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PDBsum entry 1lf9

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1lf9
Jmol PyMol
Contents
Protein chains
674 a.a. *
Ligands
ACR ×2
SO4 ×2
Waters ×674
* Residue conservation analysis
PDB id:
1lf9
Name: Hydrolase
Title: Crystal structure of bacterial glucoamylase complexed with a
Structure: Glucoamylase. Chain: a, b. Synonym: glucan 1,4-alpha-glucosidase, 1,4-alpha-d-glucan glucohydrolase, amyloglucosidase, gamma-amylase, lysosomal glucosidase, exo-1,4-alpha-glucosidase. Ec: 3.2.1.3
Source: Thermoanaerobacterium thermosaccharoly organism_taxid: 1517. Strain: dsm 571
Resolution:
2.20Å     R-factor:   0.191     R-free:   0.227
Authors: A.E.Aleshin,P.-H.Feng,R.B.Honzatko,P.J.Reilly
Key ref:
A.E.Aleshin et al. (2003). Crystal structure and evolution of a prokaryotic glucoamylase. J Mol Biol, 327, 61-73. PubMed id: 12614608 DOI: 10.1016/S0022-2836(03)00084-6
Date:
10-Apr-02     Release date:   25-Feb-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O85672  (O85672_THETR) -  Glucoamylase (Fragment)
Seq:
Struc:
 
Seq:
Struc:
695 a.a.
674 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 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     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
DOI no: 10.1016/S0022-2836(03)00084-6 J Mol Biol 327:61-73 (2003)
PubMed id: 12614608  
 
 
Crystal structure and evolution of a prokaryotic glucoamylase.
A.E.Aleshin, P.H.Feng, R.B.Honzatko, P.J.Reilly.
 
  ABSTRACT  
 
The first crystal structures of a two-domain, prokaryotic glucoamylase were determined to high resolution from the clostridial species Thermoanaerobacterium thermosaccharolyticum with and without acarbose. The N-terminal domain has 18 antiparallel strands arranged in beta-sheets of a super-beta-sandwich. The C-terminal domain is an (alpha/alpha)(6) barrel, lacking the peripheral subdomain of eukaryotic glucoamylases. Interdomain contacts are common to all prokaryotic Family GH15 proteins. Domains similar to those of prokaryotic glucoamylases in maltose phosphorylases (Family GH65) and glycoaminoglycan lyases (Family PL8) suggest evolution from a common ancestor. Eukaryotic glucoamylases may have evolved from prokaryotic glucoamylases by the substitution of the N-terminal domain with the peripheral subdomain and by the addition of a starch-binding domain.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Structures of tGA and the aGA a-domain. (a) Stereo view of the tGA b-domain. (b) Structural correspondence between the b-domain and linker region of tGA (left) and the N-glycan of aGA (right). Tan and red loops are on the catalytic side of the a-domain. Loops aL1 and aL6 of tGA that interact with the b-domain and linker are red, as are loops that interact with a corresponding N-glycosylation site of aGA. Catalytic residues are blue. Acarbose in the tGA active site is gray. Conserved N-glycosylation of fungal GAs (aGA-specific O-glycosylation sites are not shown for clarity) is in black. The conserved subdomain of fungal GAs consisting of helix aH10' (previously labeled helix 11[5]) and a b-strand hairpin is in dark green.
Figure 4.
Figure 4. Structurally homologous carbohydrases consisting of a and b-domains. (a) tGA. (b) Maltose phosphorylase (PDB entry 1H54). (c) Hyalorunate lyase (PDB entry 1EGU). The a and b-domains and linker regions are tan, blue and green, respectively. Additional C-terminal domains of maltose phosphorylase and hyaluronate lyase are brown. Conserved interfacial b-strands and a-helices are dark blue and red, respectively. Glu438 and Glu636, the catalytic acid and base of tGA; Glu487 and His671, the putative catalytic acid and phosphoryl binding residue of maltose phosphorylase; and His399, a proton acceptor of hyalorunate lyase, are black.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 327, 61-73) copyright 2003.  
  Figures were selected by the author.  

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.  
21154671 C.Luley-Goedl, and B.Nidetzky (2010).
Carbohydrate synthesis by disaccharide phosphorylases: reactions, catalytic mechanisms and application in the glycosciences.
  Biotechnol J, 5, 1324-1338.  
20713411 H.Nakai, B.O.Petersen, Y.Westphal, A.Dilokpimol, M.Abou Hachem, J...Duus, H.A.Schols, and B.Svensson (2010).
Rational engineering of Lactobacillus acidophilus NCFM maltose phosphorylase into either trehalose or kojibiose dual specificity phosphorylase.
  Protein Eng Des Sel, 23, 781-787.  
19819900 M.Hidaka, S.Fushinobu, Y.Honda, T.Wakagi, H.Shoun, and M.Kitaoka (2010).
Structural explanation for the acquisition of glycosynthase activity.
  J Biochem, 147, 237-244.
PDB codes: 2dro 2drq 2drr 2drs 3a3v
20155355 Y.Zheng, Y.Xue, Y.Zhang, C.Zhou, U.Schwaneberg, and Y.Ma (2010).
Cloning, expression, and characterization of a thermostable glucoamylase from Thermoanaerobacter tengcongensis MB4.
  Appl Microbiol Biotechnol, 87, 225-233.  
18981178 M.Kitamura, M.Okuyama, F.Tanzawa, H.Mori, Y.Kitago, N.Watanabe, A.Kimura, I.Tanaka, and M.Yao (2008).
Structural and Functional Analysis of a Glycoside Hydrolase Family 97 Enzyme from Bacteroides thetaiotaomicron.
  J Biol Chem, 283, 36328-36337.
PDB codes: 2d73 2zq0
18234665 S.Ravaud, G.Stjepanovic, K.Wild, and I.Sinning (2008).
The crystal structure of the periplasmic domain of the Escherichia coli membrane protein insertase YidC contains a substrate binding cleft.
  J Biol Chem, 283, 9350-9358.
PDB code: 3bs6
17459873 M.Nagae, A.Tsuchiya, T.Katayama, K.Yamamoto, S.Wakatsuki, and R.Kato (2007).
Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum.
  J Biol Chem, 282, 18497-18509.
PDB codes: 2eab 2eac 2ead 2eae
16817895 E.J.Rossi, L.Sim, D.A.Kuntz, D.Hahn, B.D.Johnston, A.Ghavami, M.G.Szczepina, N.S.Kumar, E.E.Sterchi, B.L.Nichols, B.M.Pinto, and D.R.Rose (2006).
Inhibition of recombinant human maltase glucoamylase by salacinol and derivatives.
  FEBS J, 273, 2673-2683.  
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
15501829 A.L.Lovering, S.S.Lee, Y.W.Kim, S.G.Withers, and N.C.Strynadka (2005).
Mechanistic and structural analysis of a family 31 alpha-glycosidase and its glycosyl-enzyme intermediate.
  J Biol Chem, 280, 2105-2115.
PDB codes: 1xsi 1xsj 1xsk
  16511025 K.Ichikawa, T.Tonozuka, M.Mizuno, Y.Tanabe, S.Kamitori, A.Nishikawa, and Y.Sakano (2005).
Crystallization and preliminary X-ray analysis of Thermoactinomyces vulgaris R-47 maltooligosaccharide-metabolizing enzyme homologous to glucoamylase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 302-304.  
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.  
15274915 M.Hidaka, Y.Honda, M.Kitaoka, S.Nirasawa, K.Hayashi, T.Wakagi, H.Shoun, and S.Fushinobu (2004).
Chitobiose phosphorylase from Vibrio proteolyticus, a member of glycosyl transferase family 36, has a clan GH-L-like (alpha/alpha)(6) barrel fold.
  Structure, 12, 937-947.
PDB codes: 1v7v 1v7w 1v7x
14660574 M.Mizuno, T.Tonozuka, S.Suzuki, R.Uotsu-Tomita, S.Kamitori, A.Nishikawa, and Y.Sakano (2004).
Structural insights into substrate specificity and function of glucodextranase.
  J Biol Chem, 279, 10575-10583.
PDB codes: 1ug9 1ulv
15240266 M.S.Kim, J.T.Park, Y.W.Kim, H.S.Lee, R.Nyawira, H.S.Shin, C.S.Park, S.H.Yoo, Y.R.Kim, T.W.Moon, and K.H.Park (2004).
Properties of a novel thermostable glucoamylase from the hyperthermophilic archaeon Sulfolobus solfataricus in relation to starch processing.
  Appl Environ Microbiol, 70, 3933-3940.  
  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.  
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
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.

 

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