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557 a.a.
Key reference
DOI no: 10.1006/jmbi.2000.3977 J Mol Biol 301:451-464 (2000) PubMed id: 10926520
Crystal structure of glycosyltrehalose trehalohydrolase from the hyperthermophilic archaeum Sulfolobus solfataricus. M.D.Feese, Y.Kato, T.Tamada, M.Kato, T.Komeda, Y.Miura, M.Hirose, K.Hondo, K.Kobayashi, R.Kuroki. ABSTRACT
The crystal structure of glycosyltrehalose trehalohydrolase from the hyperthermophilic archaeum Sulfolobus solfataricus KM1 has been solved by multiple isomorphous replacement. The enzyme is an alpha-amylase (family 13) with unique exo-amylolytic activity for glycosyltrehalosides. It cleaves the alpha-1,4 glycosidic bond adjacent to the trehalose moiety to release trehalose and maltooligo saccharide. Unlike most other family 13 glycosidases, the enzyme does not require Ca(2+) for activity, and it contains an N-terminal extension of approximately 100 amino acid residues that is homologous to N-terminal domains found in many glycosidases that recognize branched oligosaccharides. Crystallography revealed the enzyme to exist as a homodimer covalently linked by an intermolecular disulfide bond at residue C298. The existence of the intermolecular disulfide bond was confirmed by biochemical analysis and mutagenesis. The N-terminal extension forms an independent domain connected to the catalytic domain by an extended linker. The functionally essential Ca(2+) binding site found in the B domain of alpha-amylases and many other family 13 glycosidases was found to be replaced by hydrophobic packing interactions. The enzyme also contains a very unusual excursion in the (beta/alpha)(8) barrel structure of the catalytic domain. This excursion originates from the bottom of the (beta/alpha)(8) barrel between helix 6 and strand 7, but folds upward in a distorted alpha-hairpin structure to form a part of the substrate binding cleft wall that is possibly critical for the enzyme's unique substrate selectivity. Participation of an alpha-beta loop in the formation of the substrate binding cleft is a novel feature that is not observed in other known (beta/alpha)(8) enzymes.
Selected figure(s)
Figure 3.
Figure 3. Dimerization of KM1 GTHase. Stereo view of the GTHase dimer viewed down the molecular 2-fold axis to emphasize the intermolecular disulfide bond and the participation of the a6b-b7 (green) and the B domain (blue) in the dimer interface.Figure 6.
Figure 6. Comparison of the B domains of KM1 GTHase and A. oryzae a-amylase (TAA). The bound calcium ion of A. oryzae a-amylase is shown as a green sphere with three surrounding solvent ligands shown as red spheres. Residues indicated for A. oryzae are the ligands to the calcium ion and the generally conserved disulfide bond. Residues indicated for S. solfataricus form the small hydrophobic core and replace the calcium binding site in A. oryzae.The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 301, 451-464) copyright 2000. Figures were selected by an automated process.
Literature references that cite this PDB file's key reference
PubMed id Reference
19139240 M.Palomo, S.Kralj, M.J.van der Maarel, and L.Dijkhuizen (2009).
The unique branching patterns of Deinococcus glycogen branching enzymes are determined by their N-terminal domains.Appl Environ Microbiol, 75, 1355-1362.
17586772 H.Yamada, T.Tamada, M.Kosaka, K.Miyata, S.Fujiki, M.Tano, M.Moriya, M.Yamanishi, E.Honjo, H.Tada, T.Ino, H.Yamaguchi, J.Futami, M.Seno, T.Nomoto, T.Hirata, M.Yoshimura, and R.Kuroki (2007).
'Crystal lattice engineering,' an approach to engineer protein crystal contacts by creating intermolecular symmetry: crystallization and structure determination of a mutant human RNase 1 with a hydrophobic interface of leucines.Protein Sci, 16, 1389-1397.
PDB codes: 2e0j 2e0l 2e0m 2e0o
16148304 J.Eichler, and M.W.Adams (2005).
Posttranslational protein modification in Archaea.Microbiol Mol Biol Rev, 69, 393-425.
16111437 M.Beeby, B.D.O'Connor, C.Ryttersgaard, D.R.Boutz, L.J.Perry, and T.O.Yeates (2005).
The genomics of disulfide bonding and protein stabilization in thermophiles.PLoS Biol, 3, e309.
PDB code: 1rki
12482867 A.Linden, O.Mayans, W.Meyer-Klaucke, G.Antranikian, and M.Wilmanns (2003).
Differential regulation of a hyperthermophilic alpha-amylase with a novel (Ca,Zn) two-metal center by zinc.J Biol Chem, 278, 9875-9884.
PDB codes: 1mwo 1mxd 1mxg
12752453 H.B.Fritzsche, T.Schwede, and G.E.Schulz (2003).
Covalent and three-dimensional structure of the cyclodextrinase from Flavobacterium sp. no. 92.Eur J Biochem, 270, 2332-2341.
PDB code: 1h3g
12581203 S.Janecek, B.Svensson, and E.A.MacGregor (2003).
Relation between domain evolution, specificity, and taxonomy of the alpha-amylase family members containing a C-terminal starch-binding domain.Eur J Biochem, 270, 635-645.
11302176 T.Yokota, T.Tonozuka, S.Kamitori, and Y.Sakano (2001).
The deletion of amino-terminal domain in Thermoactinomyces vulgaris R-47 alpha-amylases: effects of domain N on activity, specificity, stability and dimerization.Biosci Biotechnol Biochem, 65, 401-408.
11330677 T.Yokota, T.Tonozuka, Y.Shimura, K.Ichikawa, S.Kamitori, and Y.Sakano (2001).
Structures of Thermoactinomyces vulgaris R-47 alpha-amylase II complexed with substrate analogues.Biosci Biotechnol Biochem, 65, 619-626.
PDB codes: 1jib 1jl8 The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.
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