M. tuberculosis succinyl-diaminopimelate desuccinylase, the enzyme which catalyzes the seventh step of the lysine-biosynthesis pathway, has been cloned, expressed, purified and crystallized. Preliminary X-ray diffraction analysis indicated the presence of pseudo-merohedral twinning in space group P21, resulting in possible emulation of space group C2221.
Succinyl-diaminopimelate desuccinylase from Mycobacterium tuberculosis (DapE, Rv1202) has been cloned, heterologously expressed in Escherichia coli and purified using standard chromatographic techniques. Diffraction-quality crystals were obtained at acidic pH from ammonium sulfate and PEG and diffraction data were collected from two crystals to resolutions of 2.40 and 2.58 Å, respectively. The crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 79.7, b = 76.0, c = 82.9 Å, β = 119°. The most probable content of the asymmetric unit was two molecules of DapE, which would correspond to a solvent content of 56%. Both examined crystals turned out to be pseudo-merohedrally twinned, with twin operator −h, −k, h + l and twin fractions of approximately 0.46 and 0.16, respectively.
succinyl-diaminopimelate desuccinylase; DapE; Rv1202; Mycobacterium tuberculosis
A successful MAD experiment has been conducted at the Pr L
III edge on HZB beamline BL14.2.
The use of longer X-ray wavelengths in macromolecular crystallography has grown significantly over the past few years. The main reason for this increased use of longer wavelengths has been to utilize the anomalous signal from sulfur, providing a means for the experimental phasing of native proteins. Here, another possible application of longer X-ray wavelengths is presented: MAD at the L
III edges of various lanthanide compounds. A first experiment at the L
III edge of Pr was conducted on HZB MX beamline BL14.2 and resulted in the successful structure determination of the C-terminal domain of a spliceosomal protein. This experiment demonstrates that L
III edges of lanthanides constitute potentially attractive targets for long-wavelength MAD experiments.
long-wavelength MAD; MAD phasing; lanthanide ions
The Editors of Acta F look forward to 2014.
title change; editorial
crystallization communications; editorial
crystallization ontology; editorial
The regulatory domain of M. tuberculosis aspartokinase, the enzyme which catalyses the first reaction step in the biosynthesis of the amino acids lysine, methionine and threonine, has been cloned, expressed, purified and crystallized. Preliminary X-ray diffraction analysis of several crystals revealed the presence of five distinct crystal forms.
The regulatory domain of Mycobacterium tuberculosis aspartokinase (Mtb-AK, Mtb-Ask, Rv3709c) has been cloned, heterologously expressed in Escherichia coli and purified using standard chromatographic techniques. Screening for initial crystallization conditions using the regulatory domain (AK-β) in the presence of the potential feedback inhibitor threonine identified four conditions which yielded crystals suitable for X-ray diffraction analysis. From these four conditions five different crystal forms of Mtb-AK-β resulted, three of which belonged to the orthorhombic system, one to the tetragonal system and one to the monoclinic system. The highest resolution (1.6 Å) was observed for a crystal form belonging to space group P212121, with unit-cell parameters a = 53.70, b = 63.43, c = 108.85 Å and two molecules per asymmetric unit.
aspartokinase; Rv3709c; Mycobacterium tuberculosis; tuberculosis
Crystals of the wild-type haloalkane dehalogenase DhaA derived from R. rhodochrous NCIMB 13064 and of its catalytically inactive variant DhaA13 were grown in the presence of various ligands and diffraction data were collected to high and atomic resolution.
Haloalkane dehalogenases make up an important class of hydrolytic enzymes which catalyse the cleavage of carbon–halogen bonds in halogenated aliphatic compounds. There is growing interest in these enzymes owing to their potential use in environmental and industrial applications. The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 can slowly detoxify the industrial pollutant 1,2,3-trichloropropane (TCP). Structural analysis of this enzyme complexed with target ligands was conducted in order to obtain detailed information about the structural limitations of its catalytic properties. In this study, the crystallization and preliminary X-ray analysis of complexes of wild-type DhaA with 2-propanol and with TCP and of complexes of the catalytically inactive variant DhaA13 with the dye coumarin and with TCP are described. The crystals of wild-type DhaA were plate-shaped and belonged to the triclinic space group P1, while the variant DhaA13 can form prism-shaped crystals belonging to the orthorhombic space group P212121 as well as plate-shaped crystals belonging to the triclinic space group P1. Diffraction data for crystals of wild-type DhaA grown from crystallization solutions with different concentrations of 2-propanol were collected to 1.70 and 1.26 Å resolution, respectively. A prism-shaped crystal of DhaA13 complexed with TCP and a plate-shaped crystal of the same variant complexed with the dye coumarin diffracted X-rays to 1.60 and 1.33 Å resolution, respectively. A crystal of wild-type DhaA and a plate-shaped crystal of DhaA13, both complexed with TCP, diffracted to atomic resolutions of 1.04 and 0.97 Å, respectively.
haloalkane dehalogenases; DhaA; Rhodococcus rhodochrous; microseeding; atomic resolution
The enzyme 3-isopropylmalate dehydrogenase (IPMDH) from T. thermophilus, which catalyses the penultimate reaction step of the leucine-biosynthesis pathway, has been crystallized in various states along its reaction coordinate.
The Thermus thermophilus 3-isopropylmalate dehydrogenase (Tt-IPMDH) enzyme catalyses the penultimate step of the leucine-biosynthesis pathway. It converts (2R,3S)-3-isopropylmalate to (2S)-2-isopropyl-3-oxosuccinate in the presence of divalent Mg2+ or Mn2+ and with the help of NAD+. In order to elucidate the detailed structural and functional mode of the enzymatic reaction, crystals of Tt-IPMDH were grown in the presence of various combinations of substrate and/or cofactors. Here, the crystallization, data collection and preliminary crystallographic analyses of six such complexes are reported.
isopropylmalate dehydrogenase; Thermus thermophilus; leucine-biosynthesis pathway
Glyoxalase I from L. infantum was cloned, overexpressed in E. coli, purified and crystallized.
Glyoxalase I (GLO1) is the first of the two glyoxalase-pathway enzymes. It catalyzes the formation of S-d-lactoyltrypanothione from the non-enzymatically formed hemithioacetal of methylglyoxal and reduced trypanothione. In order to understand its substrate binding and catalytic mechanism, GLO1 from Leishmania infantum was cloned, overexpressed in Escherichia coli, purified and crystallized. Two crystal forms were obtained: a cube-shaped form and a rod-shaped form. While the cube-shaped form did not diffract X-rays at all, the rod-shaped form exhibited diffraction to about 2.0 Å resolution. The crystals belonged to space group P21212, with unit-cell parameters a = 130.03, b = 148.51, c = 50.63 Å and three dimers of the enzyme per asymmetric unit.
Leishmania infantum; glyoxalase I; methylglyoxal; trypanothione
Human ADP-ribosylhydrolase 1, which cleaves the glycosidic bond between ADP-ribose and specific Arg residues in proteins, has been cloned, expressed, purified and crystallized.
Human ADP-ribosylhydrolase 1 (hARH1, ADPRH) cleaves the glycosidic bond of ADP-ribose attached to an Arg residue of a protein. hARH1 has been cloned, expressed heterologously in Escherichia coli, purified and crystallized in complex with K+ and ADP. The orthorhombic crystals contained one monomer per asymmetric unit, exhibited a solvent content of 43% and diffracted X-rays to a resolution of 1.9 Å. A prerequisite for obtaining well diffracting crystals was the performance of X-ray fluorescence analysis on poorly diffracting apo hARH1 crystals, which revealed the presence of trace amounts of K+ in the crystal. Adding K-ADP to the crystallization cocktail then resulted in a crystal of different morphology and with dramatically improved diffraction properties.
ADP-ribosylation; ADP-ribosylhydrolase; ADP-ribosylarginine hydrolase; X-ray fluorescence; ARH1; ADPRH
Two C-terminally truncated variants of the small subunit of isopropylmalate isomerase from M. tuberculosis have been cloned, expressed, purified, crystallized and examined by X-ray diffraction.
Two C-terminally truncated variants of the small subunit of Mycobacterium tuberculosis isopropylmalate isomerase (Rv2987c; LeuD), LeuD_1-156 and LeuD_1-168, have been cloned, heterologously expressed in Escherichia coli, purified using standard chromatographic techniques and crystallized. The crystals of LeuD_1-156 belonged to the hexagonal system (space group P6122 or P6522) with up to four subunits in the asymmetric unit, whereas the crystals of LeuD_1-168 belonged to the monoclinic system (space group P21) with two subunits in the asymmetric unit. Both crystals diffracted X-rays to beyond 2.0 Å resolution and were suitable for further crystallographic analysis.
isopropylmalate isomerase; Mycobacterium tuberculosis; Rv2987c
The problem of undercounting of citations that are published only in supplementary material is studied for the journals Nature, Science, Cell and the Proceedings of the National Academy of Sciences (USA).
citations; supplementary material; editorial
M. tuberculosis tetrahydrodipicolinate-N-succinyltransferase, the enzyme that catalyses the fifth reaction step of the lysine-biosynthesis pathway, has been cloned, expressed, purified and crystallized.
Tetrahydrodipicolinate-N-succinyltransferase from Mycobacterium tuberculosis (DapD, Rv1201c) has been cloned, heterologously expressed in Escherichia coli, purified using standard chromatographic techniques and crystallized in the cubic space group I23 or I213. Preliminary diffraction data analysis indicates the presence of five molecules per asymmetric unit. Furthermore, the data exhibit icosahedral point-group symmetry. One possible explanation for this is that the enzyme assembles into a 60-mer exhibiting 235 point-group symmetry and crystallizes as such in space group I23. In this case, the combination of crystallographic and noncrystallographic symmetry elements results in an arrangement of the icosahedrons in the cubic crystal with one pentamer in the asymmetric unit. Another explanation is that the packing of the molecules itself mimics icosahedral symmetry. In this case both space groups I23 and I213 would be possible.
tetrahydrodipicolinate-N-succinyltransferase; Mycobacterium tuberculosis; DapD
The enzyme aspartate semialdehyde dehydrogenase from M. tuberculosis has been expressed, purified and crystallized in two different crystal forms.
Aspartate semialdehyde dehydrogenase from Mycobacterium tuberculosis (Asd, ASADH, Rv3708c), which is the second enzyme in the lysine/homoserine-biosynthetic pathways, has been expressed heterologously in Escherichia coli. The enzyme was purified using affinity and gel-filtration chromatographic techniques and crystallized in two different crystal forms. Preliminary diffraction data analysis suggested the presence of up to four monomers in the asymmetric unit of the orthorhombic crystal form A and of one or two monomers in the cubic crystal form B.
aspartate semialdehyde dehydrogenase; Mycobacterium tuberculosis; Rv3708c