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PDBsum entry 1agm

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Hydrolase PDB id
1agm
Jmol
Contents
Protein chain
470 a.a. *
Ligands
NAG-NAG-BMA-MAN-
MAN
NAG-NAG-BMA-MAN-
MAN-MAN-MAN-MAN
MAN ×10
ACR ×2
Waters ×535
* Residue conservation analysis
PDB id:
1agm
Name: Hydrolase
Title: Refined structure for the complex of acarbose with glucoamyl aspergillus awamori var. X100 to 2.4 angstroms resolution
Structure: Glucoamylase-471. Chain: a. Engineered: yes
Source: Aspergillus awamori. Organism_taxid: 105351
Resolution:
2.30Å     R-factor:   0.124    
Authors: A.E.Aleshin,L.M.Firsov,R.B.Honzatko
Key ref: A.E.Aleshin et al. (1994). Refined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. X100 to 2.4-A resolution. J Biol Chem, 269, 15631-15639. PubMed id: 8195212
Date:
13-May-94     Release date:   30-Sep-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P69327  (AMYG_ASPAW) -  Glucoamylase
Seq:
Struc:
 
Seq:
Struc:
640 a.a.
470 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 22 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.3  - Glucan 1,4-alpha-glucosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of terminal 1,4-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     polysaccharide metabolic process   1 term 
  Biochemical function     catalytic activity     3 terms  

 

 
J Biol Chem 269:15631-15639 (1994)
PubMed id: 8195212  
 
 
Refined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. X100 to 2.4-A resolution.
A.E.Aleshin, L.M.Firsov, R.B.Honzatko.
 
  ABSTRACT  
 
The three-dimensional structure of the pseudotetrasaccharide acarbose complexed with glucoamylase II(471) from Aspergillus awamori var. X100 has been determined to 2.4-A resolution. The model includes residues corresponding to 1-471 of glucoamylase I from Aspergillus niger, a single molecule of bound acarbose, and 535 sites for water molecules. The crystallographic R factor from refinement is 0.124, and the root-mean-squared deviation in bond distances is 0.013 A. Electron density for a single molecule of bound acarbose defines what may be the first four subsites in the binding of extended maltooligosaccharides. Hydrogen bonds between acarbose and the enzyme involve Arg54, Asp55, Arg305, carbonyl177, main chain amide121, Glu179, Glu180, and carbonyl179. Glu179 forms a salt link to the imino linkage between the first and second residues of acarbose. This buried salt link probably contributes significantly to the unusually tight association (Kd approximately 10(-12) M) of acarbose with glucoamylase. In addition, a significant hydrophobic contact between the third residue of acarbose and the side chain of Trp120 distorts the three-center angle of the glucosidic linkage between the second and third residues of acarbose. A water molecule (water500) hydrogen bonds to Glu400 and the 6-hydroxyl of the valienamine moiety of acarbose and is at an approximate distance of 3.7 A from the "anomeric" carbon of the inhibitor. The relevance of the acarbose-glucoamylase complex to the mechanism of enzymic hydrolysis of oligosaccharides is discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20549574 J.A.Mertens, J.D.Braker, and D.B.Jordan (2010).
Catalytic properties of two Rhizopus oryzae 99-880 glucoamylase enzymes without starch binding domains expressed in Pichia pastoris.
  Appl Biochem Biotechnol, 162, 2197-2213.  
19484200 P.Kumar, A.Islam, F.Ahmad, and T.Satyanarayana (2010).
Characterization of a neutral and thermostable glucoamylase from the thermophilic mold Thermomucor indicae-seudaticae: activity, stability, and structural correlation.
  Appl Biochem Biotechnol, 160, 879-890.  
18074341 A.D.Hill, and P.J.Reilly (2008).
A Gibbs free energy correlation for automated docking of carbohydrates.
  J Comput Chem, 29, 1131-1141.  
18083888 E.Kainz, A.Gallmetzer, C.Hatzl, J.H.Nett, H.Li, T.Schinko, R.Pachlinger, H.Berger, Y.Reyes-Dominguez, A.Bernreiter, T.Gerngross, S.Wildt, and J.Strauss (2008).
N-glycan modification in Aspergillus species.
  Appl Environ Microbiol, 74, 1076-1086.  
17938981 M.Michelin, R.Ruller, R.J.Ward, L.A.Moraes, J.A.Jorge, H.F.Terenzi, and M.d.e. .L.Polizeli (2008).
Purification and biochemical characterization of a thermostable extracellular glucoamylase produced by the thermotolerant fungus Paecilomyces variotii.
  J Ind Microbiol Biotechnol, 35, 17-25.  
17887954 B.Sterner, R.Singh, and B.Berger (2007).
Predicting and annotating catalytic residues: an information theoretic approach.
  J Comput Biol, 14, 1058-1073.  
16649993 J.Sevcík, E.Hostinová, A.Solovicová, J.Gasperík, Z.Dauter, and K.S.Wilson (2006).
Structure of the complex of a yeast glucoamylase with acarbose reveals the presence of a raw starch binding site on the catalytic domain.
  FEBS J, 273, 2161-2171.
PDB codes: 2f6d 2fba
16001416 A.Laederach, and P.J.Reilly (2005).
Modeling protein recognition of carbohydrates.
  Proteins, 60, 591-597.  
14981306 K.Ichikawa, T.Tonozuka, R.Uotsu-Tomita, H.Akeboshi, A.Nishikawa, and Y.Sakano (2004).
Purification, characterization, and subsite affinities of Thermoactinomyces vulgaris R-47 maltooligosaccharide-metabolizing enzyme homologous to glucoamylases.
  Biosci Biotechnol Biochem, 68, 413-420.  
16233603 N.Morimoto, Y.Yasukawa, K.Watanabe, T.Unno, H.Ito, and H.Matsui (2004).
Cloning and heterologous expression of a glucodextranase gene from Arthrobacter globiformis I42, and experimental evidence for the catalytic diad of the recombinant enzyme.
  J Biosci Bioeng, 97, 127-130.  
12892492 R.Soriano, L.F.Bautista, M.Martínez, and J.Aracil (2003).
Use of a diffusion model for mono- and bicomponent anion-exchange of two isoenzymes of glucoamylase from Aspergillus niger in a fixed bed.
  Biotechnol Prog, 19, 1283-1291.  
16233198 I.Maru, J.Ohnishi, Y.Ohta, and Y.Tsukada (2002).
Why is sialic acid attracting interest now? Complete enzymatic synthesis of sialic acid with N-acylglucosamine 2-epimerase.
  J Biosci Bioeng, 93, 258-265.  
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.  
  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
10913265 M.R.Sierks, and B.Svensson (2000).
Energetic and mechanistic studies of glucoamylase using molecular recognition of maltose OH groups coupled with site-directed mutagenesis.
  Biochemistry, 39, 8585-8592.  
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.  
10630989 T.Weimar, B.Stoffer, B.Svensson, and B.M.Pinto (2000).
Complexes of glucoamylase with maltoside heteroanalogues: bound ligand conformations by use of transferred NOE experiments and molecular modeling.
  Biochemistry, 39, 300-306.  
10491121 A.Solovicová, T.Christensen, E.Hostinová, J.Gasperík, J.Sevcĭk, and B.Svensson (1999).
Structure-function relationships in glucoamylases encoded by variant Saccharomycopsis fibuligera genes.
  Eur J Biochem, 264, 756-764.  
10614065 K.D.Randell, T.P.Frandsen, B.Stoffer, M.A.Johnson, B.Svensson, and B.M.Pinto (1999).
Synthesis and glycosidase inhibitory activity of 5-thioglucopyranosylamines. Molecular modeling of complexes with glucoamylase.
  Carbohydr Res, 321, 143-156.  
10220320 M.O'Reilly, K.A.Watson, and L.N.Johnson (1999).
The crystal structure of the Escherichia coli maltodextrin phosphorylase-acarbose complex.
  Biochemistry, 38, 5337-5345.
PDB code: 2ecp
10320360 T.Christensen, B.Svensson, and B.W.Sigurskjold (1999).
Thermodynamics of reversible and irreversible unfolding and domain interactions of glucoamylase from Aspergillus niger studied by differential scanning and isothermal titration calorimetry.
  Biochemistry, 38, 6300-6310.  
  10103262 T.J.Kim, M.J.Kim, B.C.Kim, J.C.Kim, T.K.Cheong, J.W.Kim, and K.H.Park (1999).
Modes of action of acarbose hydrolysis and transglycosylation catalyzed by a thermostable maltogenic amylase, the gene for which was cloned from a Thermus strain.
  Appl Environ Microbiol, 65, 1644-1651.  
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
9972233 A.Tanaka, S.Karita, Y.Kosuge, K.Senoo, H.Obata, and N.Kitamoto (1998).
Thermal unfolding of the starch binding domain of Aspergillus niger glucoamylase.
  Biosci Biotechnol Biochem, 62, 2127-2132.  
9671514 B.W.Sigurskjold, T.Christensen, N.Payre, S.Cottaz, H.Driguez, and B.Svensson (1998).
Thermodynamics of binding of heterobidentate ligands consisting of spacer-connected acarbose and beta-cyclodextrin to the catalytic and starch-binding domains of glucoamylase from Aspergillus niger shows that the catalytic and starch-binding sites are in close proximity in space.
  Biochemistry, 37, 10446-10452.  
9521694 H.P.Fierobe, A.J.Clarke, D.Tull, and B.Svensson (1998).
Enzymatic properties of the cysteinesulfinic acid derivative of the catalytic-base mutant Glu400-->Cys of glucoamylase from Aspergillus awamori.
  Biochemistry, 37, 3753-3759.  
9521693 H.P.Fierobe, E.Mirgorodskaya, K.A.McGuire, P.Roepstorff, B.Svensson, and A.J.Clarke (1998).
Restoration of catalytic activity beyond wild-type level in glucoamylase from Aspergillus awamori by oxidation of the Glu400-->Cys catalytic-base mutant to cysteinesulfinic acid.
  Biochemistry, 37, 3743-3752.  
10209866 K.H.Park, M.J.Kim, H.S.Lee, N.S.Han, D.Kim, and J.F.Robyt (1998).
Transglycosylation reactions of Bacillus stearothermophilus maltogenic amylase with acarbose and various acceptors.
  Carbohydr Res, 313, 235-246.  
9860832 R.Mosi, H.Sham, J.C.Uitdehaag, R.Ruiterkamp, B.W.Dijkstra, and S.G.Withers (1998).
Reassessment of acarbose as a transition state analogue inhibitor of cyclodextrin glycosyltransferase.
  Biochemistry, 37, 17192-17198.  
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
9061788 P.M.Coutinho, M.K.Dowd, and P.J.Reilly (1997).
Automated docking of monosaccharide substrates and analogues and methyl alpha-acarviosinide in the glucoamylase active site.
  Proteins, 27, 235-248.  
9365988 P.M.Coutinho, and P.J.Reilly (1997).
Glucoamylase structural, functional, and evolutionary relationships.
  Proteins, 29, 334-347.  
9461285 T.Christensen, B.B.Stoffer, B.Svensson, and U.Christensen (1997).
Some details of the reaction mechanism of glucoamylase from Aspergillus niger--kinetic and structural studies on Trp52-->Phe and Trp317-->Phe mutants.
  Eur J Biochem, 250, 638-645.  
8679589 A.E.Aleshin, B.Stoffer, L.M.Firsov, B.Svensson, and R.B.Honzatko (1996).
Crystallographic complexes of glucoamylase with maltooligosaccharide analogs: relationship of stereochemical distortions at the nonreducing end to the catalytic mechanism.
  Biochemistry, 35, 8319-8328.
PDB codes: 1gah 1gai
8679632 H.P.Fierobe, B.B.Stoffer, T.P.Frandsen, and B.Svensson (1996).
Mutational modulation of substrate bond-type specificity and thermostability of glucoamylase from Aspergillus awamori by replacement with short homologue active site sequences and thiol/disulfide engineering.
  Biochemistry, 35, 8696-8704.  
8879556 J.W.Darrow, and D.G.Drueckhammer (1996).
A cyclic phosphonamidate analogue of glucose as a selective inhibitor of inverting glycosidases.
  Bioorg Med Chem, 4, 1341-1348.  
  8935166 L.A.van den Broek, M.W.Kat-Van Den Nieuwenhof, T.D.Butters, and C.A.Van Boeckel (1996).
Synthesis of alpha-glucosidase I inhibitors showing antiviral (HIV-1) and immunosuppressive activity.
  J Pharm Pharmacol, 48, 172-178.  
8639668 M.R.Sierks, and B.Svensson (1996).
Catalytic mechanism of glucoamylase probed by mutagenesis in conjunction with hydrolysis of alpha-D-glucopyranosyl fluoride and maltooligosaccharides.
  Biochemistry, 35, 1865-1871.  
8958087 P.M.Coutinho, M.K.Dowd, and P.J.Reilly (1996).
Automated docking of glucoamylase substrates and inhibitors.
  Ann N Y Acad Sci, 799, 164-171.  
8608145 S.Natarajan, and M.R.Sierks (1996).
Functional and structural roles of the highly conserved Trp120 loop region of glucoamylase from Aspergillus awamori.
  Biochemistry, 35, 3050-3058.  
8942667 U.Christensen, K.Olsen, B.B.Stoffer, and B.Svensson (1996).
Substrate binding mechanism of Glu180-->Gln, Asp176-->Asn, and wild-type glucoamylases from Aspergillus niger.
  Biochemistry, 35, 15009-15018.  
7588803 A.J.Jacks, K.Sorimachi, M.F.Le Gal-Coëffet, G.Williamson, D.B.Archer, and M.P.Williamson (1995).
1H and 15N assignments and secondary structure of the starch-binding domain of glucoamylase from Aspergillus niger.
  Eur J Biochem, 233, 568-578.  
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.  
8574695 G.S.Jacob (1995).
Glycosylation inhibitors in biology and medicine.
  Curr Opin Struct Biol, 5, 605-611.  
  7795519 S.G.Withers, and R.Aebersold (1995).
Approaches to labeling and identification of active site residues in glycosidases.
  Protein Sci, 4, 361-372.  
7712292 J.D.McCarter, and S.G.Withers (1994).
Mechanisms of enzymatic glycoside hydrolysis.
  Curr Opin Struct Biol, 4, 885-892.  
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.