Crystal structure of a putative short-chain dehydrogenase/reductase from Paraburkholderia xenovorans
Paraburkholderia xenovorans degrades organic wastes, including polychlorinated biphenyls. The atomic structure of a putative dehydrogenase/reductase (SDR) from P. xenovorans (PxSDR) was determined in space group P21 at a resolution of 1.45 Å . PxSDR shares less than 37% sequence identity with any known structure and assembles as a prototypical SDR tetramer. As expected, there is some conformational flexibility and difference in the substrate-binding cavity, which explains the substrate specificity. Uniquely, the cofactor-binding cavity of PxSDR is not well conserved and differs from those of other SDRs. PxSDR has an a...
Source: Acta Crystallographica Section F - December 17, 2021 Category: Biochemistry Authors: Davidson, J. Nicholas, K. Young, J. Conrady, D.G. Mayclin, S. Subramanian, S. Staker, B.L. Myler, P.J. Asojo, O.A. Tags: SSGCID structural genomics Paraburkholderia xenovorans oxidoreductases education and training detoxification Seattle Structural Genomics Center for Infectious Disease research communications Source Type: research
X-ray structure of a human cardiac muscle troponin C/troponin I chimera in two crystal forms
The X-ray crystal structure of a human cardiac muscle troponin C/troponin I chimera has been determined in two different crystal forms and shows a conformation of the complex that differs from that previously observed by NMR. The chimera consists of the N-terminal domain of troponin C (cTnC; residues 1 – 80) fused to the switch region of troponin I (cTnI; residues 138 – 162). In both crystal forms, the cTnI residues form a six-turn α -helix that lays across the hydrophobic groove of an adjacent cTnC molecule in the crystal structure. In contrast to previous models, the cTnI helix runs in a parallel direction relative ...
Source: Acta Crystallographica Section F - December 16, 2021 Category: Biochemistry Authors: Yan, C. Sack, J.S. Tags: human cardiac muscle troponin C troponin C/troponin I chimera calcium regulation cardiac muscle contraction research communications Source Type: research
Cryotrapping peroxide in the active site of human mitochondrial manganese superoxide dismutase crystals for neutron diffraction
Structurally identifying the enzymatic intermediates of redox proteins has been elusive due to difficulty in resolving the H atoms involved in catalysis and the susceptibility of ligand complexes to photoreduction from X-rays. Cryotrapping ligands for neutron protein crystallography combines two powerful tools that offer the advantage of directly identifying hydrogen positions in redox-enzyme intermediates without radiolytic perturbation of metal-containing active sites. However, translating cryogenic techniques from X-ray to neutron crystallography is not straightforward due to the large crystal volumes and long data-coll...
Source: Acta Crystallographica Section F - December 16, 2021 Category: Biochemistry Authors: Azadmanesh, J. Lutz, W.E. Coates, L. Weiss, K.L. Borgstahl, G.E.O. Tags: human manganese superoxide dismutase neutron diffraction large unit cell cryotrapping research communications Source Type: research
The crystal structure of DynF from the dynemicin-biosynthesis pathway of Micromonospora chersina
Dynemicin is an enediyne natural product from Micromonospora chersina ATCC53710. Access to the biosynthetic gene cluster of dynemicin has enabled the in vitro study of gene products within the cluster to decipher their roles in assembling this unique molecule. This paper reports the crystal structure of DynF, the gene product of one of the genes within the biosynthetic gene cluster of dynemicin. DynF is revealed to be a dimeric eight-stranded β -barrel structure with palmitic acid bound within a cavity. The presence of palmitic acid suggests that DynF may be involved in binding the precursor polyene heptaene, which is cen...
Source: Acta Crystallographica Section F - December 16, 2021 Category: Biochemistry Authors: Kosgei, A.J. Miller, M.D. Bhardwaj, M. Xu, W. Thorson, J.S. Van Lanen, S.G. Phillips, G.N. Tags: dynemicin natural products biosynthetic gene clusters enediynes polyketides anthraquinone β -barrel unknown function Micromonospora chersina ATCC53710 research communications Source Type: research
Submission of structural biology data for review purposes
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - December 1, 2021 Category: Biochemistry Authors: Baker, E.N. Bond, C.S. Garman, E.F. Newman, J. Read, R.J. van Raaij, M.J. Tags: structural biology data peer review editorial Source Type: research
Structures of additional crystal forms of Satellite tobacco mosaic virus grown from a variety of salts
The structures of new crystal forms of Satellite tobacco mosaic virus (STMV) are described. These belong to space groups I2, P21212 (a low-resolution form), R3 (H3) and P23. The R3 crystals are 50%/50% twinned, as are two instances of the P23 crystals. The I2 and P21212 crystals were grown from ammonium sulfate solutions, as was one crystal in space group P23, while the R3 and the other P23 crystals were grown from sodium chloride, sodium bromide and sodium nitrate. The monoclinic and orthorhombic crystals have half a virus particle as the asymmetric unit, while the rhombohedral and cubic crystals have one third of a virus...
Source: Acta Crystallographica Section F - November 29, 2021 Category: Biochemistry Authors: McPherson, A. Tags: Satellite tobacco mosaic virus STMV ion channels crystallization symmetry decapsidation anions research communications Source Type: research
The X-ray structure of juvenile hormone diol kinase from the silkworm Bombyx mori
Insect juvenile hormones (JHs) are a family of sesquiterpenoid molecules that are secreted into the haemolymph. JHs have multiple roles in insect development, metamorphosis and sexual maturation. A number of pesticides work by chemically mimicking JHs, thus preventing insects from developing and reproducing normally. The haemolymph levels of JH are governed by the rates of its biosynthesis and degradation. One enzyme involved in JH catabolism is JH diol kinase (JHDK), which uses ATP (or GTP) to phosphorylate JH diol to JH diol phosphate, which can be excreted. The X-ray structure of JHDK from the silkworm Bombyx mori has b...
Source: Acta Crystallographica Section F - November 25, 2021 Category: Biochemistry Authors: Guo, J. Keegan, R.M. Rigden, D.J. Erskine, P.T. Wood, S.P. Li, S. Cooper, J.B. Tags: kinases EF-hand motifs molecular replacement insect juvenile hormones metamorphosis Bombyx mori research communications Source Type: research
Structure of mitogen-activated protein kinase kinase 1 in the DFG-out conformation
Eukaryotic protein kinases contain an Asp-Phe-Gly (DFG) motif, the conformation of which is involved in controlling the catalytic activity, at the N-terminus of the activation segment. The motif can be switched between active-state (DFG-in) and inactive-state (DFG-out) conformations: however, the mechanism of conformational change is poorly understood, partly because there are few reports of the DFG-out conformation. Here, a novel crystal structure of nonphosphorylated human mitogen-activated protein kinase kinase 1 (MEK1; amino acids 38 – 381) complexed with ATP- γ S is reported in which MEK1 adopts the DFG-out conform...
Source: Acta Crystallographica Section F - November 25, 2021 Category: Biochemistry Authors: Nakae, S. Kitamura, M. Fujiwara, D. Sawa, M. Shirai, T. Fujii, I. Tada, T. Tags: MAP kinases human mitogen-activated protein kinase kinase 1 MEK1 DFG motif X-ray crystallography research communications Source Type: research
Improved resolution crystal structure of Acanthamoeba actophorin reveals structural plasticity not induced by microgravity
Actophorin, a protein that severs actin filaments isolated from the amoeba Acanthamoeba castellanii, was employed as a test case for crystallization under microgravity. Crystals of purified actophorin were grown under microgravity conditions aboard the International Space Station (ISS) utilizing an interactive crystallization setup between the ISS crew and ground-based experimenters. Crystals grew in conditions similar to those grown on earth. The structure was solved by molecular replacement at a resolution of 1.65 Å . Surprisingly, the structure reveals conformational changes in a remote β -turn region that were pr...
Source: Acta Crystallographica Section F - November 11, 2021 Category: Biochemistry Authors: Quirk, S. Lieberman, R.L. Tags: microgravity actophorin actin Acanthamoeba castellanii cofilin conformational change research communications Source Type: research
Roles of the hydroxy group of tyrosine in crystal structures of Sulfurisphaera tokodaiiO6-methylguanine-DNA methyltransferase
In this study, the function of Tyr91 was investigated in detail by comparing the crystal structures of mutants and their complexes with substrate analogs. In this study, tyrosine, a conserved amino acid near the active-site loop in the C-terminal domain of Sulfurisphaera tokodaii MGMT (StoMGMT), was mutated to phenylalanine to produce a Y91F mutant, and the cysteine which is responsible for receiving the methyl group in the active site was mutated to a serine to produce a C120S mutant. A Y91F/C120S double-mutant StoMGMT was also created. The function of tyrosine is discussed based on the crystal structure of Y91F mutant St...
Source: Acta Crystallographica Section F - November 11, 2021 Category: Biochemistry Authors: Kikuchi, M. Yamauchi, T. Iizuka, Y. Tsunoda, M. Tags: O6-methylguanine-DNA methyltransferases DNA repair tyrosine Sulfurisphaera tokodaii hydroxy group research communications Source Type: research
Crystal structure of oligoribonuclease from Vibrio cholerae O1 El Tor with bound peptide
Oligoribonuclease (Orn), a member of the DEDDh superfamily, can hydrolyse 2 – 5 nt nanoRNAs to mononucleotides. It is involved in maintaining the intracellular levels of RNA, c-di-GMP signalling and transcription initiation in many bacterial species. Here, the crystal structure of Orn from Vibrio cholerae O1 El Tor (VcOrn) is reported at a resolution of 1.7 Å . VcOrn, which consists of nine α -helices and six β -strands, crystallizes with a single monomer in the asymmetric unit but forms a homodimer via crystallographic twofold symmetry. Electron density is observed in the active pocket that corresponds to ...
Source: Acta Crystallographica Section F - November 11, 2021 Category: Biochemistry Authors: Zhang, J. Sun, L. Zhang, Q. Bartlam, M. Tags: oligoribonucleases Vibrio cholerae crystal structure active pocket N-terminal tag research communications Source Type: research
Finding order in chaos – nanocrystals in amorphous protein gels
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - November 1, 2021 Category: Biochemistry Authors: Bowler, M.W. Tags: nanocrystals amorphous protein gels scientific commentaries Source Type: research
Topical Reviews in Acta Crystallographica F Structural Biology Communications
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - November 1, 2021 Category: Biochemistry Authors: Helliwell, J.R. Newman, J. van Raaij, M.J. Tags: topical reviews editorial Source Type: research
Crystal structure of N-terminal degron-truncated human glutamine synthetase
Glutamine synthetase (GS) is a decameric enzyme that plays a key role in nitrogen metabolism. Acetylation of the N-terminal degron (N-degron) of GS is essential for ubiquitylation and subsequent GS degradation. The full-length GS structure showed that the N-degron is buried inside the GS decamer and is inaccessible to the acetyltransferase. The structure of N-degron-truncated GS reported here reveals that the N-degron is not essential for GS decamer formation. It is also shown that the N-degron can be exposed to a solvent region through a series of conformational adjustments upon ligand binding. In summary, this study eluc...
Source: Acta Crystallographica Section F - October 29, 2021 Category: Biochemistry Authors: Chek, M.F. Kim, S.-Y. Mori, T. Kojima, H. Hakoshima, T. Tags: glutamine synthetase N-terminal degron crystal structure research communications Source Type: research
Crystal structures of glycogen-debranching enzyme mutants in complex with oligosaccharides
Debranching is a critical step in the mobilization of the important energy store glycogen. In eukaryotes, including fungi and animals, the highly conserved glycogen-debranching enzyme (GDE) debranches glycogen by a glucanotransferase (GT) reaction followed by a glucosidase (GC) reaction. Previous work indicated that these reactions are catalyzed by two active sites located more than 50 Å apart and provided insights into their catalytic mechanisms and substrate recognition. Here, five crystal structures of GDE in complex with oligosaccharides with 4 – 9 glucose residues are presented. The data suggest that the glycog...
Source: Acta Crystallographica Section F - October 29, 2021 Category: Biochemistry Authors: Shen, M. Gong, X. Xiang, S. Tags: glycogen-debranching enzymes Candida glabrata research communications Source Type: research
