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PDBsum entry 1e3x

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protein metals links
Hydrolase PDB id
1e3x
Jmol
Contents
Protein chain
483 a.a. *
Metals
_NA
_CA ×4
Waters ×682
* Residue conservation analysis
PDB id:
1e3x
Name: Hydrolase
Title: Native structure of chimaeric amylase from b. Amyloliquefaciens and b. Licheniformis at 1.92a
Structure: Alpha-amylase. Chain: a. Engineered: yes. Other_details: chimaeric structure consisting of residues 1 - 300 of b. Amyloliquefaciens and residues 301 - 483 of b. Licheniformis
Source: Bacillus amyloliquefaciens. Organism_taxid: 1390. Expressed in: bacillus amyloliquefaciens. Expression_system_taxid: 1390. Other_details: synthetic gene
Resolution:
1.90Å     R-factor:   0.140     R-free:   0.200
Authors: A.M.Brzozowski,D.M.Lawson,J.P.Turkenburg, H.Bisgaard-Frantzen,A.Svendsen,T.V.Borchert,Z.Dauter, K.S.Wilson,G.J.Davies
Key ref:
A.M.Brzozowski et al. (2000). Structural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes. Biochemistry, 39, 9099-9107. PubMed id: 10924103 DOI: 10.1021/bi0000317
Date:
26-Jun-00     Release date:   21-Jun-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00692  (AMY_BACAM) -  Alpha-amylase
Seq:
Struc:
514 a.a.
483 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 32 residue positions (black crosses)

 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     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     4 terms  

 

 
DOI no: 10.1021/bi0000317 Biochemistry 39:9099-9107 (2000)
PubMed id: 10924103  
 
 
Structural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes.
A.M.Brzozowski, D.M.Lawson, J.P.Turkenburg, H.Bisgaard-Frantzen, A.Svendsen, T.V.Borchert, Z.Dauter, K.S.Wilson, G.J.Davies.
 
  ABSTRACT  
 
Several chimeric alpha-amylases genes were constructed by an in vivo recombination technique from the Bacillus amyloliquefaciens and Bacillus licheniformis genes. One of the fusion amylases (hereafter BA2), consisting of residues 1-300 from B. amyloliquefaciens and 301-483 from B. licheniformis, has been extensively studied by X-ray crystallography at resolutions between 2.2 and 1.7 A. The 3-dimensional structure of the native enzyme was solved by multiple isomorphous replacement, and refined at a resolution of 1.7 A. It consists of 483 amino acids, organized similarly to the known B. lichiniformis alpha-amylase structure [Machius et al. (1995) J. Mol. Biol. 246, 545-559], but features 4 bound calcium ions. Two of these form part of a linear cluster of three ions, the central ion being attributed to sodium. This cluster lies at the junction of the A and B domains with one calcium of the cluster structurally equivalent to the major Ca(2+) binding site of fungal alpha-amylases. The third calcium ion is found at the interface of the A and C domains. BA2 contains a fourth calcium site, not observed in the B. licheniformis alpha-amylase structure. It is found on the C domain where it bridges the two beta-sheets. Three acid residues (Glu261, Asp328, and Asp231) form an active site similar to that seen in other amylases. In the presence of TRIS buffer, a single molecule of TRIS occupies the -1 subsite of the enzyme where it is coordinated by the three active-center carboxylates. Kinetic data reveal that BA2 displays properties intermediate to those of its parents. Data for crystals soaked in maltooligosaccharides reveal the presence of a maltotriose binding site on the N-terminal face of the (beta/alpha)(8) barrel of the molecule, not previously described for any alpha-amylase structure, the biological function of which is unclear. Data for a complex soaked with the tetrasaccharide inhibitor acarbose, at 1.9 A, reveal a decasaccharide moiety, spanning the -7 to +3 subsites of the enzyme. The unambiguous presence of three unsaturated rings in the (2)H(3) half-chair/(2)E envelope conformation, adjacent to three 6-deoxypyranose units, clearly demonstrates synthesis of this acarbose-derived decasaccharide by a two-step transglycosylation mechanism.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21426903 L.C.Tsai, C.H.Hsiao, W.Y.Liu, L.M.Yin, and L.F.Shyur (2011).
Structural basis for the inhibition of 1,3-1,4-β-d-glucanase by noncompetitive calcium ion and competitive Tris inhibitors.
  Biochem Biophys Res Commun, 407, 593-598.  
19763902 O.Prakash, and N.Jaiswal (2010).
alpha-Amylase: an ideal representative of thermostable enzymes.
  Appl Biochem Biotechnol, 160, 2401-2414.  
19841977 Y.Liu, W.Shen, G.Y.Shi, and Z.X.Wang (2010).
Role of the calcium-binding residues Asp231, Asp233, and Asp438 in alpha-amylase of Bacillus amyloliquefaciens as revealed by mutational analysis.
  Curr Microbiol, 60, 162-166.  
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.  
18799462 A.Cartmell, E.Topakas, V.M.Ducros, M.D.Suits, G.J.Davies, and H.J.Gilbert (2008).
The Cellvibrio japonicus Mannanase CjMan26C Displays a Unique exo-Mode of Action That Is Conferred by Subtle Changes to the Distal Region of the Active Site.
  J Biol Chem, 283, 34403-34413.
PDB codes: 2vx4 2vx5 2vx6 2vx7
18443744 J.L.Uma Maheswar Rao, and T.Satyanarayana (2008).
Biophysical and biochemical characterization of a hyperthermostable and Ca2+ -independent alpha-Amylase of an extreme thermophile Geobacillus thermoleovorans.
  Appl Biochem Biotechnol, 150, 205-219.  
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.  
18848471 T.M.Gloster, J.P.Turkenburg, J.R.Potts, B.Henrissat, and G.J.Davies (2008).
Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora.
  Chem Biol, 15, 1058-1067.
PDB codes: 2jka 2jke 2jkp
18473149 Y.Xu, M.Yang, J.Sun, J.Qian, D.Zhang, Y.Sun, L.Ma, and C.Zhu (2008).
Glycogen branching enzyme: a novel deltamethrin resistance-associated gene from Culex pipiens pallens.
  Parasitol Res, 103, 449-458.  
17287210 L.E.Tailford, V.A.Money, N.L.Smith, C.Dumon, G.J.Davies, and H.J.Gilbert (2007).
Mannose foraging by Bacteroides thetaiotaomicron: structure and specificity of the beta-mannosidase, BtMan2A.
  J Biol Chem, 282, 11291-11299.
PDB code: 2je8
17598074 R.Priyadharshini, and P.Gunasekaran (2007).
Site-directed mutagenesis of the calcium-binding site of alpha-amylase of Bacillus licheniformis.
  Biotechnol Lett, 29, 1493-1499.  
17803687 S.Bozonnet, M.T.Jensen, M.M.Nielsen, N.Aghajari, M.H.Jensen, B.Kramhøft, M.Willemoës, S.Tranier, R.Haser, and B.Svensson (2007).
The 'pair of sugar tongs' site on the non-catalytic domain C of barley alpha-amylase participates in substrate binding and activity.
  FEBS J, 274, 5055-5067.
PDB codes: 2qps 2qpu
17166853 Y.Tanaka, K.Morikawa, Y.Ohki, M.Yao, K.Tsumoto, N.Watanabe, T.Ohta, and I.Tanaka (2007).
Structural and mutational analyses of Drp35 from Staphylococcus aureus: a possible mechanism for its lactonase activity.
  J Biol Chem, 282, 5770-5780.
PDB codes: 2dg0 2dg1 2dso
17492665 Y.Tanaka, T.Sasaki, I.Kumagai, Y.Yasutake, M.Yao, I.Tanaka, and K.Tsumoto (2007).
Molecular properties of two proteins homologous to PduO-type ATP:cob(I)alamin adenosyltransferase from Sulfolobus tokodaii.
  Proteins, 68, 446-457.
PDB code: 1wvt
16172888 H.Bach, and D.L.Gutnick (2006).
Novel polysaccharide-protein-based amphipathic formulations.
  Appl Microbiol Biotechnol, 71, 34-38.  
16452622 R.Kanai, K.Haga, T.Akiba, K.Yamane, and K.Harata (2006).
Role of Trp140 at subsite -6 on the maltohexaose production of maltohexaose-producing amylase from alkalophilic Bacillus sp.707.
  Protein Sci, 15, 468-477.
PDB codes: 2d3l 2d3n
15681870 G.J.Davies, A.M.Brzozowski, Z.Dauter, M.D.Rasmussen, T.V.Borchert, and K.S.Wilson (2005).
Structure of a Bacillus halmapalus family 13 alpha-amylase, BHA, in complex with an acarbose-derived nonasaccharide at 2.1 A resolution.
  Acta Crystallogr D Biol Crystallogr, 61, 190-193.
PDB code: 1w9x
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
15819888 W.Ubhayasekera, I.G.Muñoz, A.Vasella, J.Ståhlberg, and S.L.Mowbray (2005).
Structures of Phanerochaete chrysosporium Cel7D in complex with product and inhibitors.
  FEBS J, 272, 1952-1964.
PDB codes: 1z3t 1z3v 1z3w
16030022 X.Robert, R.Haser, H.Mori, B.Svensson, and N.Aghajari (2005).
Oligosaccharide binding to barley alpha-amylase 1.
  J Biol Chem, 280, 32968-32978.
PDB codes: 1rp8 1rp9 1rpk
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.  
15274914 S.B.Gabelli, M.A.Bianchet, H.F.Azurmendi, Z.Xia, V.Sarawat, A.S.Mildvan, and L.M.Amzel (2004).
Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus.
  Structure, 12, 927-935.
PDB code: 1rya
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.  
14617662 M.Kagawa, Z.Fujimoto, M.Momma, K.Takase, and H.Mizuno (2003).
Crystal structure of Bacillus subtilis alpha-amylase in complex with acarbose.
  J Bacteriol, 185, 6981-6984.
PDB code: 1ua7
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
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.  
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
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.  
11856334 T.P.Frandsen, M.M.Palcic, and B.Svensson (2002).
Substrate recognition by three family 13 yeast alpha-glucosidases.
  Eur J Biochem, 269, 728-734.  
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.  
11150610 J.E.Nielsen, and T.V.Borchert (2000).
Protein engineering of bacterial alpha-amylases.
  Biochim Biophys Acta, 1543, 253-274.  
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.