2004 Fiscal Year Final Research Report Summary
Biochemical significance of the non-common amino acid sequences specifying the common functions of enzymes, polysaccharide lyases
| Project/Area Number |
14360052
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
応用微生物学・応用生物化学
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| Research Institution | Kyoto University |
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Principal Investigator |
MURATA Kousaku Kyoto University, Graduate School of Agriculture, Professor, 農学研究科, 教授 (90142299)
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| Co-Investigator(Kenkyū-buntansha) |
MIKAMI Bunzo Kyoto University, Graduate School of Agriculture, Associate professor, 農学研究科, 助教授 (40135611)
HASHIMOTO Wataru Kyoto University, Graduate School of Agriculture, Associate professor, 農学研究科, 助教授 (30273519)
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| Project Period (FY) |
2002 – 2004
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| Keywords | Polysaccharide lyase / Structural biology / X-ray crystallography / Structure / function relationship of protein / Sphingomonas / Bacillus / Primary structure / Protein module |
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| Research Abstract |
Polysaccharide lyase is an enzyme catalyzing the depolymerization of polysaccharides such as alginate, xanthan, gellan, and hyarunonate, all of which are produced by bacteria, and gives rise oligosaccharides or monosaccharides as reaction products. The enzyme strictly recognizes uronic acids scattered on the polysaccharide molecules and splits the polysaccharides at the acid site through β-elimination reaction. However, these enzymes have no similarities in their primary structures, thus suggesting that the function of these enzymes are written by different amino acid sequences. To elucidate the reason why the enzymes with the different primary structures could show the same substrate recognition and β-elimination reaction, the X-ray crystal structures of Sphingomonas sp. A1 alginate lyase (A1-III), Pseudomonas aeruginosa PAO1 alginate lyase (PA1167), and Bacillus sp.GL1 xanthan lyase were determined and compared with those of porcine kidney N-acyl-D-glucoamine 2-epimerase and Bacillus
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sp.GL1 unsaturated glucuronylhydrolase. The structural comparison of these enzymes indicated that (1)A1-III expresses β-eliination activity by using a lid-loop module. Such the structure is also found in XL, although PA1167 has not. (2) A1-III has α/α -barell structure. PA1167 shows anti-parallel β-sheet structure. XL shows a combined structure of α/α -barrell structure and anti-paralell β-sheet structure. (3)In all the polysaccharide lyases examined, Tyr is an essential catalytic amino acid residue, and His and Arg are involved in the recognition and stabilization of substrate. From these results, it was concluded that, even though the primary structure is different, similar structure for catalytic site and substrate recognition are created through the movement of protein modules. This notion indicates that the estimation of protein function on the basis of primary structure is not always reliable and definitive function of proteins should be determined in combination with the three-dimensional structures of them. Less
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