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PDBsum entry 1qho

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protein ligands metals links
Hydrolase PDB id
1qho
Jmol
Contents
Protein chain
686 a.a. *
Ligands
MAL ×2
ABD
SO4
Metals
_CA ×3
Waters ×1106
* Residue conservation analysis
PDB id:
1qho
Name: Hydrolase
Title: Five-domain alpha-amylase from bacillus stearothermophilus, maltose/acarbose complex
Structure: Alpha-amylase. Chain: a. Fragment: intact protein, all 5 domains. Synonym: "maltogenic" alpha amylase. Engineered: yes. Other_details: contains an acarbose-derived hexasaccharide and maltose
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: bacillus subtilis. Expression_system_taxid: 1423
Resolution:
1.70Å     R-factor:   0.151     R-free:   0.175
Authors: Z.Dauter,M.Dauter,A.M.Brzozowski,S.Christensen,T.V.Borchert, L.Beier,K.S.Wilson,G.J.Davies
Key ref:
Z.Dauter et al. (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. PubMed id: 10387084 DOI: 10.1021/bi990256l
Date:
25-May-99     Release date:   31-May-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P19531  (AMYM_GEOSE) -  Maltogenic alpha-amylase
Seq:
Struc:
 
Seq:
Struc:
719 a.a.
686 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.133  - Glucan 1,4-alpha-maltohydrolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive alpha-maltose residues from the non-reducing ends of the chains.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     4 terms  

 

 
DOI no: 10.1021/bi990256l Biochemistry 38:8385-8392 (1999)
PubMed id: 10387084  
 
 
X-ray structure of Novamyl, the five-domain "maltogenic" alpha-amylase from Bacillus stearothermophilus: maltose and acarbose complexes at 1.7A resolution.
Z.Dauter, M.Dauter, A.M.Brzozowski, S.Christensen, T.V.Borchert, L.Beier, K.S.Wilson, G.J.Davies.
 
  ABSTRACT  
 
The three-dimensional structure of the Bacillus stearothermophilus "maltogenic" alpha-amylase, Novamyl, has been determined by X-ray crystallography at a resolution of 1.7 A. Unlike conventional alpha-amylases from glycoside hydrolase family 13, Novamyl exhibits the five-domain structure more usually associated with cyclodextrin glycosyltransferase. Complexes of the enzyme with both maltose and the inhibitor acarbose have been characterized. In the maltose complex, two molecules of maltose are found in the -1 to -2 and +2 to +3 subsites of the active site, with two more on the C and E domains. The C-domain maltose occupies a position identical to one previously observed in the Bacillus circulans CGTase structure [Lawson, C. L., et al. (1994) J. Mol. Biol. 236, 590-600], suggesting that the C-domain plays a genuine biological role in saccharide binding. In the acarbose-maltose complex, the tetrasaccharide inhibitor acarbose is found as an extended hexasaccharide species, bound in the -3 to +3 subsites. The transition state mimicking pseudosaccharide is bound in the -1 subsite of the enzyme in a 2H3 half-chair conformation, as expected. The active site of Novamyl lies in an open gully, fully consistent with its ability to perform internal cleavage via an endo as opposed to an exo activity.
 

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
19682075 C.Christiansen, M.Abou Hachem, S.Janecek, A.Viksø-Nielsen, A.Blennow, and B.Svensson (2009).
The carbohydrate-binding module family 20--diversity, structure, and function.
  FEBS J, 276, 5006-5029.  
19367403 R.M.Kelly, L.Dijkhuizen, and H.Leemhuis (2009).
The evolution of cyclodextrin glucanotransferase product specificity.
  Appl Microbiol Biotechnol, 84, 119-133.  
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
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.  
17879332 S.Rana, B.Kundu, and S.Durani (2007).
A mixed-alpha,beta miniprotein stereochemically reprogrammed to high-binding affinity for acetylcholine.
  Biopolymers, 87, 231-243.  
16262690 M.Machovic, B.Svensson, E.A.MacGregor, and S.Janecek (2005).
A new clan of CBM families based on bioinformatics of starch-binding domains from families CBM20 and CBM21.
  FEBS J, 272, 5497-5513.  
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
15239057 D.Hoffmeister, and J.S.Thorson (2004).
Mechanistic implications of Escherichia coli galactokinase structure-based engineering.
  Chembiochem, 5, 989-992.  
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.  
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
12624092 H.R.Mott, D.Nietlispach, L.J.Hopkins, G.Mirey, J.H.Camonis, and D.Owen (2003).
Structure of the GTPase-binding domain of Sec5 and elucidation of its Ral binding site.
  J Biol Chem, 278, 17053-17059.
PDB code: 1hk6
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
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.  
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.  
12364331 L.K.Skov, O.Mirza, D.Sprogøe, I.Dar, M.Remaud-Simeon, C.Albenne, P.Monsan, and M.Gajhede (2002).
Oligosaccharide and sucrose complexes of amylosucrase. Structural implications for the polymerase activity.
  J Biol Chem, 277, 47741-47747.
PDB codes: 1mvy 1mw0 1mw1 1mw2 1mw3
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.  
12323357 O.Kirk, T.V.Borchert, and C.C.Fuglsang (2002).
Industrial enzyme applications.
  Curr Opin Biotechnol, 13, 345-351.  
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.  
11551466 B.Höcker, C.Jürgens, M.Wilmanns, and R.Sterner (2001).
Stability, catalytic versatility and evolution of the (beta alpha)(8)-barrel fold.
  Curr Opin Biotechnol, 12, 376-381.  
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.  
11828460 S.Fort, A.Varrot, M.Schülein, S.Cottaz, H.Driguez, and G.J.Davies (2001).
Mixed-linkage cellooligosaccharides: a new class of glycoside hydrolase inhibitors.
  Chembiochem, 2, 319-325.
PDB code: 1e5j
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
  11082203 I.Przylas, Y.Terada, K.Fujii, T.Takaha, W.Saenger, and N.Sträter (2000).
X-ray structure of acarbose bound to amylomaltase from Thermus aquaticus. Implications for the synthesis of large cyclic glucans.
  Eur J Biochem, 267, 6903-6913.
PDB code: 1esw
11150610 J.E.Nielsen, and T.V.Borchert (2000).
Protein engineering of bacterial alpha-amylases.
  Biochim Biophys Acta, 1543, 253-274.  
10877806 K.Ohdan, T.Kuriki, H.Takata, H.Kaneko, and S.Okada (2000).
Introduction of raw starch-binding domains into Bacillus subtilis alpha-amylase by fusion with the starch-binding domain of Bacillus cyclomaltodextrin glucanotransferase.
  Appl Environ Microbiol, 66, 3058-3064.  
10705452 N.Ichikawa, R.Fujisaka, and R.Kuribayashi (2000).
Requirement for lysine-19 of the yeast mitochondrial ATPase inhibitor for the stability of the inactivated inhibitor-F1Fo complex at higher pH.
  Biosci Biotechnol Biochem, 64, 89-95.  
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.