Crystal structure of the catalytic domain of human RPTPH
Receptor-type protein tyrosine phosphatases (RPTPs) receive extracellular stimuli and transfer them into cells. They regulate cell growth, differentiation and death via specific signals. They have also been implicated in cancer, diabetes and neurological diseases. RPTPH, a member of the type 3 RPTP (R3-PTP) family, is an important regulator of colorectal cancer and hepatic carcinoma. Despite its importance in drug development, the structure of RPTPH has not yet been resolved. Here, the crystal structure of the catalytic domain of RPTPH was determined at 1.56   Å resolution. Despite similarities to other R3-PTPs in its o...
Source: Acta Crystallographica Section F - June 15, 2022 Category: Biochemistry Authors: Kim, M. Ryu, S.E. Tags: human RPTPH crystal structure specific inhibitor development loop conformation colorectal cancer hepatic carcinoma research communications Source Type: research

Identification, structure determination and analysis of Mycobacterium smegmatis acyl-carrier protein synthase (AcpS) crystallized serendipitously
The unintended crystallization of proteins which generally originate from the expression host instead of the target recombinant proteins is periodically reported. Despite the massive technological advances in the field, assigning a structural model to the corresponding diffraction data is not a trivial task. Here, the structure of acyl-carrier protein synthase (AcpS) from Mycobacterium smegmatis (msAcpS), which crystallized inadvertently in an experimental setup to grow crystals of a Mycobacterium tuberculosis protein using M. smegmatis as an expression system, is reported. After numerous unsuccessful attempts to solve the...
Source: Acta Crystallographica Section F - June 15, 2022 Category: Biochemistry Authors: Bhatia, I. Yadav, S. Biswal, B.K. Tags: X-ray crystallography Mycobacterium smegmatis fatty-acid biosynthesis acyl-carrier protein synthase Mycobacterium tuberculosis research communications Source Type: research

In situ crystal data-collection and ligand-screening system at SPring-8
In situ diffraction data collection using crystallization plates has been utilized for macromolecules to evaluate crystal quality without requiring additional sample treatment such as cryocooling. Although it is difficult to collect complete data sets using this technique due to the mechanical limitation of crystal rotation, recent advances in methods for data collection from multiple crystals have overcome this issue. At SPring-8, an in situ diffraction measurement system was constructed consisting of a goniometer for a plate, an articulated robot and plate storage. Using this system, complete data sets were obtained util...
Source: Acta Crystallographica Section F - May 27, 2022 Category: Biochemistry Authors: Okumura, H. Sakai, N. Murakami, H. Mizuno, N. Nakamura, Y. Ueno, G. Masunaga, T. Kawamura, T. Baba, S. Hasegawa, K. Yamamoto, M. Kumasaka, T. Tags: protein crystallography in situ X-ray diffraction room-temperature data collection crystallization plates ligand screening methods communications Source Type: research

Crystal structure of an extracellular superoxide dismutase from Onchocerca volvulus and implications for parasite-specific drug development
Superoxide dismutases (SODs) are metalloproteins that are responsible for the dismutation of superoxide anion radicals. SODs are consequently protective against oxidative damage to cellular components. Among other protective mechanisms, the filarial parasite Onchocerca volvulus has a well developed defense system to scavenge toxic free radicals using SODs during migration and sojourning of the microfilariae and adult worms in the human body. O. volvulus is responsible for the neglected disease onchocerciasis or `river blindness'. In the present study, an extracellular Cu/Zn-SOD from O. volvulus (OvEC-SOD) was cloned, purif...
Source: Acta Crystallographica Section F - May 27, 2022 Category: Biochemistry Authors: Moustafa, A. Perbandt, M. Liebau, E. Betzel, C. Falke, S. Tags: X-ray crystallography Cu/Zn superoxide dismutases metal ion coordination Onchocerca volvulus parasites docking drug targets research communications Source Type: research

Preliminary XFEL data from spontaneously grown endo-1,4- β -xylanase crystals from Hypocrea virens
The enzymatic degradation of semi-cellulosic substrates has recently received immense attention. The enzyme endo-1,4- β -xylanase is essential for the complete digestion of complex and heterogeneous hemicellulose. Here, the purification, crystallization and preliminary X-ray free-electron laser (XFEL) diffraction analysis of endo-1,4- β -xylanase from the fungus Hypocrea virens (HviGH11) are reported. Codon-optimized HviGH11 was overexpressed in Escherichia coli and spontaneously crystallized after His-tag purification and concentration. Preliminary XFEL diffraction data were collected at the Pohang Accelerator Laborator...
Source: Acta Crystallographica Section F - May 27, 2022 Category: Biochemistry Authors: Nam, K.H. Park, S. Park, J. Tags: endo-1,4- β -xylanase xylanases GH11 X-ray free-electron lasers Hypocrea virens research communications Source Type: research

Crystal structure of thermally stable homodimeric cytochrome c ′ - β from Thermus thermophilus
Cytochrome c ′ - β is a heme protein that belongs to the cytochrome P460 family and consists of homodimeric subunits with a predominantly antiparallel β -sheet fold. Here, the crystal structure of cytochrome c ′ - β from the thermophilic Thermus thermophilus (TTCP- β ) is reported at 1.74   Å resolution. TTCP- β has a typical antiparallel β -sheet fold similar to that of cytochrome c ′ - β from the moderately thermophilic Methylococcus capsulatus (MCCP- β ). The phenylalanine cap structure around the distal side of the heme is also similar in TTCP- β and MCCP- β , indicating that both proteins similarly ...
Source: Acta Crystallographica Section F - May 27, 2022 Category: Biochemistry Authors: Yoshimi, T. Fujii, S. Oki, H. Igawa, T. Adams, H.R. Ueda, K. Kawahara, K. Ohkubo, T. Hough, M.A. Sambongi, Y. Tags: crystal structure cytochrome c ′ - β protein thermal stability homodimeric interface Thermus thermophilus research communications Source Type: research

Crystal structure of the PX domain of Vps17p from Saccharomyces cerevisiae
The structure determination of the PX (phox homology) domain of the Saccharomyces cerevisiae Vps17p protein presented a challenging case for molecular replacement because it has noncrystallographic symmetry close to a crystallographic axis. The combination of diffraction-quality crystals grown under microgravity on the International Space Station and a highly accurate template structure predicted by AlphaFold2 provided the key to successful crystal structure determination. Although the structure of the Vps17p PX domain is seen in many PX domains, no basic residues are found around the canonical phosphatidylinositol phospha...
Source: Acta Crystallographica Section F - April 30, 2022 Category: Biochemistry Authors: Obita, T. Inaka, K. Kohda, D. Maita, N. Tags: AlphaFold2 International Space Station microgravity phox homology PX domain Vps17p Saccharomyces cerevisiae research communications Source Type: research

Effects of the T337M and G391V disease-related variants on human phosphoglucomutase 1: structural disruptions large and small
Phosphoglucomutase 1 (PGM1) plays a central role in glucose homeostasis in human cells. Missense variants of this enzyme cause an inborn error of metabolism, which is categorized as a congenital disorder of glycosylation. Here, two disease-related variants of PGM1, T337M and G391V, which are both located in domain 3 of the four-domain protein, were characterized via X-ray crystallography and biochemical assays. The studies show multiple impacts resulting from these dysfunctional variants, including both short- and long-range structural perturbations. In the T337M variant these are limited to a small shift in an active-site...
Source: Acta Crystallographica Section F - April 25, 2022 Category: Biochemistry Authors: Stiers, K.M. Owuocha, L.F. Beamer, L.J. Tags: missense variants enzymes inherited diseases X-ray crystallography congenital disorders of glycosylation structural perturbation human phosphoglucomutase 1 research communications Source Type: research

Biochemical and crystallization analysis of the CENP-SX – DNA complex
The CENP-SX (MHF) complex is a conserved histone-fold protein complex that is involved in chromosome segregation and DNA repair. It can bind to DNA on its own as well as in complex with other proteins such as CENP-TW and FANCM to recognize specific substrates. CENP-SX binds nonspecifically to dsDNA, similar to other histone-fold proteins. Several low-resolution structures of CENP-SX in complex with DNA are known, but a high-resolution structure is still lacking. The DNA-binding properties of CENP-SX and FANCM – CENP-SX complexes with various lengths of dsDNA were compared and the band-shift patterns and migration positio...
Source: Acta Crystallographica Section F - April 22, 2022 Category: Biochemistry Authors: Ito, S. Nishino, T. Tags: protein – DNA interactions histone-fold complexes DNA repair chromosome segregation crystallization CENP-SX DNA complex research communications Source Type: research

Crystal structure of the kringle domain of human receptor tyrosine kinase-like orphan receptor 1 (hROR1)
Receptor tyrosine kinase-like orphan receptors (RORs) are monotopic membrane proteins belonging to the receptor tyrosine kinase (RTK) family. RTKs play a role in the control of most basic cellular processes, including cell proliferation, differentiation, migration and metabolism. New emerging roles for RORs in cancer progression have recently been proposed: RORs have been shown to be overexpressed in various malignancies but not in normal tissues, and moreover an abnormal expression level of RORs on the cellular surface is correlated with high levels of cytotoxicity in primary cancer cells. Monoclonal antibodies against th...
Source: Acta Crystallographica Section F - April 22, 2022 Category: Biochemistry Authors: Guarino, S.R. Di Bello, A. Palamini, M. Capillo, M.C. Forneris, F. Tags: receptor tyrosine kinases cancer kringle domains human ROR1 immunotherapy research communications Source Type: research

The structure of Synechococcus elongatus enolase reveals key aspects of phosphoenolpyruvate binding
A structure – function characterization of Synechococcus elongatus enolase (SeEN) is presented, representing the first structural report on a cyanobacterial enolase. X-ray crystal structures of SeEN in its apoenzyme form and in complex with phosphoenolpyruvate are reported at 2.05 and 2.30   Å resolution, respectively. SeEN displays the typical fold of enolases, with a conformationally flexible loop that closes the active site upon substrate binding, assisted by two metal ions that stabilize the negatively charged groups. The enzyme exhibits a catalytic efficiency of 1.2 × 105   M − 1   s − 1 for the dehydrat...
Source: Acta Crystallographica Section F - April 3, 2022 Category: Biochemistry Authors: Gonz á lez, J.M. Mart í -Arbona, R. Chen, J.C.-H. Unkefer, C.J. Tags: enolases Synechococcus elongatus cyanobacteria phosphoenolpyruvate research communications Source Type: research

Crystal structure of the ternary complex of Leishmania major pteridine reductase 1 with the cofactor NADP+/NADPH and the substrate folic acid
Pteridine reductase 1 (PTR1) is a key enzyme of the folate pathway in protozoan parasites of the genera Leishmania and Trypanosoma and is a valuable drug target for tropical diseases. This enzyme is able to catalyze the NADPH-dependent reduction of both conjugated (folate) and unconjugated (biopterin) pterins to their tetrahydro forms, starting from oxidized- or dihydro-state substrates. The currently available X-ray structures of Leishmania major PTR1 (LmPTR1) show the enzyme in its unbound, unconjugated substrate-bound (with biopterin derivatives) and inhibitor-bound forms. However, no structure has yet been determined o...
Source: Acta Crystallographica Section F - March 30, 2022 Category: Biochemistry Authors: Dello Iacono, L. Di Pisa, F. Mangani, S. Tags: pteridine reductase Leishmania major cofactors folic acid catalysis research communications Source Type: research

Expression, purification and crystallization of a novel metagenome-derived salicylaldehyde dehydrogenase from Alpine soil
Salicylaldehyde dehydrogenase (SALD) catalyses the last reaction in the upper pathway of naphthalene degradation: the oxidation of salicylaldehyde to salicylate. This enzyme has been isolated and studied from a few organisms that belong to the betaproteobacteria and gammaproteobacteria, predominantly Pseudomonas putida. Furthermore, there is only one crystal structure of this enzyme, which was obtained from P. putida G7. Here, crystallographic studies and analysis of the crystal structure of an Alpine soil metagenome-derived SALD (SALDAP) from an alphaproteobacterium are presented. The SALDAP gene was discovered using gene...
Source: Acta Crystallographica Section F - March 28, 2022 Category: Biochemistry Authors: Dandare, S.U. H å kansson, M. Svensson, L.A. Timson, D.J. Allen, C.C.R. Tags: metagenome salicylaldehyde dehydrogenase alphaproteobacteria Alpine soil purification crystallography research communications Source Type: research

Structure and activity of a thermally stable mutant of Acanthamoeba actophorin
Actophorin, which was recently tested for crystallization under microgravity on the International Space Station, was subjected to mutagenesis to identify a construct with improved biophysical properties that were expected to improve the extent of diffraction. First, 20 mutations, including one C-terminal deletion of three residues, were introduced individually into actophorin, resulting in modest increases in thermal stability of between +0.5 ° C and +2.2 ° C. All but two of the stabilizing mutants increased both the rates of severing F-actin filaments and of spontaneous polymerization of pyrenyl G-actin in vitro. When t...
Source: Acta Crystallographica Section F - March 28, 2022 Category: Biochemistry Authors: Quirk, S. Lieberman, R.L. Tags: actin filaments microgravity mutagenesis stability actophorin research communications Source Type: research

Structure of BrxA from Staphylococcus aureus, a bacilliredoxin involved in redox homeostasis in Firmicutes
Bacilliredoxins are small proteins that are involved in redox homeostasis in bacillithiol-producing bacteria. They reduce mixed bacillithiol disulfides on protected proteins through a disulfide-exchange reaction, restoring the thiol group on the target protein. Bacilliredoxins contain an unusual conserved CGC motif, and their exact catalytic mechanism remains unclear. Here, a 1.6   Å resolution X-ray crystallographic structure of the bacilliredoxin BrxA (YphP) from Staphylococcus aureus is presented. The structure contains bacillithiol in a mixed disulfide with Cys54, as well as a disulfide linkage at Cys56, which may p...
Source: Acta Crystallographica Section F - March 28, 2022 Category: Biochemistry Authors: McHugh, C.S. Cook, P.D. Tags: BrxA Staphylococcus aureus bacillithiol thioredoxins Gram-positive bacteria oxidative stress redox homeostasis research communications Source Type: research