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PDBsum entry 1amy

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protein metals links
Hydrolase (o-glycosyl) PDB id
1amy
Jmol
Contents
Protein chain
403 a.a. *
Metals
_CA ×3
Waters ×152
* Residue conservation analysis
PDB id:
1amy
Name: Hydrolase (o-glycosyl)
Title: Crystal and molecular structure of barley alpha-amylase
Structure: 1,4-alpha-d-glucan glucanohydrolase. Chain: a. Engineered: yes
Source: Hordeum vulgare. Organism_taxid: 4513
Resolution:
2.80Å     R-factor:   0.153    
Authors: A.Kadziola,R.Haser
Key ref: A.Kadziola et al. (1994). Crystal and molecular structure of barley alpha-amylase. J Mol Biol, 239, 104-121. PubMed id: 8196040
Date:
10-Mar-94     Release date:   13-May-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04063  (AMY2_HORVU) -  Alpha-amylase type B isozyme
Seq:
Struc:
427 a.a.
403 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: 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     metabolic process   2 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
J Mol Biol 239:104-121 (1994)
PubMed id: 8196040  
 
 
Crystal and molecular structure of barley alpha-amylase.
A.Kadziola, J.Abe, B.Svensson, R.Haser.
 
  ABSTRACT  
 
The three-dimensional structure of barley malt alpha-amylase (isoform AMY2-2) was determined by multiple isomorphous replacement using three heavy-atom derivatives and solvent flattening. The model was refined using a combination of simulated annealing and conventional restrained least-squares crystallographic refinement to an R-factor of 0.153 based on 18,303 independent reflections with F(o) > sigma(F(o)) between 10 and 2.8 A resolution, with root-mean-square deviations of 0.016 A and 3.3 degrees from ideal bond lengths and bond angles, respectively. The final model consists of 403 amino acid residues, three calcium ions and 153 water molecules. The polypeptide chain folds into three domains: a central domain forming a (beta alpha)8-barrel of 286 residues, with a protruding irregular structured loop domain of 64 residues (domain B) connecting strand beta 3 and helix alpha 3 of the barrel, and a C-terminal domain of 53 residues forming a five stranded anti-parallel beta-sheet. Unlike the previously known alpha-amylase structures, AMY2-2 contains three Ca2+ binding sites co-ordinated by seven or eight oxygen atoms from carboxylate groups, main-chain carbonyl atoms and water molecules, all calcium ions being bound to domain B and therefore essential for the structural integrity of that domain. Two of the Ca2+ sites are located only 7.0 A apart with one Asp residue serving as ligand for both. One Ca2+ site located at about 20 A from the other two was found to be exchangeable with Eu3+. By homology with other alpha-amylases, some important active site residues are identified as Asp179, Glu204 and Asp289, and are situated at the C-terminal end of the central beta-barrel. A starch granule binding site, previously identified as Trp276 and Trp277, is situated on alpha-helix 6 in the central (beta alpha)8-barrel, at the surface of the enzyme. This binding site region is associated with a considerable disruption of the (beta alpha)8-barrel 8-fold symmetry.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21111049 X.Qin, L.Ren, X.Yang, F.Bai, L.Wang, P.Geng, G.Bai, and Y.Shen (2011).
Structures of human pancreatic α-amylase in complex with acarviostatins: Implications for drug design against type II diabetes.
  J Struct Biol, 174, 196-202.
PDB codes: 3old 3ole 3olg 3oli
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
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.  
17683331 I.Matsui, and K.Harata (2007).
Implication for buried polar contacts and ion pairs in hyperthermostable enzymes.
  FEBS J, 274, 4012-4022.  
17437525 K.S.Bak-Jensen, S.Laugesen, O.Ostergaard, C.Finnie, P.Roepstorff, and B.Svensson (2007).
Spatio-temporal profiling and degradation of alpha-amylase isozymes during barley seed germination.
  FEBS J, 274, 2552-2565.  
17013936 R.Buckow, U.Weiss, V.Heinz, and D.Knorr (2007).
Stability and catalytic activity of alpha-amylase from barley malt at different pressure-temperature conditions.
  Biotechnol Bioeng, 97, 1.  
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
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.  
15062085 J.Allouch, W.Helbert, B.Henrissat, and M.Czjzek (2004).
Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose.
  Structure, 12, 623-632.
PDB code: 1urx
14660599 K.S.Bak-Jensen, G.André, T.E.Gottschalk, G.Paës, V.Tran, and B.Svensson (2004).
Tyrosine 105 and threonine 212 at outermost substrate binding subsites -6 and +4 control substrate specificity, oligosaccharide cleavage patterns, and multiple binding modes of barley alpha-amylase 1.
  J Biol Chem, 279, 10093-10102.  
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
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
  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
14511369 N.Oudjeriouat, Y.Moreau, M.Santimone, B.Svensson, G.Marchis-Mouren, and V.Desseaux (2003).
On the mechanism of alpha-amylase.
  Eur J Biochem, 270, 3871-3879.  
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.  
12834286 S.S.Mar, H.Mori, J.H.Lee, K.Fukuda, W.Saburi, A.Fukuhara, M.Okuyama, S.Chiba, and A.Kimura (2003).
Purification, characterization, and sequence analysis of two alpha-amylase isoforms from azuki bean, Vigna angularis, showing different affinity towards beta-cyclodextrin sepharose.
  Biosci Biotechnol Biochem, 67, 1080-1093.  
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
12906828 X.Robert, R.Haser, T.E.Gottschalk, F.Ratajczak, H.Driguez, B.Svensson, and N.Aghajari (2003).
The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs.
  Structure, 11, 973-984.
PDB codes: 1ht6 1p6w
12220178 G.Parsiegla, A.Belaïch, J.P.Belaïch, and R.Haser (2002).
Crystal structure of the cellulase Cel9M enlightens structure/function relationships of the variable catalytic modules in glycoside hydrolases.
  Biochemistry, 41, 11134-11142.
PDB codes: 1ia6 1ia7
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.  
11914496 X.Robert, T.E.Gottschalk, R.Haser, B.Svensson, and N.Aghajari (2002).
Expression, purification and preliminary crystallographic studies of alpha-amylase isozyme 1 from barley seeds.
  Acta Crystallogr D Biol Crystallogr, 58, 683-686.  
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.  
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.  
10672010 K.W.Rodenburg, F.Vallée, N.Juge, N.Aghajari, X.Guo, R.Haser, and B.Svensson (2000).
Specific inhibition of barley alpha-amylase 2 by barley alpha-amylase/subtilisin inhibitor depends on charge interactions and can be conferred to isozyme 1 by mutation.
  Eur J Biochem, 267, 1019-1029.  
10792537 L.Janda, J.Damborský, M.Petrícek, J.Spízek, and P.Tichý (2000).
Molecular characterization of the Thermomonospora curvata aglA gene encoding a thermotolerant alpha-1,4-glucosidase.
  J Appl Microbiol, 88, 773-783.  
10691968 T.Wegrzyn, K.Reilly, G.Cipriani, P.Murphy, R.Newcomb, R.Gardner, and E.MacRae (2000).
A novel alpha-amylase gene is transiently upregulated during low temperature exposure in apple fruit.
  Eur J Biochem, 267, 1313-1322.  
  10091666 E.H.Rydberg, G.Sidhu, H.C.Vo, J.Hewitt, H.C.Côte, Y.Wang, S.Numao, R.T.MacGillivray, C.M.Overall, G.D.Brayer, and S.G.Withers (1999).
Cloning, mutagenesis, and structural analysis of human pancreatic alpha-amylase expressed in Pichia pastoris.
  Protein Sci, 8, 635-643.
PDB code: 1bsi
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.  
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.  
10500994 R.Abe, K.Yoshida, M.Aoyagi, S.Kasahara, E.Ichishima, and T.Nakajima (1999).
Characterization of chimeric enzymes constructed between two distinct alpha-amylase cDNAs from cultured rice cells.
  Biosci Biotechnol Biochem, 63, 1329-1335.  
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
9755156 G.Parsiegla, M.Juy, C.Reverbel-Leroy, C.Tardif, J.P.Belaïch, H.Driguez, and R.Haser (1998).
The crystal structure of the processive endocellulase CelF of Clostridium cellulolyticum in complex with a thiooligosaccharide inhibitor at 2.0 A resolution.
  EMBO J, 17, 5551-5562.
PDB code: 1fce
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
9013553 B.X.Yan, and Y.Q.Sun (1997).
Glycine residues provide flexibility for enzyme active sites.
  J Biol Chem, 272, 3190-3194.  
9268356 C.Spiess, H.P.Happersberger, M.O.Glocker, E.Spiess, K.Rippe, and M.Ehrmann (1997).
Biochemical characterization and mass spectrometric disulfide bond mapping of periplasmic alpha-amylase MalS of Escherichia coli.
  J Biol Chem, 272, 22125-22133.  
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.  
  9416598 K.S.Devulapalle, S.D.Goodman, Q.Gao, A.Hemsley, and G.Mooser (1997).
Knowledge-based model of a glucosyltransferase from the oral bacterial group of mutans streptococci.
  Protein Sci, 6, 2489-2493.  
18576090 M.E.Himmel, P.A.Karplus, J.Sakon, W.S.Adney, J.O.Baker, and S.R.Thomas (1997).
Polysaccharide hydrolase folds diversity of structure and convergence of function.
  Appl Biochem Biotechnol, 63, 315-325.  
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.  
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.  
8944767 M.Alkazaz, V.Desseaux, G.Marchis-Mouren, F.Payan, E.Forest, and M.Santimone (1996).
The mechanism of porcine pancreatic alpha-amylase. Kinetic evidence for two additional carbohydrate-binding sites.
  Eur J Biochem, 241, 787-796.  
8958075 M.Terashima, and S.Katoh (1996).
Modification of alpha-amylase functions by protein engineering.
  Ann N Y Acad Sci, 799, 65-69.  
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.  
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
7556163 F.Casset, A.Imberty, R.Haser, F.Payan, and S.Perez (1995).
Molecular modelling of the interaction between the catalytic site of pig pancreatic alpha-amylase and amylose fragments.
  Eur J Biochem, 232, 284-293.  
  8528071 G.D.Brayer, Y.Luo, and S.G.Withers (1995).
The structure of human pancreatic alpha-amylase at 1.8 A resolution and comparisons with related enzymes.
  Protein Sci, 4, 1730-1742.
PDB code: 1hny
  7613472 M.Qian, R.Haser, and F.Payan (1995).
Carbohydrate binding sites in a pancreatic alpha-amylase-substrate complex, derived from X-ray structure analysis at 2.1 A resolution.
  Protein Sci, 4, 747-755.  
8749857 S.Knapp, A.Rüdiger, G.Antranikian, P.L.Jorgensen, and R.Ladenstein (1995).
Crystallization and preliminary crystallographic analysis of an amylopullulanase from the hyperthermophilic archaeon Pyrococcus woesei.
  Proteins, 23, 595-597.  
7712292 J.D.McCarter, and S.G.Withers (1994).
Mechanisms of enzymatic glycoside hydrolysis.
  Curr Opin Struct Biol, 4, 885-892.  
7957256 M.Terashima, A.Kubo, M.Suzawa, Y.Itoh, and S.Katoh (1994).
The roles of the N-linked carbohydrate chain of rice alpha-amylase in thermostability and enzyme kinetics.
  Eur J Biochem, 226, 249-254.  
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.