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PDBsum entry 2d3l

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protein ligands metals links
Hydrolase PDB id
2d3l
Jmol
Contents
Protein chain
481 a.a. *
Ligands
GLC-GLC-GLC-GLC-
GLC
GLC ×2
GLC-GLC-GLC
Metals
_NA
_CA ×3
Waters ×238
* Residue conservation analysis
PDB id:
2d3l
Name: Hydrolase
Title: Crystal structure of maltohexaose-producing amylase from bac sp.707 complexed with maltopentaose.
Structure: Glucan 1,4-alpha-maltohexaosidase. Chain: a. Synonym: g6-amylase, maltohexaose-producing amylase, exo- maltohexaohydrolase. Engineered: yes
Source: Bacillus sp.. Organism_taxid: 1416. Strain: 707. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.
Resolution:
2.30Å     R-factor:   0.168     R-free:   0.213
Authors: R.Kanai,K.Haga,T.Akiba,K.Yamane,K.Harata
Key ref:
R.Kanai et al. (2006). Role of Trp140 at subsite -6 on the maltohexaose production of maltohexaose-producing amylase from alkalophilic Bacillus sp.707. Protein Sci, 15, 468-477. PubMed id: 16452622 DOI: 10.1110/ps.051877006
Date:
29-Sep-05     Release date:   14-Mar-06    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P19571  (AMT6_BACS7) -  Glucan 1,4-alpha-maltohexaosidase
Seq:
Struc:
518 a.a.
481 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.98  - Glucan 1,4-alpha-maltohexaosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of 1,4-alpha-D-glucosidic linkages in amylaceous polysaccharides so as to remove successive maltohexaose residues from the non-reducing chain ends.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
DOI no: 10.1110/ps.051877006 Protein Sci 15:468-477 (2006)
PubMed id: 16452622  
 
 
Role of Trp140 at subsite -6 on the maltohexaose production of maltohexaose-producing amylase from alkalophilic Bacillus sp.707.
R.Kanai, K.Haga, T.Akiba, K.Yamane, K.Harata.
 
  ABSTRACT  
 
Maltohexaose-producing amylase (G6-amylase) from alkalophilic Bacillus sp.707 predominantly produces maltohexaose (G6) in the yield of >30% of the total products from short-chain amylose (DP=17). Our previous crystallographic study showed that G6-amylase has nine subsites, from -6 to +3, and pointed out the importance of the indole moiety of Trp140 in G6 production. G6-amylase has very low levels of hydrolytic activities for oligosaccharides shorter than maltoheptaose. To elucidate the mechanism underlying G6 production, we determined the crystal structures of the G6-amylase complexes with G6 and maltopentaose (G5). In the active site of the G6-amylase/G5 complex, G5 is bound to subsites -6 to -2, while G1 and G6 are found at subsites +2 and -7 to -2, respectively, in the G6-amylase/G6 complex. In both structures, the glucosyl residue located at subsite -6 is stacked to the indole moiety of Trp140 within a distance of 4A. The measurement of the activities of the mutant enzymes when Trp140 was replaced by leucine (W140L) or by tyrosine (W140Y) showed that the G6 production from short-chain amylose by W140L is lower than that by W140Y or wild-type enzyme. The face-to-face short contact between Trp140 and substrate sugars is suggested to regulate the disposition of the glucosyl residue at subsite -6 and to govern product specificity for G6 production.
 
  Selected figure(s)  
 
Figure 1.
Crystal structures of the G6-amylase/G5 (A) and G6-amylase/G6 (B) complexes. The G6-amylase is composed of three domains: A (blue), B (yellow), and C (green). Three calcium ions and one sodium ion are shown by cyan and by purple spheres, respectively, and sugar molecules are represented by balls and sticks. This figure was drawn using the program Molscript (Kraulis 1991).
Figure 2.
Stereo views of ligand binding at the active site. (A) G6-amylase/G5 complex. (B) G6-amylase/G6 complex.(C) Subsite +2 of the G6-amylase/G6 complex. Omit |F[o] [minus sign]F[c]| electron density maps in A, B, and C are contoured at the 1.5 [sigma]level. Sugar ligands are shown in green. (D) The structural comparison of G5 in the G6-amylase/G5 complex (red lines) and G6 in the G6-amylase/G6 complex (green lines) with pG9 in the G6-amylase/pG9 complex (blue lines). These figures were prepared by using the program TURBO-FRODO (A. Roussel and C. Cambillau, LCCMB, Marseilles).
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2006, 15, 468-477) copyright 2006.  
  Figures were selected by an automated process.