Structural analysis of free and liganded forms of the Fab fragment of a high-affinity anti-cocaine antibody, h2E2
A high-affinity anti-cocaine monoclonal antibody, designated h2E2, is entering phase 1 clinical trials for cocaine abuse therapy. To gain insight into the molecular details of its structure that are important for binding cocaine and cocaine metabolites, the Fab fragment was generated and crystallized with and without ligand. Structures of the unliganded Fab and the Fab fragment bound to benzoylecgonine were determined, and were compared with each other and with other crystallized anti-cocaine antibodies. The affinity of the h2E2 antibody for cocaine is 4 β€… nM, while that of the cocaine metabolite benzoylecgonine is 20 β€...
Source: Acta Crystallographica Section F - November 4, 2019 Category: Biochemistry Authors: Tan, K. Zhou, M. Ahrendt, A.J. Duke, N.E.C. Tabaja, N. Ball, W.J. Kirley, T.L. Norman, A.B. Joachimiak, A. Schiffer, M. Wilton, R. Pokkuluri, P.R. Tags: high-affinity anti-cocaine antibody antigen-binding fragment crystal structure benzoylecgonine complex h2E2 Fab fragment research communications Source Type: research

Major conformational changes in the structure of lysozyme obtained from a crystal with a very low solvent content
A new crystal form of lysozyme with a very low solvent content (26.35%) has been obtained in the orthorhombic space group P212121 (with unit-cell parameters a = 30.04, b = 51.68, c = 61.53 β€… Å ). The lysozyme structure obtained from these crystals does not show the typical overall fold. Instead, major conformational changes take place in some elements of the secondary structure and in the hydrophobic core of the protein. At the end of the central α -helix ( α 2), Glu35 is usually buried in the catalytic site and shows an abnormally high pKa value, which is key to the activity of the enzyme. The high pKa...
Source: Acta Crystallographica Section F - November 4, 2019 Category: Biochemistry Authors: Salinas-Garcia, M.C. Plaza-Garrido, M. Alba-Elena, D. Camara-Artigas, A. Tags: low solvent content lysozyme folding intermediate research communications Source Type: research

Inexpensive robotic system for standard and fluorescent imaging of protein crystals
Protein-crystallization imaging and classification is a labor-intensive process typically performed either by humans or by instruments that currently cost well over $100 β€… 000. This cost puts the use of crystallization-trial imaging outside the reach of most academic laboratories, and also start-up biotechnology firms, where resources are scarce. An imaging system has been designed and prototyped which automatically captures images from multi-well protein-crystallization experiments using both standard and fluorescent imaging techniques at a cost 28 times lower than current market rates. The machine uses a Panowin F1 3D ...
Source: Acta Crystallographica Section F - November 4, 2019 Category: Biochemistry Authors: Handzlik, D. Larson, E.T. Munschy, E. Obmolova, G. Collin, D. Craig, T.K. Tags: fluorescent imaging automated microscope imaging system open source robotics methods communications Source Type: research

Automatic annotation of protein residues in published papers
This work presents an annotation tool that automatically locates mentions of particular amino-acid residues in published papers and identifies the protein concerned. These matches can be provided in context or in a searchable format in order for researchers to better use the existing and future literature. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - November 4, 2019 Category: Biochemistry Authors: Firth, R. Talo, F. Venkatesan, A. Mukhopadhyay, A. McEntyre, J. Velankar, S. Morris, C. Tags: NLP natural language processing named entity recognizer residue methods communications Source Type: research

Taking biological structure communications into the third dimension
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - October 31, 2019 Category: Biochemistry Authors: van Raaij, M. Newman, J. Tags: annotation online structure visualization augmented reality integrated multimedia editorial Source Type: research

Crystal structure of the N-terminal domain of the fibronectin-binding protein PavA from Streptococcus pneumoniae
In this study, the crystal structure of the N-terminal domain of PavA (SpPavA-N) determined at a resolution of 2.39 β€… Å is reported. Each monomer of the dimeric protein consists of two domains (domains I and II) and a short α -helix ( α 6) at the C-terminus that are connected by elongated loops. Comparison of the SpPavA-N structure with that of its homolog from Streptococcus suis (FBPS-N) revealed differences in α 5, α 6 and the domain II/ α 6 inter-loop region within domain II. The α 5 helix of FBPS-N folds back toward domain I, whereas in SpPavA-N it adopts an elongated rod sha...
Source: Acta Crystallographica Section F - September 23, 2019 Category: Biochemistry Authors: Manne, K. Narayana, S. Chattopadhyay, D. Tags: fibronectin-binding protein Streptococcus pneumoniae X-ray crystallography pneumococcal adherence and virulence factor A PavA crystal structure research communications Source Type: research

Structure of an RNA helix with pyrimidine mismatches and cross-strand stacking
The structure of a 22-base-pair RNA helix with mismatched pyrimidine base pairs is reported. The helix contains two symmetry-related CUG sequences: a triplet-repeat motif implicated in myotonic dystrophy type 1. The CUG repeat contains a U – U mismatch sandwiched between Watson – Crick pairs. Additionally, the center of the helix contains a dimerized UUCG motif with tandem pyrimidine (U – C/C – U) mismatches flanked by U – G wobble pairs. This region of the structure is significantly different from previously observed structures that share the same sequence and neighboring base pairs. The tand...
Source: Acta Crystallographica Section F - September 23, 2019 Category: Biochemistry Authors: Montemayor, E.J. Virta, J.M. Hagler, L.D. Zimmerman, S.C. Butcher, S.E. Tags: RNA myotonic dystrophy type 1 pyrimidine mismatches research communications Source Type: research

Rv0100, a proposed acyl carrier protein in Mycobacterium tuberculosis: expression, purification and crystallization
Acyl carrier proteins (ACPs) are important components in fatty-acid biosynthesis in prokaryotes. Rv0100 is predicted to be an essential ACP in Mycobacterium tuberculosis, the pathogen that is the causative agent of tuberculosis, and therefore has the potential to be a novel antituberculosis drug target. Here, the successful cloning and purification of Rv0100 using Mycobacterium smegmatis as a host is reported. Crystals of the purified protein were obtained that diffracted to a resolution of 1.9 β€… Å . Overall, this work lays the foundation for the future pursuit of drug discovery and development against this potenti...
Source: Acta Crystallographica Section F - September 23, 2019 Category: Biochemistry Authors: Bondoc, J.M.G. Gutka, H.J. Almutairi, M.M. Patwell, R. Rutter, M.W. Wolf, N.M. Samudrala, R. Mehboob, S. Movahedzadeh, F. Tags: acyl carrier protein Mycobacterium tuberculosis Mycobacterium smegmatis Rv0100 research communications Source Type: research

The structure of bovine Ξ² -lactoglobulin in crystals grown at pH 3.8 exhibiting novel threefold twinning
Bovine β -lactoglobulin was crystallized from 3 β€… M NaCl buffered at pH 3.8 with sodium citrate as thick hexagonal prisms of greater than 1 β€… mm in edge length. Analyses of the X-ray diffraction intensities using three different current algorithms were unanimous in specifying the space group to be P6322, with unit-cell dimensions a = b = 75.47, c = 140.79 β€… Å . No progress could be made, however, towards an acceptable solution by molecular replacement using this symmetry. In the end, it was found that the true space group was C2221, a subgroup of P6322, with a = 65.89, b = 114.12, c = 140.51 β€… Å , ...
Source: Acta Crystallographica Section F - September 19, 2019 Category: Biochemistry Authors: Yeates, T.O. McPherson, A. Tags: Ξ² -lactoglobulin milk tritohedral twinning symmetry whey proteins space group determination research communications Source Type: research

Crystal structure of the Fab region of a neutralizing antibody against granulocyte-macrophage colony-stimulating factor
An increased level of granulocyte-macrophage colony-stimulating factor has a potential role in the development of autoimmune diseases, and the neutralization of its activity by monoclonal antibodies is a promising therapy for some diseases. Here, the crystal structure of the Fab region of EV1007, a fully human antibody expressed in Chinese hamster ovary cells that was developed from human peripheral blood mononuclear cells, is described. The structure closely resembles that of MB007, which is the Fab region of the same antibody expressed in Escherichia coli [Blech et al. (2012), Biochem. J. 447, 205 – 215], except at...
Source: Acta Crystallographica Section F - September 19, 2019 Category: Biochemistry Authors: Angkawidjaja, C. Torashima, T. Tags: monoclonal antibodies Fab region granulocyte-macrophage colony-stimulating factor anti-GM-CSF EV1007 research communications Source Type: research

Structural characterization of a prolyl aminodipeptidase (PepX) from Lactobacillus helveticus
Prolyl aminodipeptidase (PepX) is an enzyme that hydrolyzes peptide bonds from the N-terminus of substrates when the penultimate amino-acid residue is a proline. Prolyl peptidases are of particular interest owing to their ability to hydrolyze food allergens that contain a high percentage of proline residues. PepX from Lactobacillus helveticus was cloned and expressed in Escherichia coli as an N-terminally His-tagged recombinant construct and was crystallized by hanging-drop vapor diffusion in a phosphate buffer using PEG 3350 as a precipitant. The structure was determined at 2.0 β€… Å resolution by molecular replacem...
Source: Acta Crystallographica Section F - September 19, 2019 Category: Biochemistry Authors: Ojennus, D.D. Bratt, N.J. Jones, K.L. Juers, D.H. Tags: prolyl aminodipeptidase PepX Ξ± / Ξ² -hydrolases protein structure calcium binding calcium-blade zone gluten Lactobacillus helveticus research communications Source Type: research

Structure of GTP cyclohydrolase I from Listeria monocytogenes, a potential anti-infective drug target
A putative open reading frame encoding GTP cyclohydrolase I from Listeria monocytogenes was expressed in a recombinant Escherichia coli strain. The recombinant protein was purified and was confirmed to convert GTP to dihydroneopterin triphosphate (Km = 53 β€… µ M; vmax = 180 β€… nmol β€… mg − 1 β€… min − 1). The   protein was crystallized from 1.3 β€… M sodium citrate pH 7.3 and the crystal structure was solved at a resolution of 2.4 β€… Å (Rfree = 0.226) by molecular replacement using human GTP cyclohydrolase I as a template. The protein is a D5-symmetric decamer with ten topologically equival...
Source: Acta Crystallographica Section F - August 29, 2019 Category: Biochemistry Authors: Sch ΓΌ ssler, S. Haase, I. Perbandt, M. Illarionov, B. Siemens, A. Richter, K. Bacher, A. Fischer, M. Gr Γ€ wert, T. Tags: GTP cyclohydrolase I Listeria monocytogenes crystal structure high-throughput screening tetrahydrofolate biosynthesis listeriosis research communications Source Type: research

Structure of the archaeal chemotaxis protein CheY in a domain-swapped dimeric conformation
In this study, two new crystal forms and protein structures of CheY are reported. In both crystal forms, CheY is arranged in a domain-swapped conformation. CheF, the protein bridging the chemotaxis signal transduction system and the motility apparatus, was recombinantly expressed, purified and subjected to X-ray data collection. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 29, 2019 Category: Biochemistry Authors: Paithankar, K.S. Enderle, M. Wirthensohn, D.C. Miller, A. Schlesner, M. Pfeiffer, F. Rittner, A. Grininger, M. Oesterhelt, D. Tags: chemotaxis signal transduction response regulator CheY CheF archaellum protein evolution research communications Source Type: research

Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant
The crystallization of amidase, the ultimate enzyme in the Trp-dependent auxin-biosynthesis pathway, from Arabidopsis thaliana was attempted using protein samples with at least 95% purity. Cube-shaped crystals that were assumed to be amidase crystals that belonged to space group I4 (unit-cell parameters a = b = 128.6, c = 249.7 β€… Å ) were obtained and diffracted to 3.0 β€… Å resolution. Molecular replacement using structures from the PDB containing the amidase signature fold as search models was unsuccessful in yielding a convincing solution. Using the Sequence-Independent Molecular replacement Based on Avail...
Source: Acta Crystallographica Section F - August 28, 2019 Category: Biochemistry Authors: Andi, B. Soares, A.S. Shi, W. Fuchs, M.R. McSweeney, S. Liu, Q. Tags: dihydrolipoamide succinyltransferase auxin amidase contaminant crystallization protein crystallography molecular replacement research communications Source Type: research

Crystal structure of UDP-glucose pyrophosphorylase from Yersinia pestis, a potential therapeutic target against plague
Yersinia pestis, the causative agent of bubonic plague, is one of the most lethal pathogens in recorded human history. Today, the concern is the possible misuse of Y. pestis as an agent in bioweapons and bioterrorism. Current therapies for the treatment of plague include the use of a small number of antibiotics, but clinical cases of antibiotic resistance have been reported in some areas of the world. Therefore, the discovery of new drugs is required to combat potential Y.   pestis infection. Here, the crystal structure of the Y. pestis UDP-glucose pyrophosphorylase (UGP), a metabolic enzyme implicated in the survival...
Source: Acta Crystallographica Section F - August 27, 2019 Category: Biochemistry Authors: Gibbs, M.E. Lountos, G.T. Gumpena, R. Waugh, D.S. Tags: Yersinia pestis galU UDP-glucose pyrophosphorylase plague drug targets research communications Source Type: research

Structural basis for the substrate recognition of aminoglycoside 7 β€² β€² -phosphotransferase-Ia from Streptomyces hygroscopicus
Hygromycin B (HygB) is one of the aminoglycoside antibiotics, and it is widely used as a reagent in molecular-biology experiments. Two kinases are known to inactivate HygB through phosphorylation: aminoglycoside 7 ′ ′ -phosphotransferase-Ia [APH(7 ′ ′ )-Ia] from Streptomyces hygroscopicus and aminoglycoside 4-phosphotransferase-Ia [APH(4)-Ia] from Escherichia coli. They phosphorylate the hydroxyl groups at positions 7 ′ ′ and 4 of the HygB molecule, respectively. Previously, the crystal structure of APH(4)-Ia was reported as a ternary complex with HygB and 5 ′ -adenylyl- β , &...
Source: Acta Crystallographica Section F - August 27, 2019 Category: Biochemistry Authors: Takenoya, M. Shimamura, T. Yamanaka, R. Adachi, Y. Ito, S. Sasaki, Y. Nakamura, A. Yajima, S. Tags: aminoglycoside antibiotics enzyme-mediated resistance kinases SAD phasing selenomethionine hygromycin B Streptomyces hygroscopicus research communications Source Type: research

No magnesium is needed for binding of the stimulator of interferon genes to cyclic dinucleotides
Stimulator of interferon genes (STING) binds cyclic dinucleotides (CDNs), which induce a large conformational change of the protein. The structural basis of activation of STING by CDNs is rather well understood. Unliganded STING forms an open dimer that undergoes a large conformational change ( ∼ 10 β€… Å ) to a closed conformation upon the binding of a CDN molecule. This event activates downstream effectors of STING and subsequently leads to activation of the type 1 interferon response. However, a previously solved structure of STING with 3 ′ ,3 ′ -c-di-GMP shows Mg atoms mediating the interaction of...
Source: Acta Crystallographica Section F - August 27, 2019 Category: Biochemistry Authors: Smola, M. Birkus, G. Boura, E. Tags: STING cGAS CDN 3 β€² ,3 -c-di-GMP crystal structure research communications Source Type: research

Crystal structure of TchmY from Actinoplanes teichomyceticus
Moenomycin-type antibiotics are phosphoglycolipids that are notable for their unique modes of action and have proven to be useful in animal nutrition. The gene clusters tchm from Actinoplanes teichomyceticus and moe from Streptomyces are among a limited number of known moenomycin-biosynthetic pathways. Most genes in tchm have counterparts in the moe cluster, except for tchmy and tchmz, the functions of which remain unknown. Sequence analysis indicates that TchmY belongs to the isoprenoid enzyme C2-like superfamily and may serve as a prenylcyclase. The enzyme was proposed to be involved in terminal cyclization of the moenoc...
Source: Acta Crystallographica Section F - August 27, 2019 Category: Biochemistry Authors: Yang, Z. Zhang, L. Yu, X. Wu, S. Yang, Y. Hu, Y. Li, Q. Shang, N. Guo, R.-T. Chen, C.-C. Dai, L. Liu, W. Tags: crystal structure prenylcyclases Actinoplanes teichomyceticus research communications Source Type: research

AMi: a GUI-based, open-source system for imaging samples in multi-well plates
Described here are instructions for building and using an inexpensive automated microscope (AMi) that has been specifically designed for viewing and imaging the contents of multi-well plates. The X, Y, Z translation stage is controlled through dedicated software (AMiGUI) that is being made freely available. Movements are controlled by an Arduino-based board running grbl, and the graphical user interface and image acquisition are controlled via a Raspberry Pi microcomputer running Python. Images can be written to the Raspberry Pi or to a remote disk. Plates with multiple sample wells at each row/column position are supporte...
Source: Acta Crystallographica Section F - August 5, 2019 Category: Biochemistry Authors: Bohm, A. Tags: AMi AMiGUI automated microscopy multi-well plates crystallography methods communications Source Type: research

The Rel stringent factor from Thermus thermophilus: crystallization and X-ray analysis
The stringent response, controlled by (p)ppGpp, enables bacteria to trigger a strong phenotypic resetting that is crucial to cope with adverse environmental changes and is required for stress survival and virulence. In the bacterial cell, (p)ppGpp levels are regulated by the concerted opposing activities of RSH (RelA/SpoT homologue) enzymes that can transfer a pyrophosphate group of ATP to the 3 ′ position of GDP (or GTP) or remove the 3 ′ pyrophosphate moiety from (p)ppGpp. Bifunctional Rel enzymes are notoriously difficult to crystallize owing to poor stability and a propensity for aggregation, usually leadin...
Source: Acta Crystallographica Section F - August 1, 2019 Category: Biochemistry Authors: Van Nerom, K. Tamman, H. Takada, H. Hauryliuk, V. Garcia-Pino, A. Tags: stringent response Rel/RelA/SpoT (p)ppGpp bacterial alarmone Thermus thermophilus research communications Source Type: research

Crystal structure of the Schizosaccharomyces pombe U7BR E2-binding region in complex with Ubc7
Endoplasmic reticulum (ER)-associated degradation (ERAD) is a protein quality-control pathway in eukaryotes in which misfolded ER proteins are polyubiquitylated, extracted and ultimately degraded by the proteasome. This process involves ER membrane-embedded ubiquitin E2 and E3 enzymes, as well as a soluble E2 enzyme (Ubc7 in Saccharomyces cerevisiae and UBE2G2 in mammals). E2-binding regions (E2BRs) that recruit these soluble ERAD E2s to the ER have been identified in humans and S. cerevisiae, and structures of E2 – E2BR complexes from both species have been determined. In addition to sequence and structural differen...
Source: Acta Crystallographica Section F - August 1, 2019 Category: Biochemistry Authors: Hann, Z.S. Metzger, M.B. Weissman, A.M. Lima, C.D. Tags: endoplasmic reticulum ERAD ubiquitin protein degradation ubiquitin-conjugating enzyme E2 E2-binding protein Schizosaccharomyces pombe research communications Source Type: research

Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser
Turn-on aptamers are in vitro-selected RNAs that bind to conditionally fluorescent small molecules and enhance their fluorescence. Upon binding TO1-biotin, the iMango-III aptamer achieves the largest fluorescence enhancement reported for turn-on aptamers (over 5000-fold). This aptamer was generated by structure-guided engineering and functional reselection of the parental aptamer Mango-III. Structures of both Mango-III and iMango-III have previously been determined by conventional cryocrystallography using synchrotron X-radiation. Using an X-ray free-electron laser (XFEL), the room-temperature iMango-III – TO1-biotin...
Source: Acta Crystallographica Section F - August 1, 2019 Category: Biochemistry Authors: Trachman, R.J. Stagno, J.R. Conrad, C. Jones, C.P. Fischer, P. Meents, A. Wang, Y.-X. Ferr Γ© -D'Amar Γ© , A.R. Tags: RNA structure fluorescence turn-on aptamers X-ray free-electron lasers iMango-III XFELS room temperature research communications Source Type: research

Introducing Methods Communications, a new category of contributions to Acta Crystallographica F
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - July 31, 2019 Category: Biochemistry Authors: Newman, J. van Raaij, M.J. Tags: methods communications topical reviews multimedia editorial Source Type: research

Crystal structure of the inhibitor-free form of the serine protease kallikrein-4
In this study, an inhibitor-free form of KLK4 was crystallized. The crystals obtained belonged to space group P1, contained four molecules in the asymmetric unit and diffracted to 1.64 β€… Å resolution. Interestingly, a nonstandard rotamer of the specificity-determining residue Asp189 was observed in all chains. This model will provide a useful unliganded structure for the future structure-guided design of KLK4 inhibitors. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - July 15, 2019 Category: Biochemistry Authors: Riley, B.T. Hoke, D.E. McGowan, S. Buckle, A.M. Tags: kallikrein-related peptidase 4 KLK4 apo structure unliganded research communications Source Type: research

The crystal structure of haemoglobin from Atlantic cod
has been solved to 2.54 β€… Å resolution. The structure consists of two tetramers in the crystallographic asymmetric unit. The structure of haemoglobin obtained from one individual cod suggests polymorphism in the tetrameric assembly. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - July 15, 2019 Category: Biochemistry Authors: Helland, R. Bj ΓΈ rkeng, E.K. Rothweiler, U. Sydnes, M.O. Pampanin, D.M. Tags: haemoglobin Gadus morhua Atlantic cod research communications Source Type: research

Structural insights into the substrate specificity of SP_0149, the substrate-binding protein of a methionine ABC transporter from Streptococcus pneumoniae
Successful pathogenesis is a cumulative effect of the virulence factors of a pathogen and its capability to efficiently utilize the available nutrients from the host. Streptococcus pneumoniae, a Gram-positive opportunistic pathogen, may either reside asymptomatically as a nasopharyngeal commensal inside the human host or cause lethal diseases, including pneumonia, meningitis and sepsis. S. pneumoniae is known to acquire methionine (Met) from its host through a Met importer. Here, the crystal structure of the substrate-binding protein (SBP; SP_0149) of an ABC importer with Met bound is reported at a resolution of 1.95 β€… &...
Source: Acta Crystallographica Section F - July 3, 2019 Category: Biochemistry Authors: Jha, B. Vyas, R. Bhushan, J. Sehgal, D. Biswal, B.K. Tags: Streptococcus pneumoniae ABC transporter substrate-binding protein methionine X-ray crystallography research communications Source Type: research

A promiscuous kinase inhibitor delineates the conspicuous structural features of protein kinase CK2a1
Protein kinase CK2a1 is a serine/threonine kinase that plays a crucial role in the growth, proliferation and survival of cells and is a well known target for tumour and glomerulonephritis therapies. Here, the crystal structure of the kinase domain of CK2a1 complexed with 5-iodotubercidin (5IOD), an ATP-mimetic inhibitor, was determined at 1.78 β€… Å resolution. The structure shows distinct structural features and, in combination with a comparison of the crystal structures of five off-target kinases complexed with 5IOD, provides valuable information for the development of highly selective inhibitors. (Source: Acta Cry...
Source: Acta Crystallographica Section F - July 3, 2019 Category: Biochemistry Authors: Tsuyuguchi, M. Nakaniwa, T. Sawa, M. Nakanishi, I. Kinoshita, T. Tags: protein kinase CK2 ATP-analogue inhibitor selectivity off-target kinases structural comparison research communications Source Type: research

Structural comparison of p-hydroxybenzoate hydroxylase (PobA) from Pseudomonas putida with PobA from other Pseudomonas spp. and other monooxygenases
The crystal structure is reported of p-hydroxybenzoate hydroxylase (PobA) from Pseudomonas putida, a possible drug target to combat tetracycline resistance, in complex with flavin adenine dinucleotide (FAD). The structure was refined at 2.2 β€… Å resolution with four polypeptide chains in the asymmetric unit. Based on the results of pairwise structure alignments, PobA from P. putida is structurally very similar to PobA from P. fluorescens and from P. aeruginosa. Key residues in the FAD-binding and substrate-binding sites of PobA are highly conserved spatially across the proteins from all three species. Additionally, ...
Source: Acta Crystallographica Section F - July 1, 2019 Category: Biochemistry Authors: Lazar, J.T. Shuvalova, L. Rosas-Lemus, M. Kiryukhina, O. Satchell, K.J.F. Minasov, G. Tags: Pseudomonas oxygenases antibiotic resistance PobA pHBH research communications Source Type: research

Crystal structure of the glycoside hydrolase PssZ from Listeria monocytogenes
In this study, the crystal structure of PssZ has been determined at 1.6 β€… Å resolution. PssZ belongs to glycoside hydrolase family 8 and adopts a classical ( α / α )6-barrel fold. This architecture forms a deep groove which may serve as the substrate-binding pocket. The conserved catalytic residues (Glu72, Trp110, Asn119, Phe167, Tyr183 and Asp232) are localized at the centre of the groove. This crystal structure will help to improve the understanding of the hydrolytic mechanism of PssZ and its application as a biofilm disrupter. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - June 27, 2019 Category: Biochemistry Authors: Wu, H. Qiao, S. Li, D. Guo, L. Zhu, M. Ma, L.Z. Tags: Listeria monocytogenes glycoside hydrolases SAD phasing PssZ ( Ξ± / )6-barrel fold biofilms research communications Source Type: research

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 β€… Å resolution. This model, which was refined against a data set from &s...
Source: Acta Crystallographica Section F - June 27, 2019 Category: Biochemistry Authors: Jones, C. Tran, B. Conrad, C. Stagno, J. Trachman, R. Fischer, P. Meents, A. Ferr Γ© -D'Amar Γ© , 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 25, 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 β€… Å resolution from a single AcFeSOD crystal. The crystal belonged to the hexagonal space group P61 and co...
Source: Acta Crystallographica Section F - June 25, 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 β€… 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 25, 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 – Ο€ 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 9, 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 9, 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 β€… 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 5, 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 20, 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 β€… Å using the Macromolecular Neutron Diffractometer (MaNDi) is reporte...
Source: Acta Crystallographica Section F - May 20, 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 β€… 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 β€… 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 12, 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 β€… 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 12, 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 9, 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 9, 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 β€… Å resolution, and bound to the inhibitors phosphoramidon and thiorphan at 2.8 and 3.0 β€… 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 9, 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 Ξ² -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 9, 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 Ξ² -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 29, 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 28, 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 β€… 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 25, 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 25, 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 β€… MDa calcium-dependent adhesion protein using the anomalous diffraction of the chelated calcium io...
Source: Acta Crystallographica Section F - April 25, 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 25, 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