spacer
spacer

PDBsum entry 1lwj

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1lwj
Jmol
Contents
Protein chains
441 a.a. *
Ligands
ACG ×2
Metals
_CA ×2
Waters ×41
* Residue conservation analysis
PDB id:
1lwj
Name: Transferase
Title: Crystal structure of t. Maritima 4-alpha- glucanotransferase/acarbose complex
Structure: 4-alpha-glucanotransferase. Chain: a, b. Synonym: maltodextrin glycosyltransferase, amylomaltase, d- enzyme, disproportionating enzyme, oligo-1,4-1,4- glucantransferase. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: mgt. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.225     R-free:   0.302
Authors: A.Roujeinikova,C.Raasch,S.Sedelnikova,W.Liebl,D.W.Rice
Key ref:
A.Roujeinikova et al. (2002). Crystal structure of Thermotoga maritima 4-alpha-glucanotransferase and its acarbose complex: implications for substrate specificity and catalysis. J Mol Biol, 321, 149-162. PubMed id: 12139940 DOI: 10.1016/S0022-2836(02)00570-3
Date:
31-May-02     Release date:   14-Aug-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P80099  (MGTA_THEMA) -  4-alpha-glucanotransferase
Seq:
Struc:
441 a.a.
441 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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!
  Cellular component     cytoplasm   1 term 
  Biological process     carbohydrate metabolic process   2 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
DOI no: 10.1016/S0022-2836(02)00570-3 J Mol Biol 321:149-162 (2002)
PubMed id: 12139940  
 
 
Crystal structure of Thermotoga maritima 4-alpha-glucanotransferase and its acarbose complex: implications for substrate specificity and catalysis.
A.Roujeinikova, C.Raasch, S.Sedelnikova, W.Liebl, D.W.Rice.
 
  ABSTRACT  
 
4-alpha-Glucanotransferase (GTase) is an essential enzyme in alpha-1,4-glucan metabolism in bacteria and plants. It catalyses the transfer of maltooligosaccharides from an 1,4-alpha-D-glucan molecule to the 4-hydroxyl group of an acceptor sugar molecule. The crystal structures of Thermotoga maritima GTase and its complex with the inhibitor acarbose have been determined at 2.6A and 2.5A resolution, respectively. The GTase structure consists of three domains, an N-terminal domain with the (beta/alpha)(8) barrel topology (domain A), a 65 residue domain, domain B, inserted between strand beta3 and helix alpha6 of the barrel, and a C-terminal domain, domain C, which forms an antiparallel beta-structure. Analysis of the complex of GTase with acarbose has revealed the locations of five sugar-binding subsites (-2 to +3) in the active-site cleft lying between domain B and the C-terminal end of the (beta/alpha)(8) barrel. The structure of GTase closely resembles the family 13 glycoside hydrolases and conservation of key catalytic residues previously identified for this family is consistent with a double-displacement catalytic mechanism for this enzyme. A distinguishing feature of GTase is a pair of tryptophan residues, W131 and W218, which, upon the carbohydrate inhibitor binding, form a remarkable aromatic "clamp" that captures the sugar rings at the acceptor-binding sites +1 and +2. Analysis of the structure of the complex shows that sugar residues occupying subsites from -2 to +2 engage in extensive interactions with the protein, whereas the +3 glucosyl residue makes relatively few contacts with the enzyme. Thus, the structure suggests that four subsites, from -2 to +2, play the dominant role in enzyme-substrate recognition, consistent with the observation that the smallest donor for T.maritima GTase is maltotetraose, the smallest chain transferred is a maltosyl unit and that the smallest residual fragment after transfer is maltose. A close similarity between the structures of GTase and oligo-1,6-glucosidase has allowed the structural features that determine differences in substrate specificity of these two enzymes to be analysed.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. (a) Structural formulae of acarbose. The valienamine ring is labeled A, the 6-deoxyglucoside unit is labeled B, and the two glucose units are labeled C and D. (b) Stereodiagram showing (2mF[o] -DF[c]) sA-weighted[35] electron density map around the bound inhibitor in the active site of GTase. The map is contoured at the 1.0 s level. (c) Stereodrawing showing hydrogen bonds important for recognition of a carbohydrate substrate by GTase. (d) Superposition of the structures of free GTase (green) and the GTase-inhibitor complex (red) showing the movement of loop b7a8 and helix a8 on the inhibitor binding. The bound inhibitor is drawn in light blue. The positions of the side-chains of W131 and W218, which form an aromatic clamp that captures the sugar rings at the acceptor-binding sites +1 and +2, are shown (in the structure of the free enzyme the side-chain of W218 is disordered). (e) Superposition of the region around the bound acarbose-derived inhibitor in the respective complexes of GTase (black), B. circulans CGTase (green) and A. oryzae a-amylase (red). Residue labels in black refer to GTase structure, those in green refer to CGTase and those in red refer to a-amylase. (f) Stacking feature between the planes of the tryptophan rings of residues W131 and W218 and the glucosyl residue at the +2 subsite in the GTase/carbohydrate inhibitor complex.
Figure 4.
Figure 4. Stereo plot of the superposition of the active sites of GTase (green) and oligo-1,6-glucosidase (atom colors with carbon atoms colored black). The modeled position of isomaltose in the active site of oligo-1,6-glucosidase is shown. The residues that confer different substrate specificity in oligo-1,6-glucosidase are shown in a ball-and-stick representation. Residue labeling refers to oligo-1,6-glucosidase.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 321, 149-162) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20159465 N.M.Koropatkin, and T.J.Smith (2010).
SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules.
  Structure, 18, 200-215.
PDB codes: 3k8k 3k8l 3k8m
20875088 W.M.Patrick, Y.Nakatani, S.M.Cutfield, M.L.Sharpe, R.J.Ramsay, and J.F.Cutfield (2010).
Carbohydrate binding sites in Candida albicans exo-β-1,3-glucanase and the role of the Phe-Phe 'clamp' at the active site entrance.
  FEBS J, 277, 4549-4561.
PDB codes: 2pc8 2pf0 3n9k 3o6a
18387093 E.J.Oh, S.J.Choi, S.J.Lee, C.H.Kim, and T.W.Moon (2008).
Modification of granular corn starch with 4-alpha-glucanotransferase from Thermotoga maritima: effects on structural and physical properties.
  J Food Sci, 73, C158-C166.  
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
17920282 H.Park, K.Y.Hwang, K.H.Oh, Y.H.Kim, J.Y.Lee, and K.Kim (2008).
Discovery of novel alpha-glucosidase inhibitors based on the virtual screening with the homology-modeled protein structure.
  Bioorg Med Chem, 16, 284-292.  
18398906 T.Shirai, V.S.Hung, K.Morinaka, T.Kobayashi, and S.Ito (2008).
Crystal structure of GH13 alpha-glucosidase GSJ from one of the deepest sea bacteria.
  Proteins, 73, 126-133.
PDB code: 2ze0
17064285 S.B.Conners, E.F.Mongodin, M.R.Johnson, C.I.Montero, K.E.Nelson, and R.M.Kelly (2006).
Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.
  FEMS Microbiol Rev, 30, 872-905.  
16075303 C.H.Tomich, P.da Silva, I.Carvalho, and C.A.Taft (2005).
Homology modeling and molecular interaction field studies of alpha-glucosidases as a guide to structure-based design of novel proposed anti-HIV inhibitors.
  J Comput Aided Mol Des, 19, 83-92.  
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.  
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.