Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystallization and preliminary diffraction studies of CBM3b of cellobiohydrolase 9A from Clostridium thermocellum.

ABSTRACT: Family 3 carbohydrate-binding modules (CBM3s) are associated with the scaffoldin subunit of the multi-enzyme cellulosome complex and with the family 9 glycoside hydrolases, which are multimodular enzymes that act on plant cell-wall polysaccharides, notably cellulose. Here, the crystallization of CBM3b from cellobiohydrolase 9A is reported. The crystals are tetragonal and belong to space group P4(1) or P4(3). X-ray diffraction data for CBM3b have been collected to 2.68 A resolution on beamline ID14-4 at the ESRF.

SUBMITTER: Jindou S

PROVIDER: S-EPMC2344089 | biostudies-literature | 2007 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystallization and preliminary diffraction studies of CBM3b of cellobiohydrolase 9A from Clostridium thermocellum.

Jindou Sadanari S Petkun Svetlana S Shimon Linda L Bayer Edward A EA Lamed Raphael R Frolow Felix F

Acta crystallographica. Section F, Structural biology and crystallization communications 20071121 Pt 12

Family 3 carbohydrate-binding modules (CBM3s) are associated with the scaffoldin subunit of the multi-enzyme cellulosome complex and with the family 9 glycoside hydrolases, which are multimodular enzymes that act on plant cell-wall polysaccharides, notably cellulose. Here, the crystallization of CBM3b from cellobiohydrolase 9A is reported. The crystals are tetragonal and belong to space group P4(1) or P4(3). X-ray diffraction data for CBM3b have been collected to 2.68 A resolution on beamline ID ...[more]

PMID: 18084089

Similar Datasets

Crystallization and preliminary X-ray diffraction studies of the family 54 carbohydrate-binding module from laminarinase (β-1,3-glucanase) Lic16A of Clostridium thermocellum.

Project description:The crystallization and preliminary X-ray diffraction analysis of the carbohydrate-binding module (CBM) from laminarinase Lic16A of the hyperthermophilic anaerobic bacterium Clostridium thermocellum (ctCBM54) are reported. Recombinant ctCBM54 was prepared using an Escherichia coli/pQE30 overexpression system and was crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 2.1 Å resolution using synchrotron radiation. The crystals belonged to space group P6322, with unit-cell parameters a = b = 130.15, c = 131.05 Å. The three-dimensional structure of ctCBM54 will provide valuable information about the structure-function relation of the laminarinase Lic16A and will allow the exploitation of this binding module in biotechnological applications.

| S-EPMC4321479 | biostudies-literature

Multidomain structure and cellulosomal localization of the Clostridium thermocellum cellobiohydrolase CbhA.

Project description:The nucleotide sequence of the Clostridium thermocellum F7 cbhA gene, coding for the cellobiohydrolase CbhA, has been determined. An open reading frame encoding a protein of 1,230 amino acids was identified. Removal of a putative signal peptide yields a mature protein of 1,203 amino acids with a molecular weight of 135,139. Sequence analysis of CbhA reveals a multidomain structure of unusual complexity consisting of an N-terminal cellulose binding domain (CBD) homologous to CBD family IV, an immunoglobulin-like beta-barrel domain, a catalytic domain homologous to cellulase family E1, a duplicated domain similar to fibronectin type III (Fn3) modules, a CBD homologous to family III, a highly acidic linker region, and a C-terminal dockerin domain. The cellulosomal localization of CbhA was confirmed by Western blot analysis employing polyclonal antibodies raised against a truncated enzymatically active version of CbhA. CbhA was identified as cellulosomal subunit S3 by partial amino acid sequence analysis. Comparison of the multidomain structures indicates striking similarities between CbhA and a group of cellulases from actinomycetes. Average linkage cluster analysis suggests a coevolution of the N-terminal CBD and the catalytic domain and its spread by horizontal gene transfer among gram-positive cellulolytic bacteria.

| S-EPMC107808 | biostudies-literature

Preliminary X-ray diffraction analysis of a thermophilic β-1,3-1,4-glucanase from Clostridium thermocellum.

Project description:β-1,3-1,4-Glucanases catalyze the specific hydrolysis of internal β-1,4-glycosidic bonds adjacent to the 3-O-substituted glucose residues in mixed-linked β-glucans. The thermophilic glycoside hydrolase CtGlu16A from Clostridium thermocellum exhibits superior thermal profiles, high specific activity and broad pH adaptability. Here, the catalytic domain of CtGlu16A was expressed in Escherichia coli, purified and crystallized in the trigonal space group P3121, with unit-cell parameters a=b=74.5, c=182.9 Å, by the sitting-drop vapour-diffusion method and diffracted to 1.95 Å resolution. The crystal contains two protein molecules in an asymmetric unit. Further structural determination and refinement are in progress.

| S-EPMC4089538 | biostudies-literature

Purification, crystallization and preliminary X-ray characterization of the pentamodular arabinoxylanase CtXyl5A from Clostridium thermocellum.

Project description:The cellulosome, a highly elaborate extracellular multi-enzyme complex of cellulases and hemicellulases, is responsible for the degradation of plant cell walls. The xylanase CtXyl5A (Cthe_2193) is a multimodular arabinoxylanase which is one of the largest components of the Clostridium thermocellum cellulosome. The N-terminal catalytic domain of CtXyl5A, which is a member of glycoside hydrolase family 5 (GH5), is responsible for the hydrolysis of arabinoxylans. Appended after it are three noncatalytic carbohydrate-binding modules (CBMs), which belong to families 6 (CBM6), 13 (CBM13) and 62 (CBM62). In addition, CtXyl5A has a fibronectin type III-like (Fn3) module preceding the CBM62 and a type I dockerin (DOK) module following it which allows the enzyme to be integrated into the cellulosome through binding to a cohesin module of the protein scaffold CipA. Crystals of the pentamodular enzyme without the DOK module at the C-terminus, with the domain architecture CtGH5-CBM6-CBM13-Fn3-CBM62, have been obtained. The structure of this pentamodular xylanase has been determined by molecular replacement to a resolution of 2.64?Å using coordinates of CtGH5-CBM6, Fn3 and CBM62 from the PDB as search models.

| S-EPMC3144809 | biostudies-literature

Overexpression, crystallization and preliminary X-ray crystallographic analysis of glucuronoxylan xylanohydrolase (Xyn30A) from Clostridium thermocellum.

Project description:The modular carbohydrate-active enzyme belonging to glycoside hydrolase family 30 (GH30) from Clostridium thermocellum (CtXynGH30) is a cellulosomal protein which plays an important role in plant cell-wall degradation. The full-length CtXynGH30 contains an N-terminal catalytic module (Xyn30A) followed by a family 6 carbohydrate-binding module (CBM6) and a dockerin at the C-terminus. The recombinant protein has a molecular mass of 45 kDa. Preliminary structural characterization was carried out on Xyn30A crystallized in different conditions. All tested crystals belonged to space group P1 with one molecule in the asymmetric unit. Molecular replacement has been used to solve the Xyn30A structure.

| S-EPMC3855739 | biostudies-literature

Overexpression, crystallization and preliminary X-ray crystallographic analysis of D-ribose-5-phosphate isomerase from Clostridium thermocellum.

Project description:Rare sugars are used for many industrial and medical purposes and are produced by the interconversion between aldoses and ketoses catalyzed by sugar and sugar-phosphate isomerases. Recently, Clostridium thermocellum d-ribose-5-phosphate isomerase (CTRPI), an aldose-ketose isomerase, was cloned in order to synthesize d-allose and its substrate specificity was further characterized for industrial usage. CTRPI has a novel substrate specificity that differs from those of other isomerases, which have broad substrate specificities. CTRPI prefers aldose substrates such as l-talose, d-ribose and d-allose. CTRPI was purified and crystallized in order to determine its three-dimensional structure and thus to elucidate its enzymatic reaction mechanism and understand its substrate specificity. The crystal belonged to the trigonal space group P3(2)21, with unit-cell parameters a = b = 69.5, c = 154.4 angstrom, and diffracted to 1.9 angstrom resolution. According to Matthews coefficient calculations, the crystallographic structure consists of a dimer in the asymmetric unit, with a V(M) of 3.2 angstrom(3) Da(-1) and a solvent content of 61.7%.

| S-EPMC2777044 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of a novel ?-L-arabinofuranosidase (CtGH43) from Clostridium thermocellum ATCC 27405.

Project description:The truncated carbohydrate-active enzyme belonging to family 43 glycoside hydrolase from Clostridium thermocellum (CtGH43) is an ?-L-arabinofuranosidase that in combination with endoxylanase leads to complete breakdown of L-arabinosyl-substituted xylans. The recombinant enzyme CtGH43 from C. thermocellum was overexpressed in Escherichia coli and purified by immobilized metal-ion affinity chromatography. The recombinant CtGH43 has a molecular mass of 35.86 kDa. Preliminary structural characterization was carried out on CtGH43 crystallized from different conditions, which gave either cube-shaped or brick-shaped crystals. These diffracted to a resolution of 1.65 Å for the cubic form and 1.1 Å for the monoclinic form. Molecular replacement was used to solve the CtGH43 structure.

| S-EPMC4014331 | biostudies-literature

The purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Clostridium botulinum.

Project description:In recent years, dihydrodipicolinate synthase (DHDPS; EC 4.2.1.52) has received considerable attention from both mechanistic and structural viewpoints. This enzyme, which is part of the diaminopimelate pathway leading to lysine, couples (S)-aspartate-beta-semialdehyde with pyruvate via a Schiff base to a conserved active-site lysine. In this paper, the expression, purification, crystallization and preliminary X-ray diffraction analysis of DHDPS from Clostridium botulinum, an important bacterial pathogen, are presented. The enzyme was crystallized in a number of forms, predominantly using PEG precipitants, with the best crystal diffracting to beyond 1.9 A resolution and displaying P4(2)2(1)2 symmetry. The unit-cell parameters were a = b = 92.9, c = 60.4 A. The crystal volume per protein weight (V(M)) was 2.07 A(3) Da(-1), with an estimated solvent content of 41%. The structure of the enzyme will help guide the design of novel therapeutics against the C. botulinum pathogen.

| S-EPMC2374160 | biostudies-literature

Crystallization and preliminary X-ray diffraction studies of Staphylococcus aureus homoserine dehydrogenase.

Project description:Staphylococcus aureus is a Gram-positive nosocomial pathogen. The prevalence of multidrug-resistant S. aureus strains in both hospital and community settings makes it imperative to characterize new drug targets to combat S. aureus infections. In this context, enzymes involved in cell-wall maintenance and essential amino-acid biosynthesis are significant drug targets. Homoserine dehydrogenase (HSD) is an oxidoreductase that is involved in the reversible conversion of L-aspartate semialdehyde to L-homoserine in a dinucleotide cofactor-dependent reduction reaction. HSD is thus a crucial intermediate enzyme linked to the biosynthesis of several essential amino acids such as lysine, methionine, isoleucine and threonine.

| S-EPMC3818036 | biostudies-literature

Crystallization and preliminary X-ray diffraction studies of La1 from Liocheles australasiae.

Project description:A novel scorpion venom peptide, La1 from Liocheles australasiae, with a molecular weight of 7.8 kDa, is presumed to possess a single von Willebrand factor type C (VWC) domain, a common protein module, based on the position of eight Cys residues in its sequence. The biological function of La1 is still unknown. Deciphering its three-dimensional structure will be helpful in understanding its biological function. La1 was crystallized by the sitting-drop vapour-diffusion method using magnesium sulfate as a precipitant. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a=63.0, b=30.2, c=32.3 Å, β=108.5°, and diffracted to 1.9 Å resolution. The calculated VM based on one molecule per asymmetric unit was 1.87 Å3 Da(-1). The solvent content was 34.1%.

| S-EPMC4089531 | 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