Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystallization and preliminary X-ray analysis of isopentenyl diphosphate isomerase from Methanocaldococcus jannaschii.

ABSTRACT: Type 2 isopentenyl diphosphate isomerase (IDI-2) is a flavoprotein. Recently, flavin has been proposed to play a role as a general acid-base catalyst with no redox role during the enzyme reaction. To clarify the detailed enzyme reaction mechanism of IDI-2 and the unusual role of flavin, structural analysis of IDI-2 from Methanocaldococcus jannaschii (MjIDI) was performed. Recombinant MjIDI was crystallized at 293?K using calcium acetate as a precipitant. The diffraction of the crystal extended to 2.08?Å resolution at 100?K. The crystal belonged to the tetragonal space group I422, with unit-cell parameters a=126.46, c=120.03?Å. The presence of one monomer per asymmetric unit gives a crystal volume per protein weight (VM) of 3.0?Å3?Da(-1) and a solvent constant of 59.0% by volume.

SUBMITTER: Hoshino T

PROVIDER: S-EPMC3079984 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystallization and preliminary X-ray analysis of isopentenyl diphosphate isomerase from Methanocaldococcus jannaschii.

Hoshino Takeshi T Nango Eriko E Baba Seiki S Eguchi Tadashi T Kumasaka Takashi T

Acta crystallographica. Section F, Structural biology and crystallization communications 20101223 Pt 1

Type 2 isopentenyl diphosphate isomerase (IDI-2) is a flavoprotein. Recently, flavin has been proposed to play a role as a general acid-base catalyst with no redox role during the enzyme reaction. To clarify the detailed enzyme reaction mechanism of IDI-2 and the unusual role of flavin, structural analysis of IDI-2 from Methanocaldococcus jannaschii (MjIDI) was performed. Recombinant MjIDI was crystallized at 293 K using calcium acetate as a precipitant. The diffraction of the crystal extended t ...[more]

PMID: 21206036

Similar Datasets

Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate.

Project description:Archaea have been shown to produce isoprenoids from mevalonate; however, genome analysis has failed to identify several genes in the mevalonate pathway on the basis of sequence similarity. A predicted archaeal kinase, coded for by the MJ0044 gene, was associated with other mevalonate pathway genes in the archaea and was predicted to be the "missing" phosphomevalonate kinase. The MJ0044-derived protein was tested for phosphomevalonate kinase activity and was found not to catalyze this reaction. The MJ0044 gene product was found to phosphorylate isopentenyl phosphate, generating isopentenyl diphosphate. Unlike other known kinases associated with isoprene biosynthesis, Methanocaldococcus jannaschii isopentenyl phosphate kinase is predicted to be a member of the aspartokinase superfamily.

| S-EPMC1447442 | biostudies-literature

Crystallization and preliminary X-ray diffraction analysis of MJ0458, an adenylate kinase from Methanocaldococcus jannaschii.

Project description:Adenylate kinase plays a very important role in regulating adenylate species in the cell. Methanocaldococcus jannaschii is a rich resource of unique enzymes. Here, MJ0458, an adenylate kinase from M. jannaschii, was crystallized. A set of X-ray diffraction data to 2.70?Å resolution was collected on beamline BL-17U of the Shanghai Synchrotron Radiation Facility (SSRF). The crystal belonged to space group P4(1)2(1)2 or P4(3)2(1)2. The unit-cell parameters were a = b = 76.18, c = 238.70?Å, ? = ? = ? = 90°.

| S-EPMC3818051 | biostudies-literature

Expression, purification, crystallization and preliminary X-ray analysis of a nucleoside kinase from the hyperthermophile Methanocaldococcus jannaschii.

Project description:Methanocaldococcus jannaschii nucleoside kinase (MjNK) is an ATP-dependent non-allosteric phosphotransferase that shows high catalytic activity for guanosine, inosine and cytidine. MjNK is a member of the phosphofructokinase B family, but participates in the biosynthesis of nucleoside monophosphates rather than in glycolysis. MjNK was crystallized as the apoenzyme as well as in complex with an ATP analogue and Mg2+. The latter crystal form was also soaked with fructose-6-phosphate. Synchrotron-radiation data were collected to 1.70 A for the apoenzyme crystals and 1.93 A for the complex crystals. All crystals exhibit orthorhombic symmetry; however, the apoenzyme crystals contain one monomer per asymmetric unit whereas the complex crystals contain a dimer.

| S-EPMC1952333 | biostudies-literature

Cloning, expression, purification, crystallization and preliminary crystallographic analysis of NifH1 from Methanocaldococcus jannaschii.

Project description:Nitrogen fixation is catalyzed by the nitrogenase complex in Azotobacter, which is composed of dinitrogenase and dinitrogenase reductase. Dinitrogenase is an ?(2)?(2) heterotetramer of the proteins NifD and NifK. Dinitrogenase reductase is a homodimer of the protein NifH. The expression of NifD/K and NifH nitrogenase homologues (named NflD/K and NflH for Nif-like D and H, respectively) has been detected in the non-nitrogen-fixing hyperthermophilic methanogen Methanocaldococcus jannaschii. Solving the structure of MjNifH1 may help in better understanding its function and may supply some clues to understanding the evolution of nitrogenase. The full-length protein with an additional His(6) tag at the C-terminus was expressed, purified and crystallized by the hanging-drop vapour-diffusion method at 287 K. An X-ray diffraction data set was collected to a resolution of 3.3 Å. The crystal belonged to space group P4(1)32, with unit-cell parameters a = b = c = 139.45 Å, and was estimated to contain one protein molecule per asymmetric unit.

| S-EPMC3087641 | biostudies-literature

Purification, crystallization and preliminary crystallographic analysis of the CBS-domain protein MJ1004 from Methanocaldococcus jannaschii.

Project description:The purification and preliminary crystallographic analysis of the archaeal CBS-domain protein MJ1004 from Methanocaldococcus jannaschii are described. The native protein was overexpressed, purified and crystallized in the monoclinic space group P2(1), with unit-cell parameters a=54.4, b=53.8, c=82.6 Å, β=106.1°. The crystals diffracted X-rays to 2.7 Å resolution using synchrotron radiation. Matthews-volume calculations suggested the presence of two molecules in the asymmetric unit that are likely to correspond to a dimeric species, which is also observed in solution.

| S-EPMC3053155 | biostudies-literature

Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase.

Project description:Isopentenyl diphosphate:dimethylallyl diphosphate (IPP:DMAPP) isomerase catalyses a crucial activation step in the isoprenoid biosynthesis pathway. This enzyme is responsible for the isomerization of the carbon-carbon double bond of IPP to create the potent electrophile DMAPP. DMAPP then alkylates other molecules, including IPP, to initiate the extraordinary variety of isoprenoid compounds found in nature. The crystal structures of free and metal-bound Escherichia coli IPP isomerase reveal critical active site features underlying its catalytic mechanism. The enzyme requires one Mn(2+) or Mg(2+) ion to fold in its active conformation, forming a distorted octahedral metal coordination site composed of three histidines and two glutamates and located in the active site. Two critical residues, C67 and E116, face each other within the active site, close to the metal-binding site. The structures are compatible with a mechanism in which the cysteine initiates the reaction by protonating the carbon-carbon double bond, with the antarafacial rearrangement ultimately achieved by one of the glutamates involved in the metal coordination sphere. W161 may stabilize the highly reactive carbocation generated during the reaction through quadrupole- charge interaction.

| S-EPMC145486 | biostudies-literature

Isopentenyl diphosphate isomerase. Mechanism-based inhibition by diene analogues of isopentenyl diphosphate and dimethylallyl diphosphate.

Project description:Isopentenyl diphosphate isomerase (IDI) catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). This is an essential step in the mevalonate entry into the isoprenoid biosynthetic pathway. The isomerization catalyzed by type I IDI involves protonation of the carbon-carbon double bond in IPP or DMAPP to form a tertiary carbocation, followed by deprotonation. Diene analogues for DMAPP (E-2-OPP and Z-2-OPP) and IPP (4-OPP) were synthesized and found to be potent active-site-directed irreversible inhibitors of the enzyme. X-ray analysis of the E.I complex between Escherichia coli IDI and 4-OPP reveals the presence of two isomers that differ in the stereochemistry of the newly formed C3-C4 double bond in the hydrocarbon chain of the inhibitor. In both adducts C5 of the inhibitor is joined to the sulfur of C67. In these structures the methyl group formed upon protonation of the diene moiety in 4-OPP is located near E116, implicating that residue in the protonation step.

| S-EPMC2528281 | biostudies-literature

Crystallization and preliminary crystallographic studies of L30e, a ribosomal protein from Methanocaldococcus jannaschii (MJ1044).

Project description:In view of the biological significance of understanding the ribosomal machinery of both prokaryotes and eukaryotes, the L30e ribosomal protein from Methanocaldococcus jannaschii was cloned, overexpressed, purified and crystallized using the microbatch-under-oil method with the crystallization conditions 40% PEG 400, 0.1 M MES pH 6.0 and 5% PEG 3000 at 291 K. A diffraction-quality crystal (0.20 x 0.20 x 0.35 mm) was obtained that belonged to the primitive tetragonal space group P4(3), with unit-cell parameters a = 46.1, b = 46.1, c = 98.5 A, and diffracted to a resolution of 1.9 A. Preliminary calculations reveal that the asymmetric unit contains two monomers with a Matthews coefficient (V(M)) of 2.16 A(3) Da(-1).

| S-EPMC2374168 | biostudies-literature

Purification, crystallization and preliminary crystallographic analysis of protein MJ1225 from Methanocaldococcus jannaschii, a putative archaeal homologue of gamma-AMPK.

Project description:In mammals, AMP-activated protein kinase (AMPK) is a heterotrimeric protein composed of a catalytic serine/threonine kinase subunit (alpha) and two regulatory subunits (beta and gamma). The gamma subunit senses the intracellular energy status by competitively binding AMP and ATP and is thought to be responsible for allosteric regulation of the whole complex. This work describes the purification and preliminary crystallographic analysis of protein MJ1225 from Methanocaldococcus jannaschii, an archaeal homologue of gamma-AMPK. The purified protein was crystallized using the hanging-drop vapour-diffusion method. Diffraction data for MJ1225 were collected to 2.3 A resolution using synchrotron radiation. The crystals belonged to space group H32, with unit-cell parameters a = b = 108.95, c = 148.08 A, alpha = beta = 90.00, gamma = 120.00 degrees . Preliminary analysis of the X-ray data indicated that there was one molecule per asymmetric unit.

| S-EPMC2720341 | biostudies-literature

Purification, crystallization and preliminary X-ray diffraction analysis of the FeoB G domain from Methanococcus jannaschii.

Project description:The transmembrane protein FeoB plays a key role in ferrous iron acquisition in prokaryotes. The N-terminal domain of FeoB from Methanococcus jannaschii was overproduced, purified to homogeneity and crystallized in the presence of GTP and magnesium. The native protein crystallized in a tetragonal space group and the crystals diffracted to beyond 2.2 A resolution, with unit-cell parameters a = b = 84.77, c = 137.90 A. The Matthews coefficient and the solvent content were estimated to be 2.65 A(3) Da(-1) and 53.64%, respectively, which corresponds to the presence of two molecules per asymmetric unit. To obtain initial phases, selenomethionyl-substituted protein was overproduced, purified and crystallized.

| S-EPMC2705634 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data