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PDBsum entry 1kul

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Hydrolase PDB id
1kul
Jmol
Contents
Protein chain
108 a.a. *
* Residue conservation analysis
PDB id:
1kul
Name: Hydrolase
Title: Glucoamylase, granular starch-binding domain, nmr, 5 structures
Structure: Glucoamylase. Chain: a. Fragment: binding domain, residues 509 - 616. Synonym: 1,4-alpha-d-glucan glucohydrolase. Engineered: yes. Other_details: ph 5.2, 313 k
Source: Aspergillus niger. Organism_taxid: 5061. Strain: ab4.1. Gene: a. Niger glaa. Expressed in: aspergillus niger. Expression_system_taxid: 5061.
NMR struc: 5 models
Authors: K.Sorimachi,A.J.Jacks,M.-F.Le Gal-Coeffet,G.Williamson, D.B.Archer,M.P.Williamson
Key ref:
K.Sorimachi et al. (1996). Solution structure of the granular starch binding domain of glucoamylase from Aspergillus niger by nuclear magnetic resonance spectroscopy. J Mol Biol, 259, 970-987. PubMed id: 8683599 DOI: 10.1006/jmbi.1996.0374
Date:
12-Jan-96     Release date:   11-Jul-96    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P69328  (AMYG_ASPNG) -  Glucoamylase
Seq:
Struc:
 
Seq:
Struc:
640 a.a.
108 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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!
  Biochemical function     catalytic activity     3 terms  

 

 
DOI no: 10.1006/jmbi.1996.0374 J Mol Biol 259:970-987 (1996)
PubMed id: 8683599  
 
 
Solution structure of the granular starch binding domain of glucoamylase from Aspergillus niger by nuclear magnetic resonance spectroscopy.
K.Sorimachi, A.J.Jacks, M.F.Le Gal-Coëffet, G.Williamson, D.B.Archer, M.P.Williamson.
 
  ABSTRACT  
 
The solution structure of the granular starch binding domain (SBD) of glucoamylase 1 from Aspergillus niger has been determined by heteronuclear multidimensional nuclear magnetic resonance spectroscopy and simulated annealing. A total of 1092 nuclear Overhauser enhancement-derived 1H-1H distance constraints, 137 dihedral constraints and 86 hydrogen bond constraints were incorporated into an X-PLOR simulated annealing and refinement protocol. The family of calculated structures shows a well defined beta-sheet structure consisting of one parallel and six antiparallel pairs of beta-strands which forms an open-sided beta-barrel. The root-mean-square deviation (rmsd) of 53 individual structures to the calculated average structure for the backbone atoms of residues excluding the N terminus and two mobile loops is 0.57(+/-0.10) A while the rmsd for backbone atoms in beta-strands is 0.45(+/-0.08) A. Structural features of the SBD in solution are compared to the X-ray crystal structure of a homologous domain of cyclodextrin glycosyltransferase (CGTase) in the free and bound forms. Titration studies with two ligands, maltoheptaose and beta-cyclodextrin, show the existence of two binding sites. Examination of the tertiary structures shows these two sites to be at one end of the molecule on opposite faces. The majority of residues showing the largest 1H and 15N chemical shift changes are located in loop regions. Many residues implicated in binding, based on these changes, are similar in location to previously identified binding site residues in the crystal structures of CGTase. Overall, the shift changes are small indicating that the SBD does not undergo large conformational changes upon ligand binding.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Representation of the solution structure of the SBD. The N and C termini and b-strand numbers are marked. The strands are shown as arrows which also indicate their directionality. The atomic coordinates of SBDav-min were used and the molecule was oriented by eye to give the best view of the b-strands. The orientation is rotated by approximately 180° about the vertical axis compared to Figure 3. The Figure was generated using the program MOLSCRIPT (Kraulis, 1991). The position of the disulphide bond is highlighted by ball figures for S g atoms and lines for C a -C b , C b -S g (both intraresidue) and S g -S g (interresidue) bonds for residues 509 and 604.
Figure 5.
Figure 5. Representation of the direction and alignment of the b-strands (numbered 1 to 8) in SBD. The first and last residues in each strand are marked at the ends of the arrows.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 259, 970-987) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21152915 J.Marín-Navarro, and J.Polaina (2011).
Glucoamylases: structural and biotechnological aspects.
  Appl Microbiol Biotechnol, 89, 1267-1273.  
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.  
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.  
19530230 H.Sugimoto, M.Nakaura, S.Nishimura, S.Karita, H.Miyake, and A.Tanaka (2009).
Kinetically trapped metastable intermediate of a disulfide-deficient mutant of the starch-binding domain of glucoamylase.
  Protein Sci, 18, 1715-1723.  
18378674 A.D.Jørgensen, J.Nøhr, J.S.Kastrup, M.Gajhede, B.W.Sigurskjold, J.Sauer, D.I.Svergun, B.Svensson, and B.Vestergaard (2008).
Small angle X-ray studies reveal that Aspergillus niger glucoamylase has a defined extended conformation and can form dimers in solution.
  J Biol Chem, 283, 14772-14780.  
17187076 A.L.van Bueren, M.Higgins, D.Wang, R.D.Burke, and A.B.Boraston (2007).
Identification and structural basis of binding to host lung glycogen by streptococcal virulence factors.
  Nat Struct Mol Biol, 14, 76-84.
PDB codes: 2j43 2j44
17587686 H.Sugimoto, M.Nakaura, Y.Kosuge, K.Imai, H.Miyake, S.Karita, and A.Tanaka (2007).
Thermodynamic effects of disulfide bond on thermal unfolding of the starch-binding domain of Aspergillus niger glucoamylase.
  Biosci Biotechnol Biochem, 71, 1535-1541.  
17681016 T.Senoura, A.Asao, Y.Takashima, N.Isono, S.Hamada, H.Ito, and H.Matsui (2007).
Enzymatic characterization of starch synthase III from kidney bean (Phaseolus vulgaris L.).
  FEBS J, 274, 4550-4560.  
16230347 A.B.Boraston, M.Healey, J.Klassen, E.Ficko-Blean, A.Lammerts van Bueren, and V.Law (2006).
A structural and functional analysis of alpha-glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition.
  J Biol Chem, 281, 587-598.
PDB codes: 2c3g 2c3h 2c3v 2c3w 2c3x
16433931 H.T.Chang, T.W.Pai, T.C.Fan, B.H.Su, P.C.Wu, C.Y.Tang, C.T.Chang, S.H.Liu, and M.D.Chang (2006).
A reinforced merging methodology for mapping unique peptide motifs in members of protein families.
  BMC Bioinformatics, 7, 38.  
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
16041515 H.B.Huang, M.C.Chi, W.H.Hsu, W.C.Liang, and L.L.Lin (2005).
Construction and one-step purification of Bacillus kaustophilus leucine aminopeptidase fused to the starch-binding domain of Bacillus sp. strain TS-23 alpha-amylase.
  Bioprocess Biosyst Eng, 27, 389-398.  
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.  
11478902 J.Sauer, T.Christensen, T.P.Frandsen, E.Mirgorodskaya, K.A.McGuire, H.Driguez, P.Roepstorff, B.W.Sigurskjold, and B.Svensson (2001).
Stability and function of interdomain linker variants of glucoamylase 1 from Aspergillus niger.
  Biochemistry, 40, 9336-9346.  
11272837 Y.Mezaki, Y.Katsuya, M.Kubota, and Y.Matsuura (2001).
Crystallization and structural analysis of intact maltotetraose-forming exo-amylase from Pseudomonas stutzeri.
  Biosci Biotechnol Biochem, 65, 222-225.
PDB code: 1gcy
10353816 B.Mikami, M.Adachi, T.Kage, E.Sarikaya, T.Nanmori, R.Shinke, and S.Utsumi (1999).
Structure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose.
  Biochemistry, 38, 7050-7061.
PDB codes: 1b90 1b9z
10102986 M.Goto, M.Tsukamoto, I.Kwon, K.Ekino, and K.Furukawa (1999).
Functional analysis of O-linked oligosaccharides in threonine/serine-rich region of Aspergillus glucoamylase by expression in mannosyltransferase-disruptants of yeast.
  Eur J Biochem, 260, 596-602.  
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.  
9920393 C.Jensen, S.O.Andersen, and P.Roepstorff (1998).
Primary structure of two major cuticular proteins from the migratory locust, Locusta migratoria, and their identification in polyacrylamide gels by mass spectrometry.
  Biochim Biophys Acta, 1429, 151-162.  
  9521126 M.J.Bayley, G.Jones, P.Willett, and M.P.Williamson (1998).
GENFOLD: a genetic algorithm for folding protein structures using NMR restraints.
  Protein Sci, 7, 491-499.  
9200704 M.P.Williamson, M.F.Le Gal-Coëffet, K.Sorimachi, C.S.Furniss, D.B.Archer, and G.Williamson (1997).
Function of conserved tryptophans in the Aspergillus niger glucoamylase 1 starch binding domain.
  Biochemistry, 36, 7535-7539.  
9365988 P.M.Coutinho, and P.J.Reilly (1997).
Glucoamylase structural, functional, and evolutionary relationships.
  Proteins, 29, 334-347.  
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.