Three-dimensional Structure and Substrate Binding of Bacillus stearothermophilus Neopullulanase

Hondoh, Hironori; Kuriki, Takashi; Matsuura, Yoshiki

doi:10.1016/s0022-2836(02)01402-x

Cited by 132 publications

(110 citation statements)

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“…Examination of the finished genomes also reveals other likely genes and clusters devoted to plant degradation. Orthologues of a well-studied neopullulanase (Hondoh et al, 2003) are encoded within an apparent pullulan or starch utilization cluster found in eight of the ten genomes (Table 1 and Table S3). A previously studied system (Lai & Ingram, 1993) for the uptake and utilization of cellobiose, a disaccharide produced from partial cellulose hydrolysis, is found in four of the genomes, while a five-gene cluster highly similar to a well-characterized B. subtilis glucomannan utilization operon (Sadaie et al, 2008) is found in nine of the genomes.…”

Section: Lessons From Genomesmentioning

confidence: 99%

The Geobacillus paradox: why is a thermophilic bacterial genus so prevalent on a mesophilic planet?

2014

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The genus Geobacillus comprises endospore-forming obligate thermophiles. These bacteria have been isolated from cool soils and even cold ocean sediments in anomalously high numbers, given that the ambient temperatures are significantly below their minimum requirement for growth. Geobacilli are active in environments such as hot plant composts, however, and examination of their genome sequences reveals that they are endowed with a battery of sensors, transporters and enzymes dedicated to hydrolysing plant polysaccharides. Although they appear to be relatively minor members of the plant biomass-degrading microbial community, Geobacillus bacteria have achieved a significant population with a worldwide distribution, probably in large part due to adaptive features of their spores. First, their morphology and resistance properties enable them to be mobilized in the atmosphere and transported long distances. Second, their longevity, which in theory may be extreme, enables them to lie quiescent but viable for long periods of time, accumulating gradually over time to achieve surprisingly high population densities. Introduction: an environmental enigmaGeobacillus bacteria are rod-shaped, aerobic or facultatively anaerobic, endospore-forming microbes. Depending on the strain, the temperature range for growth can extend as low as 35 u C or as high as 80 u C. But for most isolates, temperatures between about 45 and 70 u C are required (Nazina et al., 2001). These characteristics make Geobacillus bacteria (geobacilli) attractive to the biotechnology industry as sources of thermostable enzymes (de Champdoré et al., 2007; Karagüler et al., 2007), as platforms for biofuel production (Cripps et al., 2009;Taylor et al., 2009) and as potential components of bioremediation strategies (Markossian et al., 2000;Obojska et al., 2002;Perfumo et al., 2007). Obligate thermophiles, however, face a significant challenge outside the lab: they must survive on a planet with an average annual land surface temperature that has only ranged between 7 and 10 uC over the past three centuries (Rohde et al., 2013). It would be logical to assume, then, that Geobacillus would only be found in substantial numbers in the warmest regions of the planet, such as equatorial deserts or naturally occurring geothermal and hydrothermal hotspots. The truth, however, is rather more complicated.As Fig. 1 illustrates, people have been able to detect Geobacillus nearly everywhere they have thought to look. (This figure is based on a survey of 146 mostly recent references describing the isolation of Geobacillus in natural or human-made environments; for full details, see Table S1, available in Microbiology Online.) One can see at a glance that these bacteria have been isolated from sources on all seven continents as well as the Pacific Ocean and the Mediterranean Sea. What may not be obvious from a twodimensional map is that there has been much diversity in the third dimension as well. Geobacillus has been isolated from the Bolivian Andes at an altitude of 3653 m (Ma...

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Section: Lessons From Genomesmentioning

confidence: 99%

The Geobacillus paradox: why is a thermophilic bacterial genus so prevalent on a mesophilic planet?

2014

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“…sp. IM6501 maltogenic ␣-amylase (7), Bacillus stearothermophilus Neopullulanase (8), and Flavobacterium cyclomaltodextrinase (9), which can hydrolyze CDs as well as TVAII, have been reported. These x-ray structures showed that all of them have an additional domain with a distorted ␤-barrel structure to three ␣-amylase-conserved domains (10).…”

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confidence: 99%

Complex Structures of Thermoactinomyces vulgaris R-47 α-Amylase 2 with Acarbose and Cyclodextrins Demonstrate the Multiple Substrate Recognition Mechanism

Ohtaki

Mizuno

Tonozuka

et al. 2004

Journal of Biological Chemistry

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Thermoactinomyces vulgaris R-47 ␣-amylase 2 (TVAII) has the unique ability to hydrolyze cyclodextrins (CDs), with various sized cavities, as well as starch. To understand the relationship between structure and substrate specificity, x-ray structures of a TVAII-acarbose complex and inactive mutant TVAII (D325N/D421N)/␣-, ␤-and ␥-CDs complexes were determined at resolutions of 2.9, 2.9, 2.8, and 3.1 Å, respectively. In all complexes, the interactions between ligands and enzymes at subsites ؊1, ؊2, and ؊3 were almost the same, but striking differences in the catalytic site structure were found at subsites ؉1 and ؉2, where Trp 356 and Tyr 374 changed the conformation of the side chain depending on the structure and size of the ligands. Trp 356 and Tyr 374 are thought to be responsible for the multiple substraterecognition mechanism of TVAII, providing the unique substrate specificity. In the ␤-CD complex, the ␤-CD maintains a regular conical structure, making it difficult for Glu 354 to protonate the O-4 atom at the hydrolyzing site as a previously proposed hydrolyzing mechanism of ␣-amylase. From the x-ray structures, it is suggested that the protonation of the O-4 atom is possibly carried out via a hydrogen atom of the inter-glucose hydrogen bond at the hydrolyzing site.

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“…Residues corresponding to Trp238 of SMDG are shown in the amino acid sequence alignment of GH family 13 enzyme representatives (Table 2). Several GH family 13 enzymes, including barley high pI α-amylase (Kadziola et al 1998), Geobacillus stearothermophilus neopullulanase (Hondoh et al 2003), and Thermoactinomyces vulgaris R-47 α-amylase II (TVAII; Yokota et al 2001), also have a tryptophan at the corresponding position (Table 2), and these residues form a stacking interaction with their substrates or analogues at subsite +2 (or at subsite +1 in TVAII) in the solved three-dimensional structures. In CGTase, an aromatic amino acid residue, phenylalanine, is in the corresponding position and contributes to high transglycosylation activity through a stacking interaction in subsite +2 (van der Veen et al 2001).…”

Section: Enzymementioning

confidence: 99%

Structure-function relationship of substrate length specificity of dextran glucosidase from Streptococcus mutans

et al. 2008

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Dextran glucosidase from Streptococcus mutans (SMDG), an exo-type glucosidase of glycoside hydrolase (GH) family 13, specifically hydrolyzes an α-1,6-glucosidic linkage at the non-reducing ends of isomaltooligosaccharides and dextran. SMDG shows the highest sequence similarity to oligo-1,6-glucosidases (O16Gs) among GH family 13 enzymes, but these enzymes are obviously different in terms of substrate chain length specificity. SMDG efficiently hydrolyzes both short-and long-chain substrates, while O16G acts on only short-chain substrates. We focused on this difference in substrate specificity between SMDG and O16G, and elucidated the structure-function relationship of substrate chain length specificity in SMDG. Crystal structure analysis revealed that SMDG consists of three domains, A, B, and C, which are commonly found in other GH family 13 enzymes. The structural comparison between SMDG and O16G from Bacillus cereus indicated that Trp238, spanning subsites +1 and +2, and short β → α loop 4, are characteristic of SMDG, and these structural elements are predicted to be important for high activity toward long-chain substrates. The substrate size preference of SMDG was kinetically analyzed using two mutants: (i) Trp238 was replaced by a smaller amino acid, alanine, asparagine or proline; and (ii) short β → α loop 4 was exchanged with the corresponding loop of O16G. Mutant enzymes showed lower preference for long-chain substrates than wild-type enzyme, indicating that these structural elements are essential for the high activity toward long-chain substrates, as implied by structural analysis.

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Three-dimensional Structure and Substrate Binding of Bacillus stearothermophilus Neopullulanase

Cited by 132 publications

References 35 publications

The Geobacillus paradox: why is a thermophilic bacterial genus so prevalent on a mesophilic planet?

The Geobacillus paradox: why is a thermophilic bacterial genus so prevalent on a mesophilic planet?

Complex Structures of Thermoactinomyces vulgaris R-47 α-Amylase 2 with Acarbose and Cyclodextrins Demonstrate the Multiple Substrate Recognition Mechanism

Structure-function relationship of substrate length specificity of dextran glucosidase from Streptococcus mutans

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