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PDBsum entry 1k1y

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1k1y
Jmol
Contents
Protein chains
636 a.a. *
Ligands
ACR
MAL
TRS
Metals
_CA ×3
Waters ×572
* Residue conservation analysis
PDB id:
1k1y
Name: Transferase
Title: Crystal structure of thermococcus litoralis 4-alpha-glucanot complexed with acarbose
Structure: 4-alpha-glucanotransferase. Chain: a, b. Engineered: yes
Source: Thermococcus litoralis. Organism_taxid: 2265. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.198     R-free:   0.256
Authors: H.Imamura,S.Fushinobu,T.Kumasaka,M.Yamamoto,B.S.Jeon,T.Wakag H.Matsuzawa
Key ref:
H.Imamura et al. (2003). Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor. J Biol Chem, 278, 19378-19386. PubMed id: 12618437 DOI: 10.1074/jbc.M213134200
Date:
26-Sep-01     Release date:   17-Jun-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O32462  (MALQ_THELI) -  4-alpha-glucanotransferase
Seq:
Struc:
 
Seq:
Struc:
659 a.a.
636 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.1.25  - 4-alpha-glucanotransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Transfers a segment of a (1,4)-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or (1,4)-alpha-D-glucan.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
DOI no: 10.1074/jbc.M213134200 J Biol Chem 278:19378-19386 (2003)
PubMed id: 12618437  
 
 
Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor.
H.Imamura, S.Fushinobu, M.Yamamoto, T.Kumasaka, B.S.Jeon, T.Wakagi, H.Matsuzawa.
 
  ABSTRACT  
 
Thermococcus litoralis 4-alpha-glucanotransferase (TLGT) belongs to glucoside hydrolase family 57 and catalyzes the disproportionation of amylose and the formation of large cyclic alpha-1,4-glucan (cycloamylose) from linear amylose. We determined the crystal structure of TLGT with and without an inhibitor, acarbose. TLGT is composed of two domains: an N-terminal domain (domain I), which contains a (beta/alpha)7 barrel fold, and a C-terminal domain (domain II), which has a twisted beta-sandwich fold. In the structure of TLGT complexed with acarbose, the inhibitor was bound at the cleft within domain I, indicating that domain I is a catalytic domain of TLGT. The acarbose-bound structure also clarified that Glu123 and Asp214 were the catalytic nucleophile and acid/base catalyst, respectively, and revealed the residues involved in substrate binding. It seemed that TLGT produces large cyclic glucans by preventing the production of small cyclic glucans by steric hindrance, which is achieved by three lids protruding into the active site cleft, as well as an extended active site cleft. Interestingly, domain I of TLGT shares some structural features with the catalytic domain of Golgi alpha-mannosidase from Drosophila melanogaster, which belongs to glucoside hydrolase family 38. Furthermore, the catalytic residue of the two enzymes is located in the same position. These observations suggest that families 57 and 38 evolved from a common ancestor.
 
  Selected figure(s)  
 
Figure 4.
FIG. 4. Bound ligands in the form II complex of TLGT. Stereoviews of the refined models of acarbose in chain A (a) and maltose in chain B(b) are presented, together with F[o] - F[c] electron density maps contoured at 4 . Each ligand was omitted from the phase calculation. c, acarbose and the two catalytic residues. a and b were generated using XtalView (26) and Raster3d (45).
Figure 7.
FIG. 7. Surface representation around the active site of TLGT. The molecular surface of chain A of the form II-complex, a bound acarbose, and a modeled maltotetradecaose are presented. The C atoms of acarbose and maltotetradecaose are colored white and yellow, respectively. The oxygen and nitrogen atoms are colored red and blue, respectively. Lid 2 is concealed behind lid 3. The figures were prepared with the programs SPOCK (49), Molscript (44), and Raster3d (45).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 19378-19386) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18074341 A.D.Hill, and P.J.Reilly (2008).
A Gibbs free energy correlation for automated docking of carbohydrates.
  J Comput Chem, 29, 1131-1141.  
18703518 E.J.Woo, S.Lee, H.Cha, J.T.Park, S.M.Yoon, H.N.Song, and K.H.Park (2008).
Structural insight into the bifunctional mechanism of the glycogen-debranching enzyme TreX from the archaeon Sulfolobus solfataricus.
  J Biol Chem, 283, 28641-28648.
PDB codes: 2vnc 2vr5 2vuy
18500431 H.Y.Lin, H.H.Chuang, and F.P.Lin (2008).
Biochemical characterization of engineered amylopullulanase from Thermoanaerobacter ethanolicus 39E-implicating the non-necessity of its 100 C-terminal amino acid residues.
  Extremophiles, 12, 641-650.  
16510973 A.Dickmanns, M.Ballschmiter, W.Liebl, and R.Ficner (2006).
Structure of the novel alpha-amylase AmyC from Thermotoga maritima.
  Acta Crystallogr D Biol Crystallogr, 62, 262-270.
PDB code: 2b5d
16172888 H.Bach, and D.L.Gutnick (2006).
Novel polysaccharide-protein-based amphipathic formulations.
  Appl Microbiol Biotechnol, 71, 34-38.  
16513741 H.S.Lee, K.R.Shockley, G.J.Schut, S.B.Conners, C.I.Montero, M.R.Johnson, C.J.Chou, S.L.Bridger, N.Wigner, S.D.Brehm, F.E.Jenney, D.A.Comfort, R.M.Kelly, and M.W.Adams (2006).
Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus.
  J Bacteriol, 188, 2115-2125.  
16517673 M.Ballschmiter, O.Fütterer, and W.Liebl (2006).
Identification and characterization of a novel intracellular alkaline alpha-amylase from the hyperthermophilic bacterium Thermotoga maritima MSB8.
  Appl Environ Microbiol, 72, 2206-2211.  
16885460 T.Murakami, T.Kanai, H.Takata, T.Kuriki, and T.Imanaka (2006).
A novel branching enzyme of the GH-57 family in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.
  J Bacteriol, 188, 5915-5924.  
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.  
15599521 S.Kang, C.Vieille, and J.G.Zeikus (2005).
Identification of Pyrococcus furiosus amylopullulanase catalytic residues.
  Appl Microbiol Biotechnol, 66, 408-413.  
16151092 T.Kaper, B.Talik, T.J.Ettema, H.Bos, M.J.van der Maarel, and L.Dijkhuizen (2005).
Amylomaltase of Pyrobaculum aerophilum IM2 produces thermoreversible starch gels.
  Appl Environ Microbiol, 71, 5098-5106.  
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
15564678 M.Nakajima, H.Imamura, H.Shoun, S.Horinouchi, and T.Wakagi (2004).
Transglycosylation activity of Dictyoglomus thermophilum amylase A.
  Biosci Biotechnol Biochem, 68, 2369-2373.  
15233783 R.Zona, F.Chang-Pi-Hin, M.J.O'Donohue, and S.Janecek (2004).
Bioinformatics of the glycoside hydrolase family 57 and identification of catalytic residues in amylopullulanase from Thermococcus hydrothermalis.
  Eur J Biochem, 271, 2863-2872.  
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.