Crystal structure of GH30-7 endoxylanase C from the filamentous fungus Talaromyces cellulolyticus
In this study, the crystal structure of a TcXyn30C mutant which lacks the CBM1 domain was determined at 1.65   Ã… resolution. The structure of the active site of TcXyn30C was compared with that of the bifunctional GH30-7 xylanase B from T. cellulolyticus (TcXyn30B), which exhibits glucuronoxylanase and xylobiohydrolase activities. The results revealed that TcXyn30C has a conserved structural feature for recognizing the 4-O-methyl- α -d-glucuronic acid (MeGlcA) substituent in subsite − 2b. Additionally, the results demonstrated that Phe47 contributes significantly to catalysis by TcXyn30C. Phe47 is located in subsite â...
Source: Acta Crystallographica Section F - July 27, 2020 Category: Biochemistry Authors: Nakamichi, Y. Fujii, T. Watanabe, M. Matsushika, A. Inoue, H. Tags: crystal structure endoxylanases glucuronoxylanases glycoside hydrolase family 30 Talaromyces cellulolyticus research communications Source Type: research
Expression, purification and crystal structure determination of a ferredoxin reductase from the actinobacterium Thermobifida fusca
The ferredoxin reductase FdR9 from Thermobifida fusca, a member of the oxygenase-coupled NADH-dependent ferredoxin reductase (FNR) family, catalyses electron transfer from NADH to its physiological electron acceptor ferredoxin. It forms part of a putative three-component cytochrome P450 monooxygenase system in T. fusca comprising CYP222A1 and the [3Fe – 4S]-cluster ferredoxin Fdx8 as well as FdR9. Here, FdR9 was overexpressed and purified and its crystal structure was determined at 1.9   Å resolution. The overall structure of FdR9 is similar to those of other members of the FNR family and is composed of an FAD-binding...
Source: Acta Crystallographica Section F - July 27, 2020 Category: Biochemistry Authors: Rodriguez Buitrago, J.A. Kl ü nemann, T. Blankenfeldt, W. Schallmey, A. Tags: ferredoxin reductase Thermobifida fusca cytochrome P450 research communications Source Type: research
Crystal structure of the FYCO1 RUN domain suggests possible interfaces with small GTPases
FYCO1 is a multidomain adaptor protein that plays an important role in autophagy by mediating the kinesin-dependent microtubule plus-end-directed transport of autophagosomes. FYCO1 contains a RUN domain, which is hypothesized to function as a specific effector for members of the Ras superfamily of small GTPases, but its role has not been well characterized and its interaction partner(s) have not been identified. Here, the crystal structure of the FYCO1 RUN domain was determined at 1.3   Å resolution. The overall structure of the FYCO1 RUN domain was similar to those of previously reported RUN domains. Detailed structura...
Source: Acta Crystallographica Section F - July 27, 2020 Category: Biochemistry Authors: Sakurai, S. Shimizu, T. Ohto, U. Tags: X-ray crystallography autophagy FYCO1 RUN domain small GTPase binding research communications Source Type: research
Innovation versus practice in biological crystallization
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - June 30, 2020 Category: Biochemistry Authors: Newman, J. van Raaij, M.J. Tags: crystallization innovation editorial Source Type: research
Proline/alanine-rich sequence (PAS) polypeptides as an alternative to PEG precipitants for protein crystallization
Proline/alanine-rich sequence (PAS) polypeptides represent a novel class of biosynthetic polymers comprising repetitive sequences of the small proteinogenic amino acids l-proline, l-alanine and/or l-serine. PAS polymers are strongly hydrophilic and highly soluble in water, where they exhibit a natively disordered conformation without any detectable secondary or tertiary structure, similar to polyethylene glycol (PEG), which constitutes the most widely applied precipitant for protein crystallization to date. To investigate the potential of PAS polymers for structural studies by X-ray crystallography, two proteins that were ...
Source: Acta Crystallographica Section F - June 30, 2020 Category: Biochemistry Authors: Schiefner, A. Walser, R. Gebauer, M. Skerra, A. Tags: disordered polypeptide PASylation protein precipitant polyamino acid polyethylene glycol proline/alanine-rich sequence protein crystallization methods communications Source Type: research
A proposed carbon-utilization and virulence protein A, CuvA (Rv1422), from Mycobacterium tuberculosis H37Rv: crystallization, X-ray diffraction analysis and ligand binding
Mycobacterium tuberculosis possesses the ability to undergo physiological adaptations in order to persist during the prolonged course of infection despite the active immune response of the host and in order to overcome multiple environmental changes. Previous studies have proposed that M. tuberculosis CuvA (Rv1422; MtCuvA) might play a critical role in the adaptation of the bacterium to environmental changes, such as nutrient utilization and alteration of the growth rate. However, the detailed function of MtCuvA still remains unclear owing to a lack of structural information. To better understand its role in host adaptatio...
Source: Acta Crystallographica Section F - June 30, 2020 Category: Biochemistry Authors: Jeong, Y.C. Lee, K.S. Tags: Mycobacterium tuberculosis CuvA (Rv1422) bacterial adaptation nutrient utilization cell-wall precursor components research communications Source Type: research
Structural characterization of borneol dehydrogenase from Pseudomonas sp. TCU-HL1
During the microbial degradation of borneol, a bicyclic plant monoterpene, it is first converted into camphor by borneol dehydrogenase (BDH) and then enters a known camphor-degradation pathway. Previously, a recombinant Pseudomonas BDH was found in inclusion bodies when expressed in Escherichia coli. After refolding, it was still unstable and was difficult to concentrate. Here, the protein-expression conditions were improved by changing the medium from lysogeny broth to Terrific Broth, yielding a soluble form of the enzyme with higher activity. The protein was crystallized and its 3D structure was determined by X-ray diffr...
Source: Acta Crystallographica Section F - June 30, 2020 Category: Biochemistry Authors: Khine, A.A. Chen, H.-P. Huang, K.-F. Ko, T.-P. Tags: plant terpenoids camphor oxidoreductases Rossmann fold NAD expression medium protein solubility research communications Source Type: research
Tartryl-CoA inhibits succinyl-CoA synthetase
Succinyl-CoA synthetase (SCS) catalyzes the only substrate-level phosphorylation step in the tricarboxylic acid cycle. Human GTP-specific SCS (GTPSCS), an α β -heterodimer, was produced in Escherichia coli. The purified protein crystallized from a solution containing tartrate, CoA and magnesium chloride, and a crystal diffracted to 1.52   Å resolution. Tartryl-CoA was discovered to be bound to GTPSCS. The CoA portion lies in the amino-terminal domain of the α -subunit and the tartryl end extends towards the catalytic histidine residue. The terminal carboxylate binds to the phosphate-binding site of GTPSCS. (Source: A...
Source: Acta Crystallographica Section F - June 30, 2020 Category: Biochemistry Authors: Huang, J. Fraser, M.E. Tags: thioesters catalysis tricarboxylic acid cycle succinyl-CoA synthetase research communications Source Type: research
Crystal structure of the catalytic subunit of bovine pyruvate dehydrogenase phosphatase
Mammalian pyruvate dehydrogenase (PDH) activity is tightly regulated by phosphorylation and dephosphorylation, which is catalyzed by PDH kinase isomers and PDH phosphatase isomers, respectively. PDH phosphatase isomer 1 (PDP1) is a heterodimer consisting of a catalytic subunit (PDP1c) and a regulatory subunit (PDP1r). Here, the crystal structure of bovine PDP1c determined at 2.1   Å resolution is reported. The crystals belonged to space group P3221, with unit-cell parameters a = b = 75.3, c = 173.2   Å . The structure was solved by molecular-replacement methods and refined to a final R factor of 21.9% (Rfree = 24.7%)...
Source: Acta Crystallographica Section F - June 30, 2020 Category: Biochemistry Authors: Guo, Y. Qiu, W. Roche, T.E. Hackert, M.L. Tags: pyruvate dehydrogenase phosphatase cis-peptide research communications Source Type: research
Novel carbohydrate-recognition mode of the invertebrate C-type lectin SPL-1 from Saxidomus purpuratus revealed by the GlcNAc-complex crystal in the presence of Ca2+
The C-type lectins SPL-1 and SPL-2 from the bivalve Saxidomus purpuratus are composed of A and B chains and of two B chains, respectively. They bind specific carbohydrates containing acetamido groups, such as N-acetylglucosamine (GlcNAc) and N-acetylgalactosamine (GalNAc), in a Ca2+-independent manner. Unlike ordinary C-type lectins, which require Ca2+ ions for carbohydrate recognition, these lectins recognize specific carbohydrates mainly through interactions with the acetamido group without Ca2+ ions, even though Ca2+ enhances the binding affinity of these lectins, especially SPL-1. In the present study, the crystal stru...
Source: Acta Crystallographica Section F - June 4, 2020 Category: Biochemistry Authors: Unno, H. Higuchi, S. Goda, S. Hatakeyama, T. Tags: lectins bivalve C-type lectin Saxidomus purpuratus research communications Source Type: research
Crystal structure of the SH3 domain of growth factor receptor-bound protein 2
This study presents the crystal structure of the N-terminal SH3 (SH3N) domain of growth factor receptor-bound protein 2 (Grb2) at 2.5   Å resolution. Grb2 is a small (215-amino-acid) adaptor protein that is widely expressed and involved in signal transduction/cell communication. The crystal structure of full-length Grb2 has previously been reported (PDB entry 1gri). The structure of the isolated SH3N domain is consistent with the full-length structure. The structure of the isolated SH3N domain was solved at a higher resolution (2.5   Å compared with 3.1   Å for the previously deposited structure) and made it possi...
Source: Acta Crystallographica Section F - June 4, 2020 Category: Biochemistry Authors: Bolgov, A. Korban, S. Luzik, D. Zhemkov, V. Kim, M. Rogacheva, O. Bezprozvanny, I. Tags: SH3 domain Grb2 adaptor protein growth factor receptor-bound protein 2 research communications Source Type: research
Enhanced X-ray diffraction of in vivo-grown μ NS crystals by viscous jets at XFELs
μ NS is a 70   kDa major nonstructural protein of avian reoviruses, which cause significant economic losses in the poultry industry. They replicate inside viral factories in host cells, and the μ NS protein has been suggested to be the minimal viral factor required for factory formation. Thus, determining the structure of μ NS is of great importance for understanding its role in viral infection. In the study presented here, a fragment consisting of residues 448 – 605 of μ NS was expressed as an EGFP fusion protein in Sf9 insect cells. EGFP- μ NS(448 – 605) crystallization in Sf9 cells was monitored and verified ...
Source: Acta Crystallographica Section F - May 28, 2020 Category: Biochemistry Authors: Nagaratnam, N. Tang, Y. Botha, S. Saul, J. Li, C. Hu, H. Zaare, S. Hunter, M. Lowry, D. Weierstall, U. Zatsepin, N. Spence, J.C.H. Qiu, J. LaBaer, J. Fromme, P. Martin-Garcia, J.M. Tags: μ NS avian reovirus in vivo crystallization high-viscosity jets serial crystallography X-ray free-electron lasers methods communications Source Type: research
Expression, purification, crystallization and X-ray diffraction studies of a novel root-induced secreted protein from Trichoderma virens
Small secreted cysteine-rich proteins (SSCPs) from fungi play an important role in fungi – host interactions. The plant-beneficial fungi Trichoderma spp. are in use worldwide as biocontrol agents and protect the host plant from soil-borne as well as foliar pathogens. Recently, a novel SSCP, Tsp1, has been identified in the secreted protein pool of T. virens and is overinduced upon its interaction with the roots of the maize plant. The protein was observed to be well conserved in the Ascomycota division of fungi, and its homologs are present in many plant-pathogenic fungi such as Fusarium oxysporum and Magnaporthe oryzae....
Source: Acta Crystallographica Section F - May 28, 2020 Category: Biochemistry Authors: Bansal, R. Mistry, H.U. Mukherjee, P.K. Gupta, G.D. Tags: Trichoderma virens effector secreted cysteine-rich proteins protein crystallization research communications Source Type: research
Structure of heme d1-free cd1 nitrite reductase NirS
A key step in anaerobic nitrate respiration is the reduction of nitrite to nitric oxide, which is catalysed by the cd1 nitrite reductase NirS in, for example, the Gram-negative opportunistic pathogen Pseudomonas aeruginosa. Each subunit of this homodimeric enzyme consists of a cytochrome c domain and an eight-bladed β -propeller that binds the uncommon isobacteriochlorin heme d1 as an essential part of its active site. Although NirS has been well studied mechanistically and structurally, the focus of previous studies has been on the active heme d1-bound form. The heme d1-free form of NirS reported here, which represents a...
Source: Acta Crystallographica Section F - May 28, 2020 Category: Biochemistry Authors: Kl ü nemann, T. Blankenfeldt, W. Tags: cd1 nitrite reductase NirS heme d1 research communications Source Type: research
Crystal structures of the GH18 domain of the bifunctional peroxiredoxin – chitinase CotE from Clostridium difficile
CotE is a coat protein that is present in the spores of Clostridium difficile, an obligate anaerobic bacterium and a pathogen that is a leading cause of antibiotic-associated diarrhoea in hospital patients. Spores serve as the agents of disease transmission, and CotE has been implicated in their attachment to the gut epithelium and subsequent colonization of the host. CotE consists of an N-terminal peroxiredoxin domain and a C-terminal chitinase domain. Here, a C-terminal fragment of CotE comprising residues 349 – 712 has been crystallized and its structure has been determined to reveal a core eight-stranded β -barrel f...
Source: Acta Crystallographica Section F - May 28, 2020 Category: Biochemistry Authors: Whittingham, J.L. Hanai, S. Brannigan, J.A. Ferreira, W.T. Dodson, E.J. Turkenburg, J.P. Cartwright, J. Cutting, S.M. Wilkinson, A.J. Tags: Clostridium difficile spores CotE glycosyl hydrolase 3D domain swapping research communications Source Type: research
