β-N-acetylhexosaminidase from the fungus Aspergillus oryzae is a secreted extracellular enzyme that cleaves chitobiose into constituent monosaccharides. It belongs to the GH 20 glycoside hydrolase family and consists of two N-glycosylated catalytic cores noncovalently associated with two 10-kDa O-glycosylated propeptides. We used X-ray diffraction and mass spectrometry to determine the structure of A. oryzae β-N-acetylhexosaminidase isolated from its natural source. The three-dimensional structure determined and refined to a resolution of 2.3 Å revealed that this enzyme is active as a uniquely tight dimeric assembly further stabilized by N- and O-glycosylation. The propeptide from one subunit forms extensive noncovalent interactions with the catalytic core of the second subunit in the dimer, and this chain swap suggests the distinctive structural mechanism of the enzyme's activation. Unique structural features of β-N-acetylhexosaminidase from A. oryzae define a very stable and robust framework suitable for biotechnological applications. The crystal structure reported here provides structural insights into the enzyme architecture as well as the detailed configuration of the active site. These insights can be applied to rational enzyme engineering. DATABASE: Structural data are available in the PDB database under the accession number 5OAR. ENZYME: β-N-acetylhexosaminidase (EC 3.2.1.52).
- MeSH
- Aspergillus oryzae enzymologie MeSH
- beta-N-acetylhexosaminidasy chemie metabolismus MeSH
- dimerizace MeSH
- fungální proteiny chemie metabolismus MeSH
- G(M2) aktivátorový protein chemie metabolismus MeSH
- G(M2) gangliosid chemie metabolismus MeSH
- glykosylace MeSH
- interakční proteinové domény a motivy MeSH
- katalytická doména MeSH
- konzervovaná sekvence MeSH
- krystalografie rentgenová MeSH
- ligandy MeSH
- molekulární modely * MeSH
- posttranslační úpravy proteinů MeSH
- prekurzory enzymů chemie metabolismus MeSH
- sekvence aminokyselin MeSH
- sekvenční seřazení MeSH
- stabilita proteinů MeSH
- strukturní homologie proteinů MeSH
- substrátová specifita MeSH
- vazebná místa MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
α-L-Rhamnosidases cleave terminal nonreducing α-L-rhamnosyl residues from many natural rhamnoglycosides. This makes them catalysts of interest for various biotechnological applications. The X-ray structure of the GH78 family α-L-rhamnosidase from Aspergillus terreus has been determined at 1.38 Å resolution using the sulfur single-wavelength anomalous dispersion phasing method. The protein was isolated from its natural source in the native glycosylated form, and the active site contained a glucose molecule, probably from the growth medium. In addition to its catalytic domain, the α-L-rhamnosidase from A. terreus contains four accessory domains of unknown function. The structural data suggest that two of these accessory domains, E and F, might play a role in stabilizing the aglycon portion of the bound substrate.
UNLABELLED: Deoxyribonucleoside regulator (DeoR) from Bacillus subtilis negatively regulates expression of enzymes involved in the catabolism of deoxyribonucleosides and deoxyribose. The DeoR protein is homologous to the sorbitol operon regulator family of metabolic regulators and comprises an N-terminal DNA-binding domain and a C-terminal effector-binding domain. We have determined the crystal structure of the effector-binding domain of DeoR (C-DeoR) in free form and in covalent complex with its effector deoxyribose-5-phosphate (dR5P). This is the first case of a covalently attached effector molecule captured in the structure of a bacterial transcriptional regulator. The dR5P molecule is attached through a Schiff base linkage to residue Lys141. The crucial role of Lys141 in effector binding was confirmed by mutational analysis and mass spectrometry of Schiff base adducts formed in solution. Structural analyses of the free and effector-bound C-DeoR structures provided a structural explanation for the mechanism of DeoR function as a molecular switch. DATABASES: Atomic coordinates and structure factors for crystal structures of free C-DeoR and the covalent Schiff base complex of C-DeoR with dR5P have been deposited in the Protein Data Bank with accession codes 4OQQ and 4OQP, respectively. STRUCTURED DIGITAL ABSTRACT: C-DeoR and C-DeoR bind by x-ray crystallography (View interaction) DeoR and DeoR bind by molecular sieving (1, 2).
- MeSH
- Bacillus subtilis * MeSH
- bakteriální proteiny chemie genetika MeSH
- krystalografie rentgenová MeSH
- kvarterní struktura proteinů MeSH
- molekulární modely MeSH
- multimerizace proteinu MeSH
- mutageneze cílená MeSH
- represorové proteiny chemie genetika MeSH
- roztoky MeSH
- Schiffovy báze chemie MeSH
- sekundární struktura proteinů MeSH
- sekvence aminokyselin MeSH
- strukturní homologie proteinů MeSH
- substituce aminokyselin MeSH
- terciární struktura proteinů MeSH
- vazba proteinů MeSH
- vazebná místa MeSH
- vodíková vazba MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
In Bacillus subtilis, the arabinose repressor AraR negatively controls the expression of genes in the metabolic pathway of arabinose-containing polysaccharides. The protein is composed of two domains of different phylogenetic origin and function: an N-terminal DNA-binding domain belonging to the GntR family and a C-terminal effector-binding domain that shows similarity to members of the GalR/LacI family. The crystal structure of the C-terminal effector-binding domain of AraR in complex with the effector L-arabinose has been determined at 2.2 Å resolution. The L-arabinose binding affinity was characterized by isothermal titration calorimetry and differential scanning fluorimetry; the K(d) value was 8.4 ± 0.4 µM. The effect of L-arabinose on the protein oligomeric state was investigated in solution and detailed analysis of the crystal identified a dimer organization which is distinctive from that of other members of the GalR/LacI family.
- MeSH
- arabinosa metabolismus MeSH
- Bacillus subtilis chemie metabolismus MeSH
- bakteriální proteiny chemie metabolismus MeSH
- krystalografie rentgenová MeSH
- molekulární modely MeSH
- represorové proteiny chemie metabolismus MeSH
- terciární struktura proteinů MeSH
- vazba proteinů MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
HIV protease (PR) represents a prime target for rational drug design, and protease inhibitors (PI) are powerful antiviral drugs. Most of the current PIs are pseudopeptide compounds with limited bioavailability and stability, and their use is compromised by high costs, side effects, and development of resistant strains. In our search for novel PI structures, we have identified a group of inorganic compounds, icosahedral metallacarboranes, as candidates for a novel class of nonpeptidic PIs. Here, we report the potent, specific, and selective competitive inhibition of HIV PR by substituted metallacarboranes. The most active compound, sodium hydrogen butylimino bis-8,8-[5-(3-oxa-pentoxy)-3-cobalt bis(1,2-dicarbollide)]di-ate, exhibited a K(i) value of 2.2 nM and a submicromolar EC(50) in antiviral tests, showed no toxicity in tissue culture, weakly inhibited human cathepsin D and pepsin, and was inactive against trypsin, papain, and amylase. The structure of the parent cobalt bis(1,2-dicarbollide) in complex with HIV PR was determined at 2.15 A resolution by protein crystallography and represents the first carborane-protein complex structure determined. It shows the following mode of PR inhibition: two molecules of the parent compound bind to the hydrophobic pockets in the flap-proximal region of the S3 and S3' subsites of PR. We suggest, therefore, that these compounds block flap closure in addition to filling the corresponding binding pockets as conventional PIs. This type of binding and inhibition, chemical and biological stability, low toxicity, and the possibility to introduce various modifications make boron clusters attractive pharmacophores for potent and specific enzyme inhibition.
- MeSH
- aspartátové endopeptidasy chemie MeSH
- borany farmakologie chemická syntéza chemie MeSH
- financování organizované MeSH
- HIV-proteasa chemie MeSH
- inhibitory HIV-proteasy farmakologie chemická syntéza chemie MeSH
- krystalografie rentgenová MeSH
- kvantitativní vztahy mezi strukturou a aktivitou MeSH
- racionální návrh léčiv MeSH
