PDBsum entry 1acz

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Polysaccharide degradation PDB id
Protein chain
108 a.a. *
* Residue conservation analysis
PDB id:
Name: Polysaccharide degradation
Title: Glucoamylase, granular starch-binding domain complex with cyclodextrin, nmr, 5 structures
Structure: Glucoamylase. Chain: a. Fragment: starch-binding domain, residues 509 - 616. Synonym: 1,4-alpha-d-glucan glucohydrolase. Engineered: yes
Source: Aspergillus niger. Organism_taxid: 5061. Strain: ab4.1. Expressed in: aspergillus niger. Expression_system_taxid: 5061.
NMR struc: 5 models
Authors: K.Sorimachi,M.-F.Le Gal-Coeffet,G.Williamson,D.B.Archer, M.P.Williamson
Key ref:
K.Sorimachi et al. (1997). Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to beta-cyclodextrin. Structure, 5, 647-661. PubMed id: 9195884 DOI: 10.1016/S0969-2126(97)00220-7
10-Feb-97     Release date:   07-Jul-97    
Go to PROCHECK summary

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

 Enzyme reactions 
   Enzyme class: E.C.  - 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: 10.1016/S0969-2126(97)00220-7 Structure 5:647-661 (1997)
PubMed id: 9195884  
Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to beta-cyclodextrin.
K.Sorimachi, M.F.Le Gal-Coëffet, G.Williamson, D.B.Archer, M.P.Williamson.
BACKGROUND: Carbohydrate-binding domains are usually small and physically separate from the catalytic domains of hydrolytic enzymes. Glucoamylase 1 (G1) from Aspergillus niger, an enzyme used widely in the food and brewing industries, contains a granular starch binding domain (SBD) which is separated from the catalytic domain by a semi-rigid linker. The aim of this study was to determine how the SBD binds to starch, and thereby more generally to throw light on the role of carbohydrate-binding domains in the hydrolysis of insoluble polysaccharides. RESULTS: The solution structure of the SBD of A. niger G1 bound to beta-cyclodextrin (betaCD), a cyclic starch analogue, shows that the well-defined beta-sheet structure seen in the free SBD is maintained in the SBD-betaCD complex. The main differences between the free and bound states of the SBD are observed in loop regions, in or near the two starch-binding sites. The two binding sites, each of which binds one molecule of betaCD, are structurally different. Binding site 1 is small and accessible, and its structure changes very little upon ligand binding. Site 2 is longer and undergoes a significant structural change on binding. Part of this site comprises a flexible loop, which appears to allow the SBD to bind to starch strands in a range of orientations. CONCLUSIONS: The two starch-binding sites of the SBD probably differ functionally as well as structurally; site 1 probably acts as the initial starch recognition site, whereas site 2 is involved in specific recognition of appropriate regions of starch. The two starch strands are bound at approximately 90 degrees to each other. This may be functionally important, as it may force starch strands apart thus increasing the hydrolyzable surface, or alternatively it may localize the enzyme to noncrystalline (more hydrolyzable) areas of starch. The region of the SBD where the linker to the catalytic domain is attached is flexible, allowing the catalytic site to access a large surface area of the starch granules.
  Selected figure(s)  
Figure 7.
Figure 7. A view of the superimposition of SBD-bCD[av-min] (red) and the minimized average structure of free SBD (blue). The structure of free SBD was superimposed on to the N, Ca and C atoms of b strands 1-8 of SBD-bCD[av-min]. The bCD molecules are shown in yellow.
  The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 647-661) copyright 1997.  
  Figure was 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.  
21294843 M.A.Glaring, M.J.Baumann, M.Abou Hachem, H.Nakai, N.Nakai, D.Santelia, B.W.Sigurskjold, S.C.Zeeman, A.Blennow, and B.Svensson (2011).
Starch-binding domains in the CBM45 family--low-affinity domains from glucan, water dikinase and α-amylase involved in plastidial starch metabolism.
  FEBS J, 278, 1175-1185.  
19908036 D.Guillén, S.Sánchez, and R.Rodríguez-Sanoja (2010).
Carbohydrate-binding domains: multiplicity of biological roles.
  Appl Microbiol Biotechnol, 85, 1241-1249.  
19968859 N.Z.Wayllace, H.A.Valdez, R.A.Ugalde, M.V.Busi, and D.F.Gomez-Casati (2010).
The starch-binding capacity of the noncatalytic SBD2 region and the interaction between the N- and C-terminal domains are involved in the modulation of the activity of starch synthase III from Arabidopsis thaliana.
  FEBS J, 277, 428-440.  
20178562 V.Arantes, and J.N.Saddler (2010).
Access to cellulose limits the efficiency of enzymatic hydrolysis: the role of amorphogenesis.
  Biotechnol Biofuels, 3, 4.  
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.  
18611383 N.M.Koropatkin, E.C.Martens, J.I.Gordon, and T.J.Smith (2008).
Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices.
  Structure, 16, 1105-1115.
PDB codes: 3ck7 3ck8 3ck9 3ckb 3ckc
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
17203391 D.W.Wong, G.H.Robertson, C.C.Lee, and K.Wagschal (2007).
Synergistic action of recombinant alpha-amylase and glucoamylase on the hydrolysis of starch granules.
  Protein J, 26, 159-164.  
17593302 S.C.Lin, W.T.Liu, S.H.Liu, W.I.Chou, B.K.Hsiung, I.P.Lin, C.C.Sheu, and M.Dah-Tsyr Chang (2007).
Role of the linker region in the expression of Rhizopus oryzae glucoamylase.
  BMC Biochem, 8, 9.  
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
16862594 N.Palopoli, M.V.Busi, M.S.Fornasari, D.Gomez-Casati, R.Ugalde, and G.Parisi (2006).
Starch-synthase III family encodes a tandem of three starch-binding domains.
  Proteins, 65, 27-31.  
16216577 G.Polekhina, A.Gupta, B.J.van Denderen, S.C.Feil, B.E.Kemp, D.Stapleton, and M.W.Parker (2005).
Structural basis for glycogen recognition by AMP-activated protein kinase.
  Structure, 13, 1453-1462.
PDB codes: 1z0m 1z0n
  16508085 G.Polekhina, S.C.Feil, A.Gupta, P.O'Donnell, D.Stapleton, and M.W.Parker (2005).
Crystallization of the glycogen-binding domain of the AMP-activated protein kinase beta subunit and preliminary X-ray analysis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 39-42.  
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.  
15640201 R.Rodríguez-Sanoja, B.Ruiz, J.P.Guyot, and S.Sanchez (2005).
Starch-binding domain affects catalysis in two Lactobacillus alpha-amylases.
  Appl Environ Microbiol, 71, 297-302.  
15939348 R.Rodríguez-Sanoja, N.Oviedo, and S.Sánchez (2005).
Microbial starch-binding domain.
  Curr Opin Microbiol, 8, 260-267.  
15062085 J.Allouch, W.Helbert, B.Henrissat, and M.Czjzek (2004).
Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose.
  Structure, 12, 623-632.
PDB code: 1urx
12747837 G.Polekhina, A.Gupta, B.J.Michell, B.van Denderen, S.Murthy, S.C.Feil, I.G.Jennings, D.J.Campbell, L.A.Witters, M.W.Parker, B.E.Kemp, and D.Stapleton (2003).
AMPK beta subunit targets metabolic stress sensing to glycogen.
  Curr Biol, 13, 867-871.  
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.  
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.  
11980475 P.J.Simpson, S.J.Jamieson, M.Abou-Hachem, E.N.Karlsson, H.J.Gilbert, O.Holst, and M.P.Williamson (2002).
The solution structure of the CBM4-2 carbohydrate binding module from a thermostable Rhodothermus marinus xylanase.
  Biochemistry, 41, 5712-5719.
PDB codes: 1k42 1k45
  11673472 M.Czjzek, D.N.Bolam, A.Mosbah, J.Allouch, C.M.Fontes, L.M.Ferreira, O.Bornet, V.Zamboni, H.Darbon, N.L.Smith, G.W.Black, B.Henrissat, and H.J.Gilbert (2001).
The location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence is not conserved.
  J Biol Chem, 276, 48580-48587.
PDB code: 1gmm
11524680 S.Raghothama, R.Y.Eberhardt, P.Simpson, D.Wigelsworth, P.White, G.P.Hazlewood, T.Nagy, H.J.Gilbert, and M.P.Williamson (2001).
Characterization of a cellulosome dockerin domain from the anaerobic fungus Piromyces equi.
  Nat Struct Biol, 8, 775-778.
PDB codes: 1e8p 1e8q
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
10819965 S.J.Charnock, D.N.Bolam, J.P.Turkenburg, H.J.Gilbert, L.M.Ferreira, G.J.Davies, and C.M.Fontes (2000).
The X6 "thermostabilizing" domains of xylanases are carbohydrate-binding modules: structure and biochemistry of the Clostridium thermocellum X6b domain.
  Biochemistry, 39, 5013-5021.
PDB code: 1dyo
10545093 F.X.Gomis-Rüth, V.Companys, Y.Qian, L.D.Fricker, J.Vendrell, F.X.Avilés, and M.Coll (1999).
Crystal structure of avian carboxypeptidase D domain II: a prototype for the regulatory metallocarboxypeptidase subfamily.
  EMBO J, 18, 5817-5826.
PDB code: 1qmu
10425686 P.J.Simpson, D.N.Bolam, A.Cooper, A.Ciruela, G.P.Hazlewood, H.J.Gilbert, and M.P.Williamson (1999).
A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity.
  Structure, 7, 853-864.
PDB codes: 1xbd 2xbd
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.  
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.