ABSTRACT
A large-scale programme has been embarked upon aiming towards the structural determination of conserved proteins from viruses infecting hyperthermophilic archaea. Here, the crystallization of protein 14 from the archaeal virus SIFV is reported. This protein, which contains 111 residues (MW 13 465 Da), was cloned and expressed in Escherichia coli with an N-terminal His(6) tag and purified to homogeneity. The tag was subsequently cleaved and the protein was crystallized using PEG 1000 or PEG 4000 as a precipitant. Large crystals were obtained of the native and the selenomethionine-labelled protein using sitting drops of 100-300 nl. Crystals belong to space group P6(2)22 or P6(4)22, with unit-cell parameters a = b = 68.1, c = 132.4 A. Diffraction data were collected to a maximum acceptable resolution of 2.95 and 3.20 A for the SeMet-labelled and native protein, respectively.
Subject(s)
Lipothrixviridae/chemistry , Sulfolobus/virology , Viral Proteins/chemistry , Cloning, Molecular , Crystallization , Sulfolobus/genetics , Viral Proteins/genetics , X-Ray Diffraction/methodsABSTRACT
The deblocking aminopeptidase (DAP) of Pyrococcus horikoshii is a hyperthermophilic exoprotease that cleaves the N-terminal amino acid of peptide substrates with a putative deblocking activity for acylated peptides. DAP has been found to be homologous to a tetrahedral aminopeptidase from the halophilic Haloarcula marismortui. The latter enzyme is a dodecameric complex and has been revealed to be a self-compartmentalized protease whose central cavity harbouring the catalytic site is accessible through several channels of different size, unlike all other known proteolytic complexes. Three paralogues of DAP have been identified in P. horikoshii, with about 40% identity between them. Each of them has been overexpressed in Escherichia coli, purified and crystallized in the native and selenomethionine-substituted states. The results indicate that they form two kinds of assemblies, of 12 and of 24 subunits, with a molecular weight of approximately 400 and approximately 800 kDa, respectively. Crystals of the different variants of DAP and in their different oligomeric states diffract up to a resolution of 3 A.
Subject(s)
Aminopeptidases/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Pyrococcus horikoshii/enzymology , Aminopeptidases/chemistry , Aminopeptidases/isolation & purification , Bacterial Proteins/isolation & purification , Escherichia coli/enzymology , Molecular Weight , Protein Subunits/chemistry , Protein Subunits/isolation & purification , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , X-Ray DiffractionABSTRACT
The xylanase inhibitor protein I (XIP-I) from wheat Triticum aestivum is the prototype of a novel class of cereal protein inhibitors that inhibit fungal xylanases belonging to glycoside hydrolase families 10 (GH10) and 11 (GH11). The crystal structures of XIP-I in complex with Aspergillus nidulans (GH10) and Penicillium funiculosum (GH11) xylanases have been solved at 1.7 and 2.5 A resolution, respectively. The inhibition strategy is novel because XIP-I possesses two independent enzyme-binding sites, allowing binding to two glycoside hydrolases that display a different fold. Inhibition of the GH11 xylanase is mediated by the insertion of an XIP-I Pi-shaped loop (Lalpha(4)beta(5)) into the enzyme active site, whereas residues in the helix alpha7 of XIP-I, pointing into the four central active site subsites, are mainly responsible for the reversible inactivation of GH10 xylanases. The XIP-I strategy for inhibition of xylanases involves substrate-mimetic contacts and interactions occluding the active site. The structural determinants of XIP-I specificity demonstrate that the inhibitor is able to interact with GH10 and GH11 xylanases of both fungal and bacterial origin. The biological role of the xylanase inhibitors is discussed in light of the present structural data.
Subject(s)
Plant Proteins/chemistry , Xylosidases/chemistry , Amino Acid Sequence , Aspergillus nidulans , Endo-1,4-beta Xylanases/antagonists & inhibitors , Endo-1,4-beta Xylanases/chemistry , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/metabolism , Fungal Proteins/antagonists & inhibitors , Fungal Proteins/chemistry , Models, Molecular , Molecular Sequence Data , Penicillium , Plant Proteins/metabolism , Protein Conformation , Protein Folding , Sequence Homology, Amino Acid , Structure-Activity Relationship , Substrate Specificity , Xylan Endo-1,3-beta-Xylosidase/antagonists & inhibitors , Xylan Endo-1,3-beta-Xylosidase/chemistry , Xylosidases/antagonists & inhibitorsABSTRACT
Major histocompatibility complex (MHC) molecules are heterodimeric cell-surface receptors that play a crucial role in the cellular immune response by presenting epitope peptides to T-cell antigen receptors (TCR). Although the structural basis of the peptide-MHC binding mechanism is becoming better understood, it is still difficult to predict a binding mode for an MHC of unknown structure. Therefore, as the first stage of a TCR-MHC interaction study, the crystal structures of the mouse H-2K(k) molecule in complex with both an octapeptide from Influenza A virus and a nonapeptide from simian virus SV40 were solved. Here, the expression, refolding, purification and crystallization of the two complexes are reported. For the H-2K(k)-HA(259-266) complex, crystals were obtained via an extensive screen using a nanodrop-dispensing robot and diffracted to 2.5 A resolution. For the H-2K(k)-SV40(560-568) complex, microscopic needles were initially obtained and their size was improved by macroseeding and a stepwise increase in precipitant concentration. Diffraction data to a resolution of 3.0 A were collected at a synchrotron facility.
Subject(s)
H-2 Antigens/chemistry , H-2 Antigens/metabolism , Peptide Fragments/chemistry , Peptide Fragments/metabolism , Protein Folding , Animals , Crystallization , Crystallography, X-Ray , Gene Expression , H-2 Antigens/genetics , Influenza A virus/chemistry , Mice , Peptide Fragments/genetics , Protein Binding , Protein Renaturation , Simian virus 40/chemistryABSTRACT
A novel class of proteinaceous inhibitors exhibiting specificity towards microbial xylanases has recently been discovered in cereals. The three-dimensional structure of xylanase inhibitor protein I (XIP-I) from wheat (Triticum aestivum, var. Soisson) was determined by X-ray crystallography at 1.8 A (1 A=0.1 nm) resolution. The inhibitor possesses a (beta/alpha)(8) barrel fold and has structural features typical of glycoside hydrolase family 18, namely two consensus regions, approximately corresponding to the third and fourth barrel strands, and two non-proline cis -peptide bonds, Ser(36)-Phe and Trp(256)-Asp (in XIP-I numbering). However, detailed structural analysis of XIP-I revealed several differences in the region homologous with the active site of chitinases. The catalytic glutamic acid residue of family 18 chitinases [Glu(127) in hevamine, a chitinase/lysozyme from the rubber tree (Hevea brasiliensis)] is conserved in the structure of the inhibitor (Glu(128)), but its side chain is fully engaged in salt bridges with two neighbouring arginine residues. Gly(81), located in subsite -1 of hevamine, where the reaction intermediate is formed, is replaced by Tyr(80) in XIP-I. The tyrosine side chain fills the subsite area and makes a strong hydrogen bond with the side chain of Glu(190) located at the opposite side of the cleft, preventing access of the substrate to the catalytic glutamic acid. The structural differences in the inhibitor cleft structure probably account for the lack of activity of XIP-I towards chitin.
