The COP9 complex is conserved between plants and mammals and is related to the 26S proteasome regulatory complex.

The COP9 complex, genetically identified in Arabidopsis as a repressor of photomorphogenesis, is composed of multiple subunits including COP9, FUS6 (also known as COP11) and the Arabidopsis JAB1 homolog 1 (AJH1) ([1-3]; unpublished observations). We have previously demonstrated the existence of the mammalian counterpart of the COP9 complex and purified the complex by conventional biochemical and immunoaffinity procedures [4]. Here, we report the molecular identities of all eight subunits of the mammalian COP9 complex. We show that the COP9 complex is highly conserved between mammals and higher plants, and probably among most multicellular eukaryotes. It is not present in the single-cell eukaryote Saccharomyces cerevisiae, however. All of the subunits of the COP9 complex contain structural features that are also present in the components of the proteasome regulatory complex and the translation initiation factor eIF3 complex. Six subunits of the COP9 complex have overall similarity with six distinct non-ATPase regulatory subunits of the 26S proteasome, suggesting that the COP9 complex and the proteasome regulatory complex are closely related in their evolutionary origin. Subunits of the COP9 complex include regulators of the Jun N-terminal kinase (JNK) and c-Jun, a nuclear hormone receptor binding protein and a cell-cycle regulator. This suggests that the COP9 complex is an important cellular regulator modulating multiple signaling pathways.

A DNA unwinding factor involved in DNA replication in cell-free extracts of Xenopus eggs.

BACKGROUND: Alteration of chromatin structure is a key step in various aspects of DNA metabolism. DNA unwinding factors such as the high mobility group (HMG) proteins are thought to play a general role in controlling chromatin structure and a specific role in controlling DNA replication. For instance, in the in vitro simian virus 40 replication system, minichromosomes containing HMG-17 replicate more efficiently than those without it, suggesting that HMG-17 enhances the rate of replication of a chromatin template by unfolding the higher-order chromatin structure. At present, however, only limited data suggest an involvement of DNA unwinding factors in DNA replication. RESULTS: We purified from Xenopus eggs a novel heterodimeric factor, termed DNA unwinding factor (DUF), that consists of 87 kDa and 140 kDa polypeptides. DUF unwinds closed-circular duplex DNA in the presence of topoisomerase I, but it does not possess a DNA gyrase activity: it does not introduce negative supercoils into DNA at the expense of ATP hydrolysis. Cloning and sequencing of the cDNAs encoding the two polypeptides revealed that the 87 kDa polypeptide is homologous to a mammalian HMG protein, T160/structure-specific recognition protein. The 140 kDa polypeptide is homologous to yeast Cdc68, a protein that controls the expression of several genes during the G1 phase of the cell cycle by modulating chromatin structure. Immunodepletion of DUF from Xenopus egg extracts drastically reduced the ability of the extract to replicate exogenously added sperm chromatin or plasmid DNA. CONCLUSIONS: We propose that DUF plays a role in DNA replication in Xenopus egg extracts.

CIRP2, a major cytoplasmic RNA-binding protein in Xenopus oocytes.

In an attempt to isolate mRNA-binding proteins we fractionated Xenopus oocyte lysate by oligo(dT)-cellulose chromatography. A 20 kDa protein was the major component of the eluate. cDNA cloning revealed that this protein is a Xenopus homolog of the cold-inducible RNA-binding protein (CIRP) which was originally identified in mammalian cells as a protein that is overexpressed upon a temperature downshift. This Xenopus protein, termed here xCIRP2, is highly expressed in ovary, testis and brain in adult Xenopus tissues. In oocytes it is predominantly localized in the cytoplasm. By biochemical fractionation we provide evidence that xCIRP2 is associated with ribosomes, suggesting that it participates in translational regulation in oocytes. Microinjection of labeled mRNA into oocytes followed by UV cross-linking of the oocyte lysate led to identification of two major RNA-binding activities. Immunoprecipitation of the RNA-binding proteins demonstrated that one is xCIRP2 and that the other contains FRGY2. FRGY2, which is one of the principal constituents of mRNA storage particles involved in translational masking of maternal mRNA, has an RNA-binding domain conserved to those of bacterial cold shock proteins. Possible implications of the highly abundant expression in oocytes of cold shock RNA-binding proteins of both eukaryotic and prokaryotic types are discussed.

Post-translational modification is essential for catalytic activity of nitrile hydratase.

Nitrile hydratase from Rhodococcus sp. N-771 is an alphabeta heterodimer with a nonheme ferric iron in the catalytic center. In the catalytic center, alphaCys112 and alphaCys114 are modified to a cysteine sulfinic acid (Cys-SO2H) and a cysteine sulfenic acid (Cys-SOH), respectively. To understand the function and the biogenic mechanism of these modified residues, we reconstituted the nitrile hydratase from recombinant unmodified subunits. The alphabeta complex reconstituted under argon exhibited no activity. However, it gradually gained the enzymatic activity through aerobic incubation. ESI-LC/MS analysis showed that the anaerobically reconstituted alphabeta complex did not have the modification of alphaCys112-SO2H and aerobic incubation induced the modification. The activity of the reconstituted alphabeta complex correlated with the amount of alphaCys112-SO2H. Furthermore, ESI-LC/MS analyses of the tryptic digest of the reconstituted complex, removed of ferric iron at low pH and carboxamidomethylated without reduction, suggested that alphaCys114 is modified to Cys-SOH together with the sulfinic acid modification of alphaCys112. These results suggest that alphaCys112 and alphaCys114 are spontaneously oxidized to Cys-SO2H and Cys-SOH, respectively, and alphaCys112-SO2H is responsible for the catalytic activity solely or in combination with alphaCys114-SOH.

In vitro growth ability and chemosensitivity of gastric and colorectal cancer cells assessed with the human tumour clonogenic assay and the thymidine incorporation assay.

A human tumour cloning assay (HTCA) has been performed on 191 samples of gastric and 152 samples of colorectal cancers, and a thymidine incorporation assay (TIA) on 178 samples of gastric and 109 samples of colorectal cancers. The rate of evaluable assays was significantly higher in the TIA than in the HTCA (P less than 0.01). In terms of in vitro growth potential in the two assays, gastric cancer cells were less active than the colorectal cancer cells (P less than 0.05). In frequency of in vitro sensitivity to drugs, gastric cancer was more chemosensitive than colorectal cancer in both assays. The in vitro/in vivo correlations of high resistance-predictive ratios and low sensitivity-predictive ratios were similar in both assays. The results indicate that the TIA is more applicable than the HTCA to screening of active agents against fresh gastrointestinal cancers.

Stage-specific modification of G protein beta subunits in rat placenta.

We previously analysed the plasma membrane proteins of rat placenta and prepared a database of 150 plasma membrane proteins, expressed in a stage-specific manner, utilizing two-dimensional gel electrophoresis (2D/E) [Mol. Cell. Endocrinol. 115(1995)149]. In this study, we focused on the proteins, tentatively named psL-I (MW 36.2 kDa, pI 5.3) and psL-II (35.9 kDa, 5.3), which were expressed mainly in late pregnancy. Close to psL-I and psL-II on 2D/E gels, we also recognized more abundant proteins [psC-I (36.2 kDa, 5.4) and psC-II (35.9 kDa, 5.4), respectively] arranged side by side with the same MW but different pI. Expression of psL-I and psL-II was detected only in junctional zone of placenta, whereas psC-I and psC-II were expressed in both labyrinth and junctional zones. In addition, psL-I and psL-II began to increase on day 16 of pregnancy and peaked at term, whereas expression of psC-I and psC-II was relatively constant. The analysis of these four proteins (psL-I, psL-II, psC-I and psC-II) by preparative 2D/E, peptide mapping, amino acid sequence and mass spectrometry (MALDI-TOF-MS) revealed that psC-I was a G protein beta1 subunit, and psC-II was a beta2 subunit, and showed that psL-I and psL-II were molecular modified forms of psC-I and psC-II, respectively. Expression of these G protein beta subunits (psL-I, psL-II, psC-I and psC-II) was also observed in rat choriocarcinoma cells, Rcho-1 cells. Expression of psC-I and psC-II was much higher than those of psL-I and psL-II, and their level was relatively constant regardless of the stage of differentiation in vitro. Interestingly, expression of psL-I and psL-II gradually increased in association with the differentiation. Since the expression of beta1 and beta2 subunit proteins and their mRNAs was constant during the process of differentiation in Rcho-1 cells, the expression of these lower pI forms of G protein subunits (psL-I and psL-II) was thought to be post-translationally regulated. In conclusion, there are modified forms of G protein beta1 and beta2 subunits, in the placenta and Rcho-1 cells, which are expressed in a pregnancy-stage or differentiation stage specific manner.

Characterization of a thermostable lysine-specific metalloendopeptidase from the fruiting bodies of a basidiomycete, Grifola frondosa.

A zinc-metalloendopeptidase, MEP, capable of catalyzing specific cleavage of acyl-lysine bonds (-X-Lys-) in polypeptides has been purified 212-fold in a yield of 24.7% from the fruiting bodies of Grifola frondosa, which is a popular edible mushroom called "MAITA-KE" in Japan. The purified enzyme consists of a single polypeptide chain with an apparent molecular mass of 20 kDa and a pI value of 7.46, contains 1 atom of zinc/molecule and can be inactivated with EDTA or 1,10-phenanthroline. Treatment of MEP with EDTA affords an apoenzyme, whose activity can be fully restored by the addition of Mn2+, Zn2+, Ca2+, or Co2+. Prominent features of MEP are its remarkable heat stability and its high affinity for beta-D-glucans and chitin. It hydrolyzes proteins maximally at pH 9-10, liberating only lysylpeptides. Polylysine and lysine copolymers with alanine, phenylalanine, or glutamic acid can serve as good substrates. Lysylalanine was liberated from bovine insulin and its oxidized B chain by the action of MEP. Mass spectrometric analysis by Frit-FAB MS of the fragments generated from horse heart cytochrome c presented unambiguous evidence to corroborate the specificity of MEP for acyl-lysine bonds.

A monoclonal antibody, 3A10, recognizes a specific amino acid sequence present on a series of developmentally expressed brain proteins.

Immunoblotting showed that a monoclonal antibody, 3A10, binds to a series of rat brain-specific antigens with molecular masses of 150-, 120-, 118-, 106-, 104-, 79-, and 77-kDa. The expression of 3A10 antigens is dependent on the developmental stage of the brain; only the 106-kDa antigen is detected during embryonic stages of rat brain development, while the expression of the remaining 6 antigens starts after birth and reaches a maximum during postnatal days 15-21. Detection of the 3A10 antigens in cultured neuronal and glial cells derived from cerebral cortices of rat brain at embryonic day 18 showed that the 77-, 79-, 106-, and 150-kDa antigens are specifically expressed in neuronal cells. The 77-kDa antigen was purified and identified as synapsin I by amino acid sequence analyses of the peptide fragments isolated after Achromobacter protease I treatment. During the isolation of 3A10-reactive proteins by immunological screening of cDNA libraries constructed from adult rat brain, we found that all of the 3A10-reactive clones contain nucleotide sequences encoding the unique amino acid sequence TRSP(S, R,G)P. Analyses of 3A10-binding to various synthetic peptides showed that the monoclonal antibody recognizes a specific conformational structure formed by either the TRSPXP sequence or similar amino acid sequences that are expressed on a series of developmentally expressed brain proteins.

Characterization of a novel fungal protein, p15, which induces neuronal differentiation of PC12 cells.

In our previous paper, we reported that a 15 kDa protein (p15) produced by a fungus, genus Helicosporium, enhanced NGF-induced neurite outgrowth from PC12 cells. Here we further characterized the actions of p15. The complete amino acid sequence of p15 was determined and it was shown to be a hydrophilic protein composed of 118 amino acid residues with two intramolecular disulfide bridges. p15-induced neurite outgrowth was blocked by the depletion of extracellular Ca(2+) in the culture medium and was significantly inhibited by L-type Ca(2+) channel inhibitor nicardipine. p15 stimulated Src kinase and MAPK activities, and neurite outgrowth was not observed in srcDN2, a dominant negative c-src(K295R)-expressing cell line, and was significantly reduced in RasN17-expressing cells. These results suggest that p15 stimulates neurite outgrowth through the potentiation of L-type Ca(2+) channels, thereby activating the Src-Ras-MAPK cascade.

Production of homo- and hetero-dimeric isozymes from two aldehyde oxidase genes of Arabidopsis thaliana.

Polyclonal antibodies were raised against synthetic peptides or recombinant polypeptides encoded by Arabidopsis atAO-1 and atAO-2 cDNAs, which have sequences similar to maize and animal aldehyde oxidase (AO) cDNAs. Anti-atAO-1 antibodies recognized AOalpha and AObeta among the three isoforms, AOalpha, AObeta, and AOgamma, detected in Arabidopsis seedlings after native PAGE, while anti-atAO-2 antibodies reacted with AObeta and AOgamma. The polypeptide specifically recognized by each antibody was collected as the Protein-A/IgG/antigen complex. The 150- and 145-kDa polypeptides were purified by SDS-PAGE and digested with Achromobacter Protease I. From the amino acid sequences and molecular masses of the derivative peptides, it was revealed that the 150- and 145-kDa polypeptides were the products of atAO-1 and atAO-2, respectively. Molecular masses of the native forms of AOalpha, AObeta, and AOgamma were estimated as approximately 290-300 kDa. These results suggest that AOalpha and AOgamma are homodimers consisting of atAO-1 and atAO-2 products, respectively, and that AObeta is a heterodimer of the atAO-1 and atAO-2 products.

Functional expression of nitrile hydratase in Escherichia coli: requirement of a nitrile hydratase activator and post-translational modification of a ligand cysteine.

The nitrile hydratase (NHase) from Rhodococcus sp. N-771 is a photoreactive enzyme that is inactivated on nitrosylation of the non-heme iron center and activated on photo-dissociation of nitric oxide (NO). The nitrile hydratase operon consists of six genes encoding NHase regulator 2, NHase regulator 1, amidase, NHase alpha subunit, NHase beta subunit and NHase activator. We overproduced the NHase in Escherichia coli using a T7 expression system. The NHase was functionally expressed in E. coli only when the NHase activator encoded downstream of the beta subunit gene was co-expressed and the transformant was grown at 30 degrees C or less. A ligand cysteine, alphaCys112, of the recombinant NHase was also post-translationally modified to a cysteine-sulfinic acid similar to for the native NHase. Although another modification of alphaCys114 could not be identified because of the instability under acidic conditions, the recombinant NHase could be reversibly inactivated by nitric oxide.

Possible prevention from the progression of cardiotoxicity in adriamycin-treated rabbits by coenzyme Q10.

The cumulative dose-dependent cardiotoxicity induced by doxorubicin (adriamycin, ADR) and its possible prevention by coenzyme Q10 (CoQ10) were studied in rabbits. In the group that received ADR alone, ADR dose-dependent electrocardiography (ECG) abnormalities and severe myocardial damage on electron microscopic examination were observed. In the group that received ADR + CoQ10, these alterations occurred in lesser degree, and ECG changes seemed to be improved. The results indicated that CoQ10 might prevent the progression of cardiotoxicity in ADR treated rabbits.

Isolation and characterization of calmodulin in the pheromone gland of the silkworm, Bombyx mori.

Production of the sex pheromone bombykol in the silkworm, Bombyx mori, is regulated by a neurohormone termed pheromone biosynthesis activating neuropeptide (PBAN). It has been suggested that the external signal of PBAN in this species is transmitted to the intracellular cascade reactions consisting of Ca2+/calmodulin (CaM) complex and phosphoprotein phosphatase. To demonstrate the molecular mechanisms regulated by PBAN, we attempted to characterize CaM in the pheromone gland of B. mori. By using ion-exchange and RP-HPLC, B. mori CaM was purified from the cytosolic fraction of the pheromone gland. The primary structure was deduced by composition/sequence analysis and mass spectrometric analysis of the fragment peptides obtained from enzymatic and chemical fragmentations. The amino acid sequence of B. mori CaM was identical with Drosophila CaM deduced from the CaM gene of D. melanogaster, suggesting that insects have well conserved the molecule of CaM.

Amino acid sequences of metalloendopeptidases specific for acyl-lysine bonds from Grifola frondosa and Pleurotus ostreatus fruiting bodies.

The complete amino acid sequences of two lysine-specific zinc metalloendopeptidases (EC 3.4.24), Grifola frondosa metalloendopeptidase (GFMEP) and Pleurotus ostreatus metalloendopeptidase (POMEP), from the fruiting bodies of these two edible mushrooms have been established based on the sequence information of the peptides generated from the reduced and alkylated GFMEP and POMEP by proteolytic digestions using GFMEP, trypsin, and other proteinases as well as by several chemical cleavages. From the sequences, it was found that GFMEP and POMEP were polypeptides composed of 167 and 168 amino acid residues, from which their molecular weights were calculated to be 18,040.5 and 17,921.3 in accord with the observed (M+H)+ values of 18,028 and 17,927, respectively, as determined by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Two disulfide bonds in GFMEP were found to link Cys5 to Cys75 and Cys77 to Cys97. An unusual post-translational modification of GFMEP was corroborated to be a partial attachment of a single mannose to Thr42. Comparison of the sequences revealed that overall identity between the enzymes was 61.3%. Although a highly homologous sequence was not found in sequence data bases except for a consensus zinc-binding sequence, HEXXH, both metalloendopeptidases somewhat resembled a family of metalloproteinases categorized as deuterolysin. These proteases together with GFMEP and POMEP do not have conserved third and/or fourth liganding amino acid residues seen in metzincin or thermolysin superfamily proteins and belong to a novel zinc metalloendopeptidase superfamily.

The complete amino acid sequences of two serine proteinase inhibitors from the fruiting bodies of a basidiomycete, Pleurotus ostreatus.

The complete amino acid sequences of two isomeric endogenous inhibitors, IA-1 and IA-2, both of which specifically inhibit an intracellular serine proteinase (proteinase A) purified from the fruiting bodies of a higher basidiomycete, Pleurotus ostreatus, were determined. Both inhibitors are acidic polypeptides with respective molecular masses of 8307 and 8244 Da, as determined by plasma desorption mass spectral analyses, and their N-terminal serine residue is blocked by acetylation. The fragments generated from the inhibitors by proteolytic and chemical cleavages were subjected to amino acid composition, sequence, and mass spectral analyses. The sequence and molecular mass information for the peptides established that the inhibitors both consisted of 76 amino acid residues and differed from each other in that aspartic acid and glutamic acid residues at residues 12 and 15 of IA-1 were replaced by glycine and aspartic acid in IA-2, respectively. The molecular masses of IA-1 and IA-2 were calculated to be 8309 and 8237, based on the sequence data. The action of carboxypeptidase Y on IA-1 resulted in a complete loss of the inhibitory activity along with successive release of glutamine and threonine from the C-terminus. Cyanogen bromide cleavage of Met38-Pro39 and Met41-Lys42 in IA-1 and hydroxylamine degradation of IA-2 completely abolished their inhibitory activity. These results suggest that the whole molecules of both inhibitors are essential to their inhibitory activities. Their structural resemblance to propeptides of subtilisin family proteinases revealed their mechanism of action.

An automated interpretation of MALDI/TOF postsource decay spectra of oligosaccharides. 1. Automated peak assignment.

A computer program has been developed that helps the interpretation of MALDI/TOF postsource decay (PSD) spectra of N-linked oligosaccharides of a protein. The program includes routines for automated peak assignment and generation of a simulated PSD spectrum. From a raw spectrum, peaks are assigned automatically; i.e., numbers of saccharide residues removed from the parent ion are calculated. If the structure of the oligosaccharide is known, a simulated PSD spectrum of the oligosaccharide will be generated. The simulated PSD spectrum helps interpretation of the observed spectrum. While, in a case where several candidate structures are given, one can narrow the field of plausible structures for the unknown oligosaccharide by comparing the observed spectrum with the simulated PSD spectra. Using a Pentium 233-MHz microprocessor, it takes only a few seconds to interpret a spectrum.

Cloning and molecular characterization of plant aldehyde oxidase.

Primary structural information of a plant aldehyde oxidase (AO), which was purified from maize coleoptiles using indole-3-acetaldehyde as a substrate, was obtained by sequencing a series of cleavage peptides, permitting the cloning of the corresponding cDNA (zmAO-1). The complete nucleotide sequence was determined; the deduced amino acid sequence encodes a protein of 1358 amino acid residues of Mr 146,681, which is consistent with the size of the AO monomeric subunit. There is a significant similarity with AO from mammals and xanthine dehydrogenases from various sources. The maize AO polypeptide contains consensus sequences for iron-sulfur centers and a putative molybdopterin cofactor-binding domain. In addition, another cDNA (zmAO-2), highly homologous to zmAO-1 at both the nucleotide and amino acid sequence levels, was cloned. zmAO-2 would encode a protein of 1349 amino acid residues of Mr 145,173 and has molecular characteristics similar to those of zmAO-1. zmAO-1 was expressed at a high level in roots, which was closely correlated with immunoblotting results using antiserum raised against the purified maize AO protein, whereas zmAO-2 was expressed at a higher level in coleoptiles than in roots. We propose each zmAO may have a unique function during plant development.

Molecular cloning of a novel sex pheromone responsible for the release of a different sex pheromone in Closterium peracerosum-strigosum-littorale complex.

A sex pheromone, protoplast-release-inducing protein (PR-IP) inducer, of the Closterium peracerosum-strigosum-littorale complex is known to induce the release of PR-IP, from mating-type plus (mt+) cells during sexual reproduction. The purified PR-IP inducer was treated with trypsin to obtain internal peptides for determination of partial amino acid sequences. Using these sequences, oligonucleotides were synthesized and used as primers for the combined reverse transcription-PCR. A 296 bp cDNA fragment was amplified, permitting the cloning of corresponding full length cDNA (CpPI; Closterium peracerosum-strigosum-littorale complex PR-IP inducer). The deduced amino acid sequence of CpPI encodes a protein of 212 amino acid residues of M(r) 23,071 whereas portion of the peptide secreted is predicted to have 142 amino acid residues of M(r) 15,717 and shows no significant similarity with known proteins. The predicted protein has three possible consensus sequences for asparagine-linked glycosylation site. The CpPI gene was expressed when mating-type minus (mt-) cells were incubated at a low cell density in the light. Nitrogen deprivation from the medium enhances expression of the CpPI gene. An analysis by genomic Southern hybridization revealed that the cDNA probe hybridized to several DNA fragments obtained from both the genome of mt- and mt+ cells. However, in mt- cells, transcripts for the PR-IP inducer could not be detected by Northern hybridization.

S-adenosyl-L-methionine:L-methionine S-methyltransferase from germinating barley. Purification and localization.

S-Adenosyl-L-methionine:L-methionine S-methyltransferase (MMT) catalyzes the synthesis of S-methyl-L-methionine (SMM) from L-methionine and S-adenosyl-L-methionine. SMM content increases during barley (Hordeum vulgare L.) germination. Elucidating the role of this compound is important from both a fundamental and a technological standpoint, because SMM is the precursor of dimethylsulfide, a biogenic source of atmospheric S and an undesired component in beer. We present a simple purification scheme for the MMT from barley consisting of 10% to 25% polyethylene glycol fractionation, anion-exchange chromatography on diethylaminoethyl-Sepharose, and affinity chromatography on adenosine-agarose. A final activity yield of 23% and a 2765-fold purification factor were obtained. After digestion of the protein with protease, the amino acid sequence of a major peptide was determined and used to produce a synthetic peptide. A polyclonal antibody was raised against this synthetic peptide conjugated to activated keyhole limpet hemocyanin. The antibody recognized the 115-kD denatured MMT protein and native MMT. During barley germination, both the specific activity and the amount of MMT protein increased. MMT-specific activity was found to be higher in the root and shoot than in the endosperm. MMT could be localized by an immunohistochemical approach in the shoot, scutellum, and aleurone cells but not in the root or endosperm (including aleurone).

Tertiary and quaternary structures of photoreactive Fe-type nitrile hydratase from Rhodococcus sp. N-771: roles of hydration water molecules in stabilizing the structures and the structural origin of the substrate specificity of the enzyme.

The crystal structure analysis of the Fe-type nitrile hydratase from Rhodococcus sp. N-771 revealed the unique structure of the enzyme composed of the alpha- and beta-subunits and the unprecedented structure of the non-heme iron active center [Nagashima, S., et al. (1998) Nat. Struct. Biol. 5, 347-351]. A number of hydration water molecules were identified both in the interior and at the exterior of the enzyme. The study presented here investigated the roles of the hydration water molecules in stabilizing the tertiary and the quaternary structures of the enzyme, based on the crystal structure and the results from a laser light scattering experiment for the enzyme in solution. Seventy-six hydration water molecules between the two subunits significantly contribute to the alphabeta heterodimer formation by making up the surface shape, forming extensive networks of hydrogen bonds, and moderating the surface charge of the beta-subunit. In particular, 20 hydration water molecules form the extensive networks of hydrogen bonds stabilizing the unique structure of the active center. The amino acid residues hydrogen-bonded to those hydration water molecules are highly conserved among all known nitrile hydratases and even in the homologous enzyme, thiocyanate hydrolase, suggesting the structural conservation of the water molecules in the NHase family. The crystallographic asymmetric unit contained two heterodimers connected by 50 hydration water molecules. The heterotetramer formation in crystallization was clearly explained by the concentration-dependent aggregation state of NHase found in the light scattering measurement. The measurement proved that the dimer-tetramer equilibrium shifted toward the heterotetramer dominant state in the concentration range of 10(-2)-1.0 mg/mL. In the tetramer dominant state, 50 water molecules likely glue the two heterodimers together as observed in the crystal structure. Because NHase exhibits a high abundance in bacterial cells, the result suggests that the heterotetramer is physiologically relevant. In addition, it was revealed that the substrate specificity of this enzyme, recognizing small aliphatic substrates rather than aromatic ones, came from the narrowness of the entrance channel from the bulk solvent to the active center. This finding may give a clue for changing the substrate specificity of the enzyme. Under the crystallization condition described here, one 1,4-dioxane molecule plugged the channel. Through spectroscopic and crystallographic experiments, we found that the molecule prevented the dissociation of the endogenous NO molecule from the active center even when the crystal was exposed to light.