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Bacillus circulans chitinase A1 (ChiA1) has a deep substrate-binding cleft on top of its (beta/alpha)8-barrel catalytic domain and an interaction between the aromatic residues in this cleft and bound oligosaccharide has been suggested. To study the roles of these aromatic residues, especially in crystalline-chitin hydrolysis, site-directed mutagenesis of these residues was carried out. Y56A and W53A mutations at subsites -5 and -3, respectively, selectively decreased the hydrolysing activity against highly crystalline beta-chitin. W164A and W285A mutations at subsites +1 and +2, respectively, decreased the hydrolysing activity against crystalline beta-chitin and colloidal chitin, but enhanced the activities against soluble substrates. These mutations increased the K(m)-value when reduced (GlcNAc)5 (where GlcNAc is N -acetylglucosamine) was used as the substrate, but decreased substrate inhibition observed with wild-type ChiA1 at higher concentrations of this substrate. In contrast with the selective effect of the other mutations, mutations of W433 and Y279 at subsite -1 decreased the hydrolysing activity drastically against all substrates and reduced the kcat-value, measured with 4-methylumbelliferyl chitotrioside to 0.022% and 0.59% respectively. From these observations, it was concluded that residues Y56 and W53 are only essential for crystalline-chitin hydrolysis. W164 and W285 are very important for crystalline-chitin hydrolysis and also participate in hydrolysis of other substrates. W433 and Y279 are both essential for catalytic reaction as predicted from the structure.

Functional investigation of the proposed dehydratase domain of ATX, a 6-methylsalicylic acid synthase from Aspergillus terreus, revealed that the domain is not involved in dehydration of the ␤-hydroxytriketide intermediate tethered on the acyl carrier protein but catalyzes thioester hydrolysis to release the product from the acyl carrier protein. Thus, we renamed this domain the thioester hydrolase (TH) domain. The intermediate bound to the TH domain of mutant H972A formed in the presence of NADPH was released as 6-methylsalicylic acid by both the intact ATX and by THID (a 541-amino acid region containing TH domain and its downstream) protein, in trans. Furthermore, THID showed a catalytic activity to hydrolyze a model substrate, 6-methylsalicylic acid-N-acetylcysteamine. The TH domain is the first example of a product-releasing domain that is located in the middle of a multidomain iterative type I polyketide synthase. Moreover, it is functionally different from serine protease-type thioesterase domains of iterative type I polyketide synthases.Iterative type I polyketide synthases (iPKSs) 3 are large multifunctional enzymes consisting of the minimum catalytic domains for PKS reactions, the ␤-ketoacyl synthase (KS), acyl transferase (AT) and acyl carrier protein (ACP) domains, and additional domains such as a ketoreductase (KR), dehydratase (DH), enoylreductase (ER), methyltransferase, and thioesterase (TE) domain. Through iterative use of these domains in a programmed manner, each iPKS produces its specific polyketide product. However, little is known how iPKSs control their reactions (1).6-Methylsalicylic acid synthase (MSAS) was the first PKS to be purified and the first fungal iPKS whose gene was cloned (2-6). A conserved domain search indicated that MSAS consists of KS, AT, DH, KR, and ACP domains (5, 7). These domains of MSAS are thought to catalyze a series of programmed reactions, Claisen condensations, reduction, dehydration, cyclization, and product release (Fig. 1).Because MSAS is one of the simplest iPKSs, we have been studying its catalytic mechanism using ATX cloned from Aspergillus terreus (8). We previously carried out the expression of catalytic domain mutants of ATX in yeast. The KS mutant (KSm), AT domain mutant (ATm), and ACP mutant (ACPm) lost 6-methylsalicylic acid (6MSA) production, and the KR domain mutant (KRm) produced triacetic acid lactone as reported (9).The DH domain of ATX was assigned by comparison of secondary structural elements predicted by PredictProtein with discrete DHs of type II fatty acid synthase (FAS) from Escherichia coli (10). The conserved DH domain motif, HXXXGXXXXP, has been identified in FAS DH, in which the histidine residue is a catalytic residue for dehydration, (11) and the corresponding sequence H 972 XXXGXXXXP 981 was found in ATX. This His 972 is crucial for ATX reaction as indicated by our previous result that the ATX H972A mutant (DHm) did not give any product, such as the ␤-hydroxy triketide (9).Because MSAS has no apparent TE domain, it has been one of...

Fusobacterium nucleatum produces a large amount of the toxic metabolite hydrogen sulfide in the oral cavity. Here, we report the molecular basis of F. nucleatum H2S production, which is associated with two different enzymes: the previously reported Cdl (Fn1220) and the newly identified Lcd (Fn0625). SDS-PAGE analysis with activity staining revealed that crude enzyme extracts from F. nucleatum ATCC 25586 contained three major H2S-producing proteins. Two of the proteins with low molecular masses migrated similarly to purified Fn0625 and Fn1220. Their kinetic values suggested that Fn0625 had a lower enzymic capacity to produce H2S from l-cysteine (∼30 %) than Fn1220. The Fn0625 protein degraded a variety of substrates containing βC–S linkages to produce ammonia, pyruvate and sulfur-containing products. Unlike Fn0625, Fn1220 produced neither pyruvate nor ammonia from l-cysteine. Reversed-phase HPLC separation and mass spectrometry showed that incubation of l-cysteine with Fn1220 produced H2S and an uncommon amino acid, lanthionine, which is a natural constituent of the peptidoglycans of F. nucleatum ATCC 25586. In contrast, most of the sulfur-containing substrates tested, except l-cysteine, were not used by Fn1220. Real-time PCR analysis demonstrated that the fn1220 gene showed several-fold higher expression than fn0625 and housekeeping genes in exponential-phase cultures of F. nucleatum. Thus, we conclude that Fn0625 and Fn1220 produce H2S in distinct manners: Fn0625 carries out β-elimination of l-cysteine to produce H2S, pyruvate and ammonia, whereas Fn1220 catalyses the β-replacement of l-cysteine to produce H2S and lanthionine, the latter of which may be used for peptidoglycan formation in F. nucleatum.

The rice class I chitinase OsChia1b, also referred to as RCC2 or Cht‐2, is composed of an N‐terminal chitin‐binding domain (ChBD) and a C‐terminal catalytic domain (CatD), which are connected by a proline‐ and threonine‐rich linker peptide. Because of the ability to inhibit fungal growth, the OsChia1b gene has been used to produce transgenic plants with enhanced disease resistance. As an initial step toward elucidating the mechanism of hydrolytic action and antifungal activity, the full‐length structure of OsChia1b was analyzed by X‐ray crystallography and small‐angle X‐ray scattering (SAXS). We determined the crystal structure of full‐length OsChia1b at 2.00‐Å resolution, but there are two possibilities for a biological molecule with and without interdomain contacts. The SAXS data showed an extended structure of OsChia1b in solution compared to that in the crystal form. This extension could be caused by the conformational flexibility of the linker. A docking simulation of ChBD with tri‐N‐acetylchitotriose exhibited a similar binding mode to the one observed in the crystal structure of a two‐domain plant lectin complexed with a chitooligosaccharide. A hypothetical model based on the binding mode suggested that ChBD is unsuitable for binding to crystalline α‐chitin, which is a major component of fungal cell walls because of its collisions with the chitin chains on the flat surface of α‐chitin. This model also indicates the difference in the binding specificity of plant and bacterial ChBDs of GH19 chitinases, which contribute to antifungal activity. Proteins 2010. © 2010 Wiley‐Liss,Inc.