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PDBsum entry 1sma

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protein Protein-protein interface(s) links
Hydrolase PDB id
1sma
Jmol
Contents
Protein chains
588 a.a. *
Waters ×191
* Residue conservation analysis
PDB id:
1sma
Name: Hydrolase
Title: Crystal structure of a maltogenic amylase
Structure: Maltogenic amylase. Chain: a, b. Fragment: n-domain, barrel, c-domain
Source: Thermus sp. Im6501. Organism_taxid: 75891. Strain: m6501
Biol. unit: Dimer (from PQS)
Resolution:
2.80Å     R-factor:   0.209     R-free:   0.267
Authors: J.S.Kim,S.S.Cha,B.H.Oh
Key ref:
J.S.Kim et al. (1999). Crystal structure of a maltogenic amylase provides insights into a catalytic versatility. J Biol Chem, 274, 26279-26286. PubMed id: 10473583 DOI: 10.1074/jbc.274.37.26279
Date:
21-Apr-99     Release date:   26-Apr-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O69007  (O69007_9DEIN) -  Maltogenic amylase
Seq:
Struc:
 
Seq:
Struc:
588 a.a.
588 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     3 terms  

 

 
DOI no: 10.1074/jbc.274.37.26279 J Biol Chem 274:26279-26286 (1999)
PubMed id: 10473583  
 
 
Crystal structure of a maltogenic amylase provides insights into a catalytic versatility.
J.S.Kim, S.S.Cha, H.J.Kim, T.J.Kim, N.C.Ha, S.T.Oh, H.S.Cho, M.J.Cho, M.J.Kim, H.S.Lee, J.W.Kim, K.Y.Choi, K.H.Park, B.H.Oh.
 
  ABSTRACT  
 
Amylases catalyze the hydrolysis of starch material and play central roles in carbohydrate metabolism. Compared with many different amylases that are able to hydrolyze only alpha-D-(1,4)-glycosidic bonds, maltogenic amylases exhibit catalytic versatility: hydrolysis of alpha-D-(1,4)- and alpha-D-(1,6)-glycosidic bonds and transglycosylation of oligosaccharides to C3-, C4-, or C6-hydroxyl groups of various acceptor mono- or disaccharides. It has been speculated that the catalytic property of the enzymes is linked to the additional approximately 130 residues at the N terminus that are absent in other typical alpha-amylases. The crystal structure of a maltogenic amylase from a Thermus strain was determined at 2.8 A. The structure, an analytical centrifugation, and a size exclusion column chromatography proved that the enzyme is a dimer in solution. The N-terminal segment of the enzyme folds into a distinct domain and comprises the enzyme active site together with the central (alpha/beta)(8) barrel of the adjacent subunit. The active site is a narrow and deep cleft suitable for binding cyclodextrins, which are the preferred substrates to other starch materials. At the bottom of the active site cleft, an extra space, absent in the other typical alpha-amylases, is present whose size is comparable with that of a disaccharide. The space is most likely to host an acceptor molecule for the transglycosylation and to allow binding of a branched oligosaccharide for hydrolysis of alpha-D-(1,4)-glycosidic or alpha-D-(1,6)-glycosidic bond. The (alpha/beta)(8) barrel of the enzyme is the preserved scaffold in all the known amylases. The structure represents a novel example of how an enzyme acquires a different substrate profile and a catalytic versatility from a common active site and represents a framework for explaining the catalytic activities of transglycosylation and hydrolysis of alpha-D-(1,6)-glycosidic bond.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Schematic drawings of products from reaction of acarbose with ThMA . Acarbose is hydrolyzed to PTS and glucose. Three different products can be generated by transglycosylation of PTS to glucose. One of those generated by -D-(1,4)-transglycosylation is acarbose. The activity of -D-(1,4)-transglycosylation can be detected by using an acceptor molecule such as -methylglucoside.
Figure 6.
Fig. 6. Proposed mechanism for competition of transglycosylation and hydrolysis reaction at the active site of ThMA . A proposal for a double-displacement reaction is followed. The third conserved residue Asp-424, which may play a role in raising the pK[a] of Glu-357 (30), is not drawn.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 26279-26286) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21355000 F.Li, X.Zhu, Y.Li, H.Cao, and Y.Zhang (2011).
Functional characterization of a special thermophilic multifunctional amylase OPMA-N and its N-terminal domain.
  Acta Biochim Biophys Sin (Shanghai), 43, 324-334.  
19763902 O.Prakash, and N.Jaiswal (2010).
alpha-Amylase: an ideal representative of thermostable enzymes.
  Appl Biochem Biotechnol, 160, 2401-2414.  
18703518 E.J.Woo, S.Lee, H.Cha, J.T.Park, S.M.Yoon, H.N.Song, and K.H.Park (2008).
Structural insight into the bifunctional mechanism of the glycogen-debranching enzyme TreX from the archaeon Sulfolobus solfataricus.
  J Biol Chem, 283, 28641-28648.
PDB codes: 2vnc 2vr5 2vuy
18552192 J.Y.Damián-Almazo, A.Moreno, A.López-Munguía, X.Soberón, F.González-Muñoz, and G.Saab-Rincón (2008).
Enhancement of the alcoholytic activity of alpha-amylase AmyA from Thermotoga maritima MSB8 (DSM 3109) by site-directed mutagenesis.
  Appl Environ Microbiol, 74, 5168-5177.  
18981178 M.Kitamura, M.Okuyama, F.Tanzawa, H.Mori, Y.Kitago, N.Watanabe, A.Kimura, I.Tanaka, and M.Yao (2008).
Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron.
  J Biol Chem, 283, 36328-36337.
PDB codes: 2d73 2zq0
18049800 S.B.Mabrouk, E.B.Messaoud, D.Ayadi, S.Jemli, A.Roy, M.Mezghani, and S.Bejar (2008).
Cloning and sequencing of an original gene encoding a maltogenic amylase from Bacillus sp. US149 strain and characterization of the recombinant activity.
  Mol Biotechnol, 38, 211-219.  
17587692 S.H.Park, H.K.Kang, J.H.Shim, E.J.Woo, J.S.Hong, J.W.Kim, B.H.Oh, B.H.Lee, H.Cha, and K.H.Park (2007).
Modulation of substrate preference of thermus maltogenic amylase by mutation of the residues at the interface of a dimer.
  Biosci Biotechnol Biochem, 71, 1564-1567.  
17371546 T.Tonozuka, A.Sogawa, M.Yamada, N.Matsumoto, H.Yoshida, S.Kamitori, K.Ichikawa, M.Mizuno, A.Nishikawa, and Y.Sakano (2007).
Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein.
  FEBS J, 274, 2109-2120.
PDB codes: 2dfz 2zyk
16367752 H.S.Lee, J.S.Kim, K.Shim, J.W.Kim, K.Inouye, H.Oneda, Y.W.Kim, K.A.Cheong, H.Cha, E.J.Woo, J.H.Auh, S.J.Lee, J.W.Kim, and K.H.Park (2006).
Dissociation/association properties of a dodecameric cyclomaltodextrinase. Effects of pH and salt concentration on the oligomeric state.
  FEBS J, 273, 109-121.  
16857016 S.Y.Tang, Q.T.Le, J.H.Shim, S.J.Yang, J.H.Auh, C.Park, and K.H.Park (2006).
Enhancing thermostability of maltogenic amylase from Bacillus thermoalkalophilus ET2 by DNA shuffling.
  FEBS J, 273, 3335-3345.  
16310726 P.Turner, A.Labes, O.H.Fridjonsson, G.O.Hreggvidson, P.Schönheit, J.K.Kristjansson, O.Holst, and E.N.Karlsson (2005).
Two novel cyclodextrin-degrading enzymes isolated from thermophilic bacteria have similar domain structures but differ in oligomeric state and activity profile.
  J Biosci Bioeng, 100, 380-390.  
15182368 M.Mizuno, T.Tonozuka, A.Uechi, A.Ohtaki, K.Ichikawa, S.Kamitori, A.Nishikawa, and Y.Sakano (2004).
The crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) complexed with transglycosylated product.
  Eur J Biochem, 271, 2530-2538.
PDB code: 1vb9
15466542 S.J.Yang, H.S.Lee, C.S.Park, Y.R.Kim, T.W.Moon, and K.H.Park (2004).
Enzymatic analysis of an amylolytic enzyme from the hyperthermophilic archaeon Pyrococcus furiosus reveals its novel catalytic properties as both an alpha-amylase and a cyclodextrin-hydrolyzing enzyme.
  Appl Environ Microbiol, 70, 5988-5995.  
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.  
12902281 Y.W.Kim, J.H.Choi, J.W.Kim, C.Park, J.W.Kim, H.Cha, S.B.Lee, B.H.Oh, T.W.Moon, and K.H.Park (2003).
Directed evolution of Thermus maltogenic amylase toward enhanced thermal resistance.
  Appl Environ Microbiol, 69, 4866-4874.  
11916682 H.Kamasaka, K.Sugimoto, H.Takata, T.Nishimura, and T.Kuriki (2002).
Bacillus stearothermophilus neopullulanase selective hydrolysis of amylose to maltose in the presence of amylopectin.
  Appl Environ Microbiol, 68, 1658-1664.  
12423336 H.Mori, K.S.Bak-Jensen, and B.Svensson (2002).
Barley alpha-amylase Met53 situated at the high-affinity subsite -2 belongs to a substrate binding motif in the beta-->alpha loop 2 of the catalytic (beta/alpha)8-barrel and is critical for activity and substrate specificity.
  Eur J Biochem, 269, 5377-5390.  
12119024 M.J.Kim, H.S.Lee, J.S.Cho, T.J.Kim, T.W.Moon, S.T.Oh, J.W.Kim, B.H.Oh, and K.H.Park (2002).
Preparation and characterization of alpha-D-glucopyranosyl-alpha-acarviosinyl-D-glucopyranose, a novel inhibitor specific for maltose-producing amylase.
  Biochemistry, 41, 9099-9108.  
11257505 E.A.MacGregor, S.Janecek, and B.Svensson (2001).
Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes.
  Biochim Biophys Acta, 1546, 1.  
11737209 H.Mori, K.S.Bak-Jensen, T.E.Gottschalk, M.S.Motawia, I.Damager, B.L.Møller, and B.Svensson (2001).
Modulation of activity and substrate binding modes by mutation of single and double subsites +1/+2 and -5/-6 of barley alpha-amylase 1.
  Eur J Biochem, 268, 6545-6558.  
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
10650202 J.Matzke, A.Herrmann, E.Schneider, and E.P.Bakker (2000).
Gene cloning, nucleotide sequence and biochemical properties of a cytoplasmic cyclomaltodextrinase (neopullulanase) from Alicyclobacillus acidocaldarius, reclassification of a group of enzymes.
  FEMS Microbiol Lett, 183, 55-61.  
10841756 T.J.Kim, C.S.Park, H.Y.Cho, S.S.Cha, J.S.Kim, S.B.Lee, T.W.Moon, J.W.Kim, B.H.Oh, and K.H.Park (2000).
Role of the glutamate 332 residue in the transglycosylation activity of ThermusMaltogenic amylase.
  Biochemistry, 39, 6773-6780.  
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.