PDBsum entry 2d0f

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Hydrolase PDB id
Protein chain
637 a.a. *
MPD ×4
_CA ×3
Waters ×452
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of thermoactinomyces vulgaris r-47 alpha- amylase 1 (tvai) mutant d356n complexed with p2, a pullulan model oligosaccharide
Structure: Alpha-amylase i. Chain: a. Synonym: tva i. Engineered: yes. Mutation: yes
Source: Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47. Expressed in: escherichia coli. Expression_system_taxid: 562
2.08Å     R-factor:   0.154     R-free:   0.187
Authors: A.Abe,H.Yoshida,T.Tonozuka,Y.Sakano,S.Kamitori
Key ref:
A.Abe et al. (2005). Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages. FEBS J, 272, 6145-6153. PubMed id: 16302977 DOI: 10.1111/j.1742-4658.2005.05013.x
02-Aug-05     Release date:   11-Jul-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q60053  (NEPU1_THEVU) -  Neopullulanase 1
666 a.a.
637 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.  - Neopullulanase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of pullulan to panose (6-alpha-D-glucosylmaltose).
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     7 terms  


DOI no: 10.1111/j.1742-4658.2005.05013.x FEBS J 272:6145-6153 (2005)
PubMed id: 16302977  
Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages.
A.Abe, H.Yoshida, T.Tonozuka, Y.Sakano, S.Kamitori.
Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) has unique hydrolyzing activities for pullulan with sequence repeats of alpha-(1,4), alpha-(1,4), and alpha-(1,6) glycosidic linkages, as well as for starch. TVAI mainly hydrolyzes alpha-(1,4) glycosidic linkages to produce a panose, but it also hydrolyzes alpha-(1,6) glycosidic linkages with a lesser efficiency. X-ray structures of three complexes comprising an inactive mutant TVAI (D356N or D356N/E396Q) and a pullulan model oligosaccharide (P2; [Glc-alpha-(1,6)-Glc-alpha-(1,4)-Glc-alpha-(1,4)]2 or P5; [Glc-alpha-(1,6)-Glc-alpha-(1,4)-Glc-alpha-(1,4)]5) were determined. The complex D356N/P2 is a mimic of the enzyme/product complex in the main catalytic reaction of TVAI, and a structural comparison with Aspergillus oryzaealpha-amylase showed that the (-) subsites of TVAI are responsible for recognizing both starch and pullulan. D356N/E396Q/P2 and D356N/E396Q/P5 provided models of the enzyme/substrate complex recognizing the alpha-(1,6) glycosidic linkage at the hydrolyzing site. They showed that only subsites -1 and -2 at the nonreducing end of TVAI are effective in the hydrolysis of alpha-(1,6) glycosidic linkages, leading to weak interactions between substrates and the enzyme. Domain N of TVAI is a starch-binding domain acting as an anchor in the catalytic reaction of the enzyme. In this study, additional substrates were also found to bind to domain N, suggesting that domain N also functions as a pullulan-binding domain.
  Selected figure(s)  
Figure 1.
Fig. 1. Chemical structures of the repeat units of pullulan, P2 and P5. A solid arrow indicates the main hydrolysing site, and a dashed arrow indicates the minor site of pullulan hydrolysed by TVAI.
Figure 2.
Fig. 2. Overall structure of TVAI (D356N/E396Q/P5). Domains N, A, B, and C are drawn in blue, green, yellow, and pink, respectively. The binding substrates and Ca^2+ are shown by a wire-style model and as orange spheres. The catalytic site, site-N, site-NA, site-A, and site-C, are labelled. The loop region from Ser282 to Gln284 in D356N/E396Q/P2 with poor electron density is shown in red.
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS J (2005, 272, 6145-6153) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19502354 R.Suzuki, T.Katayama, M.Kitaoka, H.Kumagai, T.Wakagi, H.Shoun, H.Ashida, K.Yamamoto, and S.Fushinobu (2009).
Crystallographic and mutational analyses of substrate recognition of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum.
  J Biochem, 146, 389-398.
PDB code: 2zxq
18784084 M.E.Caines, H.Zhu, M.Vuckovic, L.M.Willis, S.G.Withers, W.W.Wakarchuk, and N.C.Strynadka (2008).
The Structural Basis for T-antigen Hydrolysis by Streptococcus pneumoniae: A TARGET FOR STRUCTURE-BASED VACCINE DESIGN.
  J Biol Chem, 283, 31279-31283.
PDB code: 3ecq
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
18473149 Y.Xu, M.Yang, J.Sun, J.Qian, D.Zhang, Y.Sun, L.Ma, and C.Zhu (2008).
Glycogen branching enzyme: a novel deltamethrin resistance-associated gene from Culex pipiens pallens.
  Parasitol Res, 103, 449-458.  
17803687 S.Bozonnet, M.T.Jensen, M.M.Nielsen, N.Aghajari, M.H.Jensen, B.Kramhøft, M.Willemoës, S.Tranier, R.Haser, and B.Svensson (2007).
The 'pair of sugar tongs' site on the non-catalytic domain C of barley alpha-amylase participates in substrate binding and activity.
  FEBS J, 274, 5055-5067.
PDB codes: 2qps 2qpu
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 code is shown on the right.