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PDBsum entry 1gai

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protein ligands links
Hydrolase PDB id
1gai
Jmol
Contents
Protein chain
472 a.a. *
Ligands
MAN ×10
NAG-NAG-BMA-MAN-
MAN
NAG-NAG-BMA-MAN-
MAN-MAN-MAN-MAN-
MAN
GAC
Waters ×1713
* Residue conservation analysis
PDB id:
1gai
Name: Hydrolase
Title: Glucoamylase-471 complexed with d-gluco-dihydroacarbose
Structure: Glucoamylase-471. Chain: a. Fragment: residues 1-471. Synonym: glucoamylase-ii, glucan 1,4-alpha-glucosidase. Other_details: complexed with d-gluco-dihydroacarbose
Source: Aspergillus awamori. Organism_taxid: 105351. Variant: x100
Resolution:
1.70Å     R-factor:   0.147     R-free:   0.167
Authors: A.E.Aleshin,B.Stoffer,L.M.Firsov,B.Svensson,R.B.Honzatko
Key ref:
A.E.Aleshin et al. (1996). Crystallographic complexes of glucoamylase with maltooligosaccharide analogs: relationship of stereochemical distortions at the nonreducing end to the catalytic mechanism. Biochemistry, 35, 8319-8328. PubMed id: 8679589 DOI: 10.1021/bi960321g
Date:
06-Mar-96     Release date:   17-Aug-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P69327  (AMYG_ASPAW) -  Glucoamylase
Seq:
Struc:
 
Seq:
Struc:
640 a.a.
472 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  

 

 
DOI no: 10.1021/bi960321g Biochemistry 35:8319-8328 (1996)
PubMed id: 8679589  
 
 
Crystallographic complexes of glucoamylase with maltooligosaccharide analogs: relationship of stereochemical distortions at the nonreducing end to the catalytic mechanism.
A.E.Aleshin, B.Stoffer, L.M.Firsov, B.Svensson, R.B.Honzatko.
 
  ABSTRACT  
 
Crystal structures at pH 4 of complexes of glucoamylase from Aspergillus awamori var. X100 with the pseudotetrasaccharides D-gluco-dihydroacarbose and acarbose have been refined to R-factors of 0.147 and 0.131 against data to 1.7- and 2.0-A resolution, respectively. The two inhibitors bind in nearly identical manners, each exhibiting a dual binding mode with respect to the location of the last sugar residues. The reduced affinity of D-gluco-dihydroacarbose (K1 = 10(-8) M) relative to acarbose (K1 = 10(-12) M) may stem in part from the weakening of hydrogen bonds of the catalytic water (Wat 500) to the enzyme. Steric contacts between the nonreducing end of D-gluco-dihydroacarbose and the catalytic water perturb Wat 500 from its site of optimal hydrogen bonding to the active site. Interactions within the active site displace the 6-hydroxymethyl group of the nonreducing end of both acarbose and D-gluco-dihydroacarbose toward a more axial position. In the case of D-gluco-dihydroacarbose the shift in the position of the 6-hydroxymethyl group occurs with a 12 degrees change in two dihedral angles of the glucopyranose ring toward a half-chair conformation. The observed conformational distortion of the first residue of D-gluco-dihydroacarbose is consistent with the generation of a glucopyranosyl cation in the transition state. Comparable distortions of stereochemistry in model compounds require approximately 2 kcal/mol, not more than 25% of the energy necessary to form the half-chair conformation in glucose. The magnitude of stereochemical distortion observed in the active site of glucoamylase suggests that favorable electrostatic interactions between the putative glucopyranosyl cation intermediate and the active site must be more important in stabilizing the transition state than mechanical distortion of the substrate.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20066263 T.M.Gloster, and G.J.Davies (2010).
Glycosidase inhibition: assessing mimicry of the transition state.
  Org Biomol Chem, 8, 305-320.  
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.  
15211513 L.L.Videau, W.B.Arendall, and J.S.Richardson (2004).
The cis-Pro touch-turn: a rare motif preferred at functional sites.
  Proteins, 56, 298-309.  
15148314 T.Itoh, S.Akao, W.Hashimoto, B.Mikami, and K.Murata (2004).
Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution.
  J Biol Chem, 279, 31804-31812.
PDB code: 1vd5
12964193 A.Laederach, and P.J.Reilly (2003).
Specific empirical free energy function for automated docking of carbohydrates to proteins.
  J Comput Chem, 24, 1748-1757.  
12005440 S.C.Garman, L.Hannick, A.Zhu, and D.N.Garboczi (2002).
The 1.9 A structure of alpha-N-acetylgalactosaminidase: molecular basis of glycosidase deficiency diseases.
  Structure, 10, 425-434.
PDB codes: 1ktb 1ktc
12022868 T.Shimizu, T.Nakatsu, K.Miyairi, T.Okuno, and H.Kato (2002).
Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.
  Biochemistry, 41, 6651-6659.
PDB codes: 1k5c 1kcc 1kcd
  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.  
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.  
10469642 K.A.Watson, C.McCleverty, S.Geremia, S.Cottaz, H.Driguez, and L.N.Johnson (1999).
Phosphorylase recognition and phosphorolysis of its oligosaccharide substrate: answers to a long outstanding question.
  EMBO J, 18, 4619-4632.
PDB codes: 1e4o 1qm5
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.  
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.  
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.  
9345622 A.White, and D.R.Rose (1997).
Mechanism of catalysis by retaining beta-glycosyl hydrolases.
  Curr Opin Struct Biol, 7, 645-651.  
9345621 B.Henrissat, and G.Davies (1997).
Structural and sequence-based classification of glycoside hydrolases.
  Curr Opin Struct Biol, 7, 637-644.  
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.  
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.