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Glycosyltransferase PDB id
1bpl
Jmol
Contents
Protein chains
179 a.a. *
290 a.a. *
Waters ×237
* Residue conservation analysis
PDB id:
1bpl
Name: Glycosyltransferase
Title: Glycosyltransferase
Structure: Alpha-1,4-glucan-4-glucanohydrolase. Chain: a. Synonym: alpha-amylase (bla). Alpha-1,4-glucan-4-glucanohydrolase. Chain: b. Synonym: alpha-amylase (bla). Ec: 3.2.1.1
Source: Bacillus licheniformis. Organism_taxid: 1402. Atcc: 27811. Atcc: 27811
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.167    
Authors: M.Machius,G.Wiegand,R.Huber
Key ref: M.Machius et al. (1995). Crystal structure of calcium-depleted Bacillus licheniformis alpha-amylase at 2.2 A resolution. J Mol Biol, 246, 545-559. PubMed id: 7877175 DOI: 10.1006/jmbi.1994.0106
Date:
13-Jul-95     Release date:   17-Aug-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06278  (AMY_BACLI) -  Alpha-amylase
Seq:
Struc: 		512 a.a.
179 a.a.*
Protein chain
Pfam   ArchSchema ?
P06278  (AMY_BACLI) -  Alpha-amylase
Seq:
Struc: 		512 a.a.
290 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.3.2.1.1  - Alpha-amylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-alpha-glucosidic linkages in oligosaccharides and polysaccharides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
DOI no: 10.1006/jmbi.1994.0106 J Mol Biol 246:545-559 (1995)
PubMed id: 7877175  
 
 
Crystal structure of calcium-depleted Bacillus licheniformis alpha-amylase at 2.2 A resolution.
M.Machius, G.Wiegand, R.Huber.
 
  ABSTRACT  
 
The three-dimensional structure of the calcium-free form of Bacillus licheniformis alpha-amylase (BLA) has been determined by multiple isomorphous replacement in a crystal of space group P4(3)2(1)2 (a = b = 119.6 A, c = 85.4 A). The structure was refined using restrained crystallographic refinement to an R-factor of 0.177 for 28,147 independent reflections with intensities FObs > 0 at 2.2 A resolution, with root mean square deviations of 0.008 A and 1.4 degrees from ideal bond lengths and bond angles, respectively. The final model contains 469 residue, 237 water molecules, and one chloride ion. The segment between Trp182 and Asn192 could not be located in the electron density, nor could the N and C termini. Cleavage of the calcium-free form of BLA was observed after Glu189, due to a Glu-C endopeptidase present in trace amounts in the preparation. BLA did not crystallize without this cleavage under the conditions applied. BLA exhibits the characteristic overall topological fold observed for other alpha-amylases and related amylolytic enzymes: a central domain A containing an alpha/beta-barrel with a large protrusion between beta-strand 3 and alpha-helix 3 (domain B) and a C-terminal greek key motif (domain C). Unlike in the other enzymes, domain B possesses a beta-sheet made up of six loosely connected, twisted beta-strands forming a kind of a barrel with a large hole in the interior. Topological comparisons to TAKA-amylase, pig pancreatic alpha-amylase and cyclodextrin glycosyltransferase reveal a very high structural equivalence for large portions of the proteins and an exceptionally pronounced structural similarity for calcium binding, chloride binding and the active site. None of the theories proposed to explain the enhanced thermostability of BLA showed a satisfactory correlation with the three-dimensional structure. Instead, sequence comparisons to the less thermostable bacterial alpha-amylase from Bacillus amyloliquefaciens (BAA) indicate that some ionic interactions present in BLA, but which cannot be formed in BAA, might be responsible for the enhanced thermostability of BLA.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21354427 K.Ito, S.Ito, T.Shimamura, S.Weyand, Y.Kawarasaki, T.Misaka, K.Abe, T.Kobayashi, A.D.Cameron, and S.Iwata (2011).
Crystal structure of glucansucrase from the dental caries pathogen Streptococcus mutans.
  J Mol Biol, 408, 177-186.
PDB codes: 3aib 3aic 3aie
19756583 F.M.Reyes-Sosa, F.P.Molina-Heredia, and M.A.De la Rosa (2010).
A novel alpha-amylase from the cyanobacterium Nostoc sp. PCC 7119.
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20812985 K.Yamamoto, H.Miyake, M.Kusunoki, and S.Osaki (2010).
Crystal structures of isomaltase from Saccharomyces cerevisiae and in complex with its competitive inhibitor maltose.
  FEBS J, 277, 4205-4214.
PDB codes: 3a4a 3aj7
20108054 N.Hmidet, H.Maalej, A.Haddar, and M.Nasri (2010).
A novel alpha-amylase from Bacillus mojavensis A21: purification and biochemical characterization.
  Appl Biochem Biotechnol, 162, 1018-1030.  
19763902 O.Prakash, and N.Jaiswal (2010).
alpha-Amylase: an ideal representative of thermostable enzymes.
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18951544 B.Khemakhem, M.B.Ali, N.Aghajari, M.Juy, R.Haser, and S.Bejar (2009).
Engineering of the alpha-amylase from Geobacillus stearothermophilus US100 for detergent incorporation.
  Biotechnol Bioeng, 102, 380-389.  
19558417 F.Ataei, S.Hosseinkhani, and K.Khajeh (2009).
Limited proteolysis of luciferase as a reporter in nanosystem biology: a comparative study.
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16391027 K.Kurosawa, T.Hosaka, N.Tamehiro, T.Inaoka, and K.Ochi (2006).
Improvement of alpha-amylase production by modulation of ribosomal component protein S12 in Bacillus subtilis 168.
  Appl Environ Microbiol, 72, 71-77.  
16703471 L.L.Lin, P.J.Chen, J.S.Liu, W.C.Wang, and H.F.Lo (2006).
Identification of glutamate residues important for catalytic activity or thermostability of a truncated Bacillus sp. strain TS-23 alpha-amylase by site-directed mutagenesis.
  Protein J, 25, 232-239.  
17009862 W.K.Kim, A.Henschel, C.Winter, and M.Schroeder (2006).
The many faces of protein-protein interactions: A compendium of interface geometry.
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15747134 C.Colin, C.Leblanc, G.Michel, E.Wagner, E.Leize-Wagner, A.Van Dorsselaer, and P.Potin (2005).
Vanadium-dependent iodoperoxidases in Laminaria digitata, a novel biochemical function diverging from brown algal bromoperoxidases.
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15610414 M.Shahhoseini, A.A.Ziaee, A.A.Pourbabai, N.Ghaemi, and N.Declerck (2005).
A natural variant of Bacillus licheniformis alpha-amylase isolated from flour mill wastewaters sheds light on the origin of high thermostability.
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16033468 M.Vitikainen, H.L.Hyyryläinen, A.Kivimäki, V.P.Kontinen, and M.Sarvas (2005).
Secretion of heterologous proteins in Bacillus subtilis can be improved by engineering cell components affecting post-translocational protein folding and degradation.
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15722449 R.Maurus, A.Begum, H.H.Kuo, A.Racaza, S.Numao, C.Andersen, J.W.Tams, J.Vind, C.M.Overall, S.G.Withers, and G.D.Brayer (2005).
Structural and mechanistic studies of chloride induced activation of human pancreatic alpha-amylase.
  Protein Sci, 14, 743-755.
PDB codes: 1xgz 1xh0 1xh1 1xh2
16003949 S.Srimathi, and G.Jayaraman (2005).
Effect of glycosylation on the catalytic and conformational stability of homologous alpha-amylases.
  Protein J, 24, 79-88.  
15378403 T.Fukushima, T.Mizuki, A.Echigo, A.Inoue, and R.Usami (2005).
Organic solvent tolerance of halophilic alpha-amylase from a Haloarchaeon, Haloarcula sp. strain S-1.
  Extremophiles, 9, 85-89.  
15356864 G.André, and V.Tran (2004).
Putative implication of alpha-amylase loop 7 in the mechanism of substrate binding and reaction products release.
  Biopolymers, 75, 95.  
15291818 K.Yamamoto, A.Nakayama, Y.Yamamoto, and S.Tabata (2004).
Val216 decides the substrate specificity of alpha-glucosidase in Saccharomyces cerevisiae.
  Eur J Biochem, 271, 3414-3420.  
15304511 S.Numao, I.Damager, C.Li, T.M.Wrodnigg, A.Begum, C.M.Overall, G.D.Brayer, and S.G.Withers (2004).
In situ extension as an approach for identifying novel alpha-amylase inhibitors.
  J Biol Chem, 279, 48282-48291.
PDB codes: 1u2y 1u30 1u33
15133166 T.Ohshiro, J.Littlechild, E.Garcia-Rodriguez, M.N.Isupov, Y.Iida, T.Kobayashi, and Y.Izumi (2004).
Modification of halogen specificity of a vanadium-dependent bromoperoxidase.
  Protein Sci, 13, 1566-1571.  
  16233519 A.Tanaka, and E.Hoshino (2003).
Secondary calcium-binding parameter of Bacillus amyloliquefaciens alpha-amylase obtained from inhibition kinetics.
  J Biosci Bioeng, 96, 262-267.  
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
12540849 M.Machius, N.Declerck, R.Huber, and G.Wiegand (2003).
Kinetic stabilization of Bacillus licheniformis alpha-amylase through introduction of hydrophobic residues at the surface.
  J Biol Chem, 278, 11546-11553.
PDB code: 1ob0
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.  
12719434 T.Nonaka, M.Fujihashi, A.Kita, H.Hagihara, K.Ozaki, S.Ito, and K.Miki (2003).
Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites.
  J Biol Chem, 278, 24818-24824.
PDB codes: 1ud2 1ud3 1ud4 1ud5 1ud6 1ud8
11856298 O.L.Franco, D.J.Rigden, F.R.Melo, and M.F.Grossi-De-Sá (2002).
Plant alpha-amylase inhibitors and their interaction with insect alpha-amylases.
  Eur J Biochem, 269, 397-412.  
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.  
11267650 K.Khajeh, H.Naderi-Manesh, B.Ranjbar, A.Moosavi-Movahedi, and M.Nemat-Gorgani (2001).
Chemical modification of lysine residues in Bacillus alpha-amylases: effect on activity and stability.
  Enzyme Microb Technol, 28, 543-549.  
10924103 A.M.Brzozowski, D.M.Lawson, J.P.Turkenburg, H.Bisgaard-Frantzen, A.Svendsen, T.V.Borchert, Z.Dauter, K.S.Wilson, and G.J.Davies (2000).
Structural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes.
  Biochemistry, 39, 9099-9107.
PDB codes: 1e3x 1e3z 1e40 1e43
10944350 J.Burke, A.Roujeinikova, P.J.Baker, S.Sedelnikova, C.Raasch, W.Liebl, and D.W.Rice (2000).
Crystallization and preliminary X-ray crystallographic studies on maltosyltransferase from Thermotoga maritima.
  Acta Crystallogr D Biol Crystallogr, 56, 1049-1050.  
11150610 J.E.Nielsen, and T.V.Borchert (2000).
Protein engineering of bacterial alpha-amylases.
  Biochim Biophys Acta, 1543, 253-274.  
10969023 J.Fitter, and J.Heberle (2000).
Structural equilibrium fluctuations in mesophilic and thermophilic alpha-amylase.
  Biophys J, 79, 1629-1636.  
11053856 J.H.Lebbink, C.Bertoldo, G.Tibbelin, J.T.Andersen, F.Duffner, G.Antranikian, and R.Ladenstein (2000).
Crystallization and preliminary X-ray crystallographic studies of the thermoactive pullulanase type I, hydrolyzing alpha-1,6 glycosidic linkages, from Fervidobacterium pennivorans Ven5.
  Acta Crystallogr D Biol Crystallogr, 56, 1470-1472.  
10867237 Y.W.Tsai, J.S.Chia, Y.Y.Shiau, H.C.Chou, Y.C.Liaw, and K.L.Lou (2000).
Three-dimensional modelling of the catalytic domain of Streptococcus mutans glucosyltransferase GtfB.
  FEMS Microbiol Lett, 188, 75-79.  
10449318 A.Shaw, R.Bott, and A.G.Day (1999).
Protein engineering of alpha-amylase for low pH performance.
  Curr Opin Biotechnol, 10, 349-352.  
10353816 B.Mikami, M.Adachi, T.Kage, E.Sarikaya, T.Nanmori, R.Shinke, and S.Utsumi (1999).
Structure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose.
  Biochemistry, 38, 7050-7061.
PDB codes: 1b90 1b9z
10547530 G.André, A.Buléon, R.Haser, and V.Tran (1999).
Amylose chain behavior in an interacting context. III. Complete occupancy of the AMY2 barley alpha-amylase cleft and comparison with biochemical data.
  Biopolymers, 50, 751-762.  
10491128 J.E.Nielsen, L.Beier, D.Otzen, T.V.Borchert, H.B.Frantzen, K.V.Andersen, and A.Svendsen (1999).
Electrostatics in the active site of an alpha-amylase.
  Eur J Biochem, 264, 816-824.  
10409823 L.Lo Leggio, S.Kalogiannis, M.K.Bhat, and R.W.Pickersgill (1999).
High resolution structure and sequence of T. aurantiacus xylanase I: implications for the evolution of thermostability in family 10 xylanases and enzymes with (beta)alpha-barrel architecture.
  Proteins, 36, 295-306.
PDB codes: 1tax 1tix
10030014 R.A.Jones, L.S.Jermiin, S.Easteal, B.K.Patel, and I.R.Beacham (1999).
Amylase and 16S rRNA genes from a hyperthermophilic archaebacterium.
  J Appl Microbiol, 86, 93.  
10383865 W.D.Crabb, and J.K.Shetty (1999).
Commodity scale production of sugars from starches.
  Curr Opin Microbiol, 2, 252-256.  
10387084 Z.Dauter, M.Dauter, A.M.Brzozowski, S.Christensen, T.V.Borchert, L.Beier, K.S.Wilson, and G.J.Davies (1999).
X-ray structure of Novamyl, the five-domain "maltogenic" alpha-amylase from Bacillus stearothermophilus: maltose and acarbose complexes at 1.7A resolution.
  Biochemistry, 38, 8385-8392.
PDB codes: 1qho 1qhp
  9667930 A.Butler (1998).
Vanadium haloperoxidases.
  Curr Opin Chem Biol, 2, 279-285.  
9558324 A.K.Schmidt, S.Cottaz, H.Driguez, and G.E.Schulz (1998).
Structure of cyclodextrin glycosyltransferase complexed with a derivative of its main product beta-cyclodextrin.
  Biochemistry, 37, 5909-5915.
PDB code: 3cgt
  9634702 F.Vallée, A.Kadziola, Y.Bourne, M.Juy, K.W.Rodenburg, B.Svensson, and R.Haser (1998).
Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution.
  Structure, 6, 649-659.
PDB code: 1ava
  9726872 K.Igarashi, Y.Hatada, H.Hagihara, K.Saeki, M.Takaiwa, T.Uemura, K.Ara, K.Ozaki, S.Kawai, T.Kobayashi, and S.Ito (1998).
Enzymatic properties of a novel liquefying alpha-amylase from an alkaliphilic Bacillus isolate and entire nucleotide and amino acid sequences.
  Appl Environ Microbiol, 64, 3282-3289.  
  9687444 K.Stephenson, and C.R.Harwood (1998).
Influence of a cell-wall-associated protease on production of alpha-amylase by Bacillus subtilis.
  Appl Environ Microbiol, 64, 2875-2881.  
9761914 M.J.Cho, S.S.Cha, J.H.Park, H.J.Cha, H.S.Lee, K.H.Park, and B.H.Oh (1998).
Preliminary X-ray crystallographic analysis of a novel maltogenic amylase from Bacillus stearothermophilus ET1.
  Acta Crystallogr D Biol Crystallogr, 54, 416-418.  
  9551551 M.Machius, N.Declerck, R.Huber, and G.Wiegand (1998).
Activation of Bacillus licheniformis alpha-amylase through a disorder-->order transition of the substrate-binding site mediated by a calcium-sodium-calcium metal triad.
  Structure, 6, 281-292.
PDB code: 1bli
  9541387 N.Aghajari, G.Feller, C.Gerday, and R.Haser (1998).
Crystal structures of the psychrophilic alpha-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor.
  Protein Sci, 7, 564-572.
PDB codes: 1aqh 1aqm
  9862804 N.Aghajari, G.Feller, C.Gerday, and R.Haser (1998).
Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level.
  Structure, 6, 1503-1516.
PDB code: 1b0i
9283074 A.M.Brzozowski, and G.J.Davies (1997).
Structure of the Aspergillus oryzae alpha-amylase complexed with the inhibitor acarbose at 2.0 A resolution.
  Biochemistry, 36, 10837-10845.
PDB code: 7taa
  9293008 G.Dong, C.Vieille, A.Savchenko, and J.G.Zeikus (1997).
Cloning, sequencing, and expression of the gene encoding extracellular alpha-amylase from Pyrococcus furiosus and biochemical characterization of the recombinant enzyme.
  Appl Environ Microbiol, 63, 3569-3576.  
9278396 I.Matsui, and B.Svensson (1997).
Improved activity and modulated action pattern obtained by random mutagenesis at the fourth beta-alpha loop involved in substrate binding to the catalytic (beta/alpha)8-barrel domain of barley alpha-amylase 1.
  J Biol Chem, 272, 22456-22463.  
8999834 M.Inohara-Ochiai, T.Nakayama, R.Goto, M.Nakao, T.Ueda, and Y.Shibano (1997).
Altering substrate specificity of Bacillus sp. SAM1606 alpha-glucosidase by comparative site-specific mutagenesis.
  J Biol Chem, 272, 1601-1607.  
9352636 T.Suganuma, Y.Maeda, K.Kitahara, and T.Nagahama (1997).
Study of the action of human salivary alpha-amylase on 2-chloro-4-nitrophenyl alpha-maltotrioside in the presence of potassium thiocyanate.
  Carbohydr Res, 303, 219-227.  
  9006052 W.Liebl, I.Stemplinger, and P.Ruile (1997).
Properties and gene structure of the Thermotoga maritima alpha-amylase AmyA, a putative lipoprotein of a hyperthermophilic bacterium.
  J Bacteriol, 179, 941-948.  
8552646 A.Messerschmidt, and R.Wever (1996).
X-ray structure of a vanadium-containing enzyme: chloroperoxidase from the fungus Curvularia inaequalis.
  Proc Natl Acad Sci U S A, 93, 392-396.
PDB code: 1vnc
8681972 C.Gilles, J.P.Astier, G.Marchis-Mouren, C.Cambillau, and F.Payan (1996).
Crystal structure of pig pancreatic alpha-amylase isoenzyme II, in complex with the carbohydrate inhibitor acarbose.
  Eur J Biochem, 238, 561-569.
PDB code: 1ose
8798613 G.Feller, O.Bussy, C.Houssier, and C.Gerday (1996).
Structural and functional aspects of chloride binding to Alteromonas haloplanctis alpha-amylase.
  J Biol Chem, 271, 23836-23841.  
8855411 J.S.Esteve-Romero, A.Bossi, and P.G.Righetti (1996).
Purification of thermamylase in multicompartment electrolyzers with isoelectric membranes: the problem of protein solubility.
  Electrophoresis, 17, 1242-1247.  
8721743 T.Suganuma, M.Ohnishi, K.Hiromi, and T.Nagahama (1996).
Elucidation of the subsite structure of bacterial saccharifying alpha-amylase and its mode of degradation of maltose.
  Carbohydr Res, 282, 171-180.  
8552644 Y.Chen, J.Inobe, V.K.Kuchroo, J.L.Baron, C.A.Janeway, and H.L.Weiner (1996).
Oral tolerance in myelin basic protein T-cell receptor transgenic mice: suppression of autoimmune encephalomyelitis and dose-dependent induction of regulatory cells.
  Proc Natl Acad Sci U S A, 93, 388-391.  
  8535789 C.Wiesmann, G.Beste, W.Hengstenberg, and G.E.Schulz (1995).
The three-dimensional structure of 6-phospho-beta-galactosidase from Lactococcus lactis.
  Structure, 3, 961-968.
PDB code: 1pbg
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.