T4 endonuclease V is a DNA repair enzyme from bacteriophage T4 that catalyzes the first reaction step of the pyrimidine dimer-specific base excision repair pathway. The crystal structure of this enzyme complexed with a duplex DNA substrate, containing a thymine dimer, has been determined at 2.75 A resolution. The atomic structure of the complex reveals the unique conformation of the DNA duplex, which exhibits a sharp kink with a 60 degree inclination at the central thymine dimer. The adenine base complementary to the 5' side of the thymine dimer is completely flipped out of the DNA duplex and trapped in a cavity on the protein surface. These structural features allow an understanding of the catalytic mechanism and implicate a general mechanism of how other repair enzymes recognize damaged DNA duplexes.
The crystal structure of a microbial transglutaminase from Streptoverticillium mobaraense has been determined at 2.4 Å resolution. The protein folds into a platelike shape, and has one deep cleft at the edge of the molecule. Its overall structure is completely different from that of the factor XIII-like transglutaminase, which possesses a cysteine protease-like catalytic triad. superimpose well on the catalytic triad "Cys-HisAsp" of the factor XIII-like transglutaminase, in this order. The secondary structure frameworks around these residues are also similar to each other. These results imply that both transglutaminases are related by convergent evolution; however, the microbial transglutaminase has developed a novel catalytic mechanism specialized for the cross-linking reaction. The structure accounts well for the catalytic mechanism, in which Asp 255 is considered to be enzymatically essential, as well as for the causes of the higher reaction rate, the broader substrate specificity, and the lower deamidation activity of this enzyme.Transglutaminase (TGase 1 ; protein-glutamine ␥-glutamyltransferase, EC 2.3.2.13) catalyzes an acyl transfer reaction in which the ␥-carboxyamide groups of peptide-bound glutamine residues act as the acyl donors. The most common acyl acceptors of TGase are the ⑀-amino groups of lysine residues within peptides or the primary amino groups of some naturally occurring polyamines (1, 2). When lysine residues in proteins serve as acyl acceptors, intermolecular or intramolecular ⑀-(␥-glutamyl)lysine bonds are formed, resulting in the polymerization of proteins.TGases are widely distributed in various organisms, including vertebrates (3-7), invertebrates (8, 9), mollusks (10), plants (11), and microorganisms (12). Among these TGases, the human blood coagulation factor XIII has been most characterized (13)(14)(15)(16)(17)(18). By catalyzing the cross-linking between fibrin molecules, factor XIII forms fibrin clots for hemostasis and heals a wound. The crystal structure of human factor XIII has been determined, revealing that it consists of four domains with a cysteine protease-like active site (19 -22). Many TGases are homologous to human factor XIII and share the common feature of Ca 2ϩ -dependent catalytic activity (3-8). A tissue-type TGase from red sea bream liver (fish-derived TGase (FTG)) is an example of such factor XIII-like TGases and shows 33% sequence homology to human factor XIII (7). The crystal structure of FTG has also been determined (23). The overall and active site structures of FTG are essentially similar to those of human factor XIII.A microbial TGase (MTG) has been isolated from the culture medium of Streptoverticillium sp. S-8112 (24), which has been identified as a variant of Sv. mobaraense. This enzyme is the first TGase obtained from a nonmammalian source. Thus far, few TGases have been identified from microorganisms, particularly from Streptoverticillium species (25). Although the physiological role of MTG is still unknown, this protein is secreted from the cytoplas...
Three mutants of Escherichia coli ribonuclease HI, in which an invariant acidic residue Asp134 was replaced, were crystallized, and their three-dimensional structures were determined by X-ray crystallography. The D134A mutant is completely inactive, whereas the other two mutants, D134H and D134N, retain 59 and 90% activities relative to the wild-type, respectively. The overall structures of these three mutant proteins are identical with that of the wild-type enzyme, except for local conformational changes of the flexible loops. The ribonuclease H family has a common active site, which is composed of four invariant acidic residues (Asp10, Glu48, Asp70 and Asp134 in E.coli ribonuclease HI), and their relative positions in the mutants, even including the side-chain atoms, are almost the same as those in the wild-type. The positions of the delta-polar atoms at residue 134 in the wild-type, as well as D134H and D134N, coincide well with each other. They are located near the imidazole side chain of His124, which is assumed to participate in the catalytic reaction, in addition to the four invariant acidic residues. Combined with the pH profiles of the enzymatic activities of the two other mutants, H124A and H124A/D134N, the crystallographic results allow us to propose a new catalytic mechanism of ribonuclease H, which includes the roles for Asp134 and His124.
Edited by Judit OvádiKeywords: Phosphoketolase Thiamine diphosphate Bifidobacterium longum a b s t r a c tThe crystal structure of Bifidobacterium longum phosphoketolase, a thiamine diphosphate (TPP) dependent enzyme, has been determined at 2.2 Å resolution. The enzyme is a dimer with the active sites located at the interface between the two identical subunits with molecular mass of 92.5 kDa. The bound TPP is almost completely shielded from solvent except for the catalytically important C2-carbon of the thiazolium ring, which can be accessed by a substrate sugar through a narrow funnel-shaped channel. In silico docking studies of B. longum phosphoketolase with its substrate enable us to propose a model for substrate binding. Structured summary:MINT-7985878: PKT (uniprotkb:Q6R2Q7) and PKT (uniprotkb:Q6R2Q7) bind (MI:0407) by X-ray crystallography (MI:0114)
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