spacer
spacer

PDBsum entry 3gly

Go to PDB code: 
protein ligands links
Hydrolase PDB id
3gly
Jmol
Contents
Protein chain
470 a.a. *
Ligands
NAG-NAG-BMA-MAN-
MAN
NAG-NAG-BMA-MAN-
MAN-MAN-MAN-MAN
MAN ×10
Waters ×673
* Residue conservation analysis
PDB id:
3gly
Name: Hydrolase
Title: Refined crystal structures of glucoamylase from aspergillus var. X100
Structure: Glucoamylase-471. Chain: a. Engineered: yes
Source: Aspergillus awamori. Organism_taxid: 105351
Resolution:
2.20Å     R-factor:   0.141    
Authors: A.E.Aleshin,C.Hoffman,L.M.Firsov,R.B.Honzatko
Key ref: A.E.Aleshin et al. (1994). Refined crystal structures of glucoamylase from Aspergillus awamori var. X100. J Mol Biol, 238, 575-591. PubMed id: 8176747
Date:
03-Jun-94     Release date:   01-Nov-94    
Supersedes: 1gly
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 Mol Biol 238:575-591 (1994)
PubMed id: 8176747  
 
 
Refined crystal structures of glucoamylase from Aspergillus awamori var. X100.
A.E.Aleshin, C.Hoffman, L.M.Firsov, R.B.Honzatko.
 
  ABSTRACT  
 
The refined crystal structures of a proteolytic fragment of glucoamylase from Aspergillus awamori var. X100 have been determined at pH 6 and 4 to a resolution of 2.2 A and 2.4 A, respectively. The models include the equivalent of residues 1 to 471 of glucoamylase from Aspergillus niger and a complete interpretation of the solvent structure. The R-factors of the pH 6 and 4 structures are 0.14 and 0.12, respectively, with root-mean-square deviations of 0.014 A and 0.012 A from expected bondlengths. The enzyme has the general shape of a doughnut. The "hole" of the doughnut consists of a barrier of hydrophobic residues at the center, which separates two water-filled voids, one of which serves as the active site. Three clusters of water molecules extend laterally from the active site. One of the lateral clusters connects the deepest recess of the active site to the surface of the enzyme. The most significant difference in the pH 4 and 6 structures is the thermal parameter of water 500, the putative nucleophile in the hydrolysis of maltooligosaccharides. Water 500 is associated more tightly with the enzyme at pH 4 (the pH of optimum catalysis) than at pH 6. In contrast to water 500, Glu179, the putative catalytic acid of glucoamylase, retains the same conformation in both structures and is in an environment that would favor the ionized, rather than the acid form of the side-chain. Glycosyl chains of 5 and 8 sugar residues are linked to Asparagines 171 and 395, respectively. The conformations of the two glycosyl chains are similar, being superimposable on each other with a root-mean-square discrepancy of 1.9 A. The N-glycosyl chains hydrogen bond to the surface of the protein through their terminal sugars, but otherwise do not interact strongly with the enzyme. The structures have ten serine/threonine residues, to each of which is linked a single mannose sugar. The structure of the ten O-glycosylated residues taken together suggests a well-defined conformation for proteins that have extensive O-glycosylation of their polypeptide chain.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20445236 Z.S.Derewenda (2010).
Application of protein engineering to enhance crystallizability and improve crystal properties.
  Acta Crystallogr D Biol Crystallogr, 66, 604-615.  
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
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.  
11828459 H.Driguez (2001).
Thiooligosaccharides as tools for structural biology.
  Chembiochem, 2, 311-318.  
11296285 N.E.Robinson, and A.B.Robinson (2001).
Prediction of protein deamidation rates from primary and three-dimensional structure.
  Proc Natl Acad Sci U S A, 98, 4367-4372.  
11106614 A.J.Orry, and B.A.Wallace (2000).
Modeling and docking the endothelin G-protein-coupled receptor.
  Biophys J, 79, 3083-3094.  
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.  
10449316 C.Ford (1999).
Improving operating performance of glucoamylase by mutagenesis.
  Curr Opin Biotechnol, 10, 353-357.  
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.  
12501412 A.Ducki, O.Grundmann, L.Konermann, F.Mayer, and M.Hoppert (1998).
Glucoamylase from Thermoanaerobacterium thermosaccharolyticum: Sequence studies and analysis of the macromolecular architecture of the enzyme.
  J Gen Appl Microbiol, 44, 327-335.  
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.  
9235002 A.L.Lomize, and H.I.Mosberg (1997).
Thermodynamic model of secondary structure for alpha-helical peptides and proteins.
  Biopolymers, 42, 239-269.  
9295271 C.M.Starks, K.Back, J.Chappell, and J.P.Noel (1997).
Structural basis for cyclic terpene biosynthesis by tobacco 5-epi-aristolochene synthase.
  Science, 277, 1815-1820.
PDB codes: 5eas 5eat 5eau
9434909 H.W.Park, and L.S.Beese (1997).
Protein farnesyltransferase.
  Curr Opin Struct Biol, 7, 873-880.  
9065406 H.W.Park, S.R.Boduluri, J.F.Moomaw, P.J.Casey, and L.S.Beese (1997).
Crystal structure of protein farnesyltransferase at 2.25 angstrom resolution.
  Science, 275, 1800-1804.
PDB code: 1ft1
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.  
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.  
9115442 T.N.Petersen, S.Kauppinen, and S.Larsen (1997).
The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix.
  Structure, 5, 533-544.
PDB code: 1rmg
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
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.  
8952477 S.K.Natarajan, and M.R.Sierks (1996).
Identification of enzyme-substrate and enzyme-product complexes in the catalytic mechanism of glucoamylase from Aspergillus awamori.
  Biochemistry, 35, 15269-15279.  
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.  
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.  
8747463 M.Sundaramoorthy, J.Terner, and T.L.Poulos (1995).
The crystal structure of chloroperoxidase: a heme peroxidase--cytochrome P450 functional hybrid.
  Structure, 3, 1367-1377.
PDB codes: 1cpo 2cpo
7712292 J.D.McCarter, and S.G.Withers (1994).
Mechanisms of enzymatic glycoside hydrolysis.
  Curr Opin Struct Biol, 4, 885-892.  
8033904 L.M.Firsov, K.N.Neustroev, A.E.Aleshin, C.M.Metzler, D.E.Metzler, R.D.Scott, B.Stoffer, T.Christensen, and B.Svensson (1994).
NMR spectroscopy of exchangeable protons of glucoamylase and of complexes with inhibitors in the 9-15-ppm range.
  Eur J Biochem, 223, 293-302.  
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.