one crystal form diffracted to 1.60 Å resolution or higher. Ficin (iso)forms B and C share a common crystal form, suggesting close sequence and structural similarity. The latter diffracted to a resolution of 1.20 Å and b...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Haesaerts, S.Rodriguez Buitrago, J.A.Loris, R.Baeyens-Volant, D.Azarkan, M. Tags: ficin cysteine protease papain Ficus carica research communications Source Type: research

Analytical ultracentrifugation and preliminary X-ray studies of the chloroplast envelope quinone oxidoreductase homologue from Arabidopsis thaliana
Quinone oxidoreductases reduce a broad range of quinones and are widely distributed among living organisms. The chloroplast envelope quinone oxidoreductase homologue (ceQORH) from Arabidopsis thaliana binds NADPH, lacks a classical N-terminal and cleavable chloroplast transit peptide, and is transported through the chloroplast envelope membrane by an unknown alternative pathway without cleavage of its internal chloroplast targeting sequence. To unravel the fold of this targeting sequence and its substrate specificity, ceQORH from A. thaliana was overexpressed in Escherichia coli, purified and crystallized. Crystals of apo ...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Mas y mas, S.Giustini, C.Ferrer, J.-L.Rolland, N.Curien, G.Cobessi, D. Tags: chloroplast envelope quinone oxidoreductase homologue analytical ultracentrifugation research communications Source Type: research

Structure of dihydrodipicolinate synthase from the commensal bacterium Bacteroides thetaiotaomicron at 2.1 Å resolution
Dihydrodipicolinate synthase (DapA) catalyzes the first committed step of the diaminopimelate biosynthetic pathway of lysine. It has been shown to be an essential enzyme in many bacteria and has been the subject of research to generate novel antibiotics. However, this pathway is present in both pathogenic and commensal bacteria, and antibiotics targeting DapA may interfere with normal gut colonization. Bacteroides thetaiotaomicron is a Gram-negative commensal bacterium that makes up a large proportion of the normal microbiota of the human gut. The structure of DapA from B. thetaiotaomicron (BtDapA) has been determined. Thi...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Mank, N.Arnette, A.Klapper, V.Offermann, L.Chruszcz, M. Tags: dihydrodipicolinate synthase Bacteroides thetaiotaomicron research communications Source Type: research

Structure of the ABL2/ARG kinase in complex with dasatinib
ABL2/ARG (ABL-related gene) belongs to the ABL (Abelson tyrosine-protein kinase) family of tyrosine kinases. ARG plays important roles in cell morphogenesis, motility, growth and survival, and many of these biological roles overlap with the cellular functions of the ABL kinase. Chronic myeloid leukemia (CML) is associated with constitutive ABL kinase activation resulting from fusion between parts of the breakpoint cluster region (BCR) and ABL1 genes. Similarly, fusion of the ETV6 (Tel) and ARG genes drives some forms of T-cell acute lymphoblastic leukemia (T-ALL) and acute myeloid leukemia (AML). Dasatinib is a tyrosine ki...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Ha, B.H.Simpson, M.A.Koleske, A.J.Boggon, T.J. Tags: ABL2 ARG research communications Source Type: research

Complex assembly, crystallization and preliminary X-ray crystallographic analysis of the human Rod–Zwilch–ZW10 (RZZ) complex
The spindle-assembly checkpoint (SAC) monitors kinetochore–microtubule attachment during mitosis. In metazoans, the three-subunit Rod–Zwilch–ZW10 (RZZ) complex is a crucial SAC component that interacts with additional SAC-activating and SAC-silencing components, including the Mad1–Mad2 complex and cytoplasmic dynein. The RZZ complex contains two copies of each subunit and has a predicted molecular mass of ∼800 kDa. Given the low abundance of the RZZ complex in natural sources, its recombinant reconstitution was attempted by co-expression of its subunits in insect cells. The RZZ complex was pur...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Altenfeld, A.Wohlgemuth, S.Wehenkel, A.Vetter, I.R.Musacchio, A. Tags: spindle-assembly checkpoint cell division mitosis RZZ complex Rod Zwilch ZW10 kinetochore Ndc80 Mis12 Knl1 KMN network research communications Source Type: research

Purification, crystallization and preliminary X-ray crystallographic analysis of the phosphatase domain (PA3346PD) of the response regulator PA3346 from Pseudomonas aeruginosa PAO1
The phosphatase domain (PA3346PD) of the response regulator PA3346 modulates the downstream anti-anti-σ factor PA3347 to regulate swarming motility in Pseudomonas aeruginosa PAO1. PA3346PD, which comprises the protein phosphatase 2C domain (PP2C), is classified as a Ser/Thr phosphatase of the Mg2+- or Mn2+-dependent protein phosphatase (PPM) family. The recombinant PA3346PD, with molecular mass 26 kDa, was overexpressed in Escherichia coli, purified on an Ni2+–NTA agarose column and crystallized by the sitting-drop vapour-diffusion method. X-ray diffraction data were collected from PA3346PD crystals to a reso...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Chen, L.-Y.Wu, P.-H.Guan, H.-H.Fun, H.-K.Chang, H.-Y.Chen, C.-J. Tags: phosphatase domain response regulator Pseudomonas aeruginosa research communications Source Type: research

Expression, purification, crystallization and preliminary crystallographic analysis of a GH20 β-N-acetylglucosaminidase from the marine bacterium Vibrio harveyi
In this study, the crystallization and preliminary crystallographic data of wild-type VhGlcNAcase and its catalytically inactive mutant D437A in the absence and the presence of substrate are reported. Crystals of wild-type VhGlcNAcase were grown in 0.1 M sodium acetate pH 4.6, 1.4 M sodium malonate, while crystals of the D437A mutant were obtained in 0.1 M bis-tris pH 7.5, 0.1 M sodium acetate, 20% PEG 3350. X-ray data from the wild-type and the mutant crystals were collected at a synchrotron-radiation light source and were complete to a resolution of 2.5 Å. All crystals were composed of the same type of di...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Meekrathok, P.Bürger, M.Porfetye, A.T.Vetter, I.R.Suginta, W. Tags: β -N-acetylglucosaminidase Vibrio harveyi GH20 glycoside hydrolase family research communications Source Type: research

Structure of the omalizumab Fab
Omalizumab is a humanized anti-IgE antibody that inhibits the binding of IgE to its receptors on mast cells and basophils, thus blocking the IgE-mediated release of inflammatory mediators from these cells. Omalizumab binds to the Fc domains of IgE in proximity to the binding site of the high-affinity IgE receptor Fc∊RI, but the epitope and the mechanisms and conformations governing the recognition remain unknown. In order to elucidate the molecular mechanism of its anti-IgE activity, the aim was to analyse the interaction of omalizumab with human IgE. Therefore, IgE Fc C∊2–4 was recombinantly produced in mammalia...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Jensen, R.K.Plum, M.Tjerrild, L.Jakob, T.Spillner, E.Andersen, G.R. Tags: IgE Fab fragment therapeutic antibody research communications Source Type: research

Crystallization and preliminary X-ray characterization of the eukaryotic replication terminator Reb1–Ter DNA complex
This study is the first to yield structural information about this important family of proteins and will provide insights into the mechanism of replication and transcription termination. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Jaiswal, R.Singh, S.K.Bastia, D.Escalante, C.R. Tags: protein – DNA complex Reb1 transcription termination eukaryotic RNA Pol I research communications Source Type: research

Cloning, expression, crystallization and preliminary X-ray studies of a superfolder GFP fusion of cyanobacterial Psb32
A fusion of Psb32 from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (TePsb32) with superfolder GFP was created for enhanced solubility and improved detection and purification. The fusion protein readily formed large hexagonal crystals belonging to space group P6122. A full data set extending to 2.3 Å resolution was collected at the Swiss Light Source. The phase problem could be solved by using only the sfGFP fusion partner or by using GFP and AtTLP18.3 from Arabidopsis thaliana as search models. Based on this expression construct, a versatile library of 24 vectors combining four different supe...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Liauw, P.Kannchen, D.Gasper, R.Dyczmons-Nowaczyk, N.Nowaczyk, M.M.Hofmann, E. Tags: Psb32 superfolder GFP Thermosynechococcus elongatus BP-1 research communications Source Type: research