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protein metals Protein-protein interface(s) links
Hydrolase PDB id
1ji1
Jmol
Contents
Protein chains
637 a.a. *
Metals
_CA ×6
Waters ×1474
* Residue conservation analysis
PDB id:
1ji1
Name: Hydrolase
Title: Crystal structure analysis of thermoactinomyces vulgaris r- 47 alpha-amylase 1
Structure: Alpha-amylase i. Chain: a, b. Engineered: yes
Source: Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.60Å     R-factor:   0.182     R-free:   0.206
Authors: S.Kamitori,A.Abe,A.Ohtaki,A.Kaji,T.Tonozuka,Y.Sakano
Key ref:
S.Kamitori et al. (2002). Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution. J Mol Biol, 318, 443-453. PubMed id: 12051850 DOI: 10.1016/S0022-2836(02)00111-0
Date:
28-Jun-01     Release date:   05-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q60053  (NEPU1_THEVU) -  Neopullulanase 1
Seq:
Struc: 		 
Seq:
Struc: 		666 a.a.
637 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.135  - 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: 10.1016/S0022-2836(02)00111-0 J Mol Biol 318:443-453 (2002)
PubMed id: 12051850  
 
 
Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution.
S.Kamitori, A.Abe, A.Ohtaki, A.Kaji, T.Tonozuka, Y.Sakano.
 
  ABSTRACT  
 
The X-ray crystal structures of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) and alpha-amylase 2 (TVAII) have been determined at 1.6 A and 2.3 A resolution, respectively. The structures of TVAI and TVAII have been refined, R-factor of 0.182 (R(free)=0.206) and 0.179 (0.224), respectively, with good chemical geometries. Both TVAI and TVAII have four domains, N, A, B and C, and all very similar in structure. However, there are some differences in the structures between them. Domain N of TVAI interacts strongly with domains A and B, giving a spherical shape structure to the enzyme, while domain N of TVAII is isolated from the other domains, which leads to the formation of a dimer. TVAI has three bound Ca ions, whereas TVAII has only one. TVAI has eight extra loops compared to TVAII, while TVAII has two extra loops compared to TVAI. TVAI can hydrolyze substrates more efficiently than TVAII with a high molecular mass such as starch, while TVAII is much more active against cyclodextrins than TVAI and other alpha-amylases. A structural comparison of the active sites has clearly revealed this difference in substrate specificity.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Comparison of thermostability of TVAI and TVAII in the presence or absence of EGTA. The curves expressed by the equation RA[calc]=100+[ -100Tn/(Hn+Tn)] are also plotted. 		Figure 4.
Figure 4. Two molecules (Mol-1 and Mol-2) in an asymmetric unit of TVAI (left) and TVAII (right) illustrated by the program MOLSCRIPT. Mol-2 is shown by light colors. The active site residues, Phe310(TVAI)/Phe286(TVAII), Asp356/325, Glu396/354, and Asp472/421, and the bound Ca ions are shown by a wire-style model and black circles, respectively.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 443-453) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21063757 M.C.Chi, T.J.Wu, T.T.Chuang, H.L.Chen, H.F.Lo, and L.L.Lin (2010).
Biophysical characterization of a recombinant α-amylase from thermophilic Bacillus sp. strain TS-23.
  Protein J, 29, 572-582.  
19490104 N.Matsumoto, M.Yamada, Y.Kurakata, H.Yoshida, S.Kamitori, A.Nishikawa, and T.Tonozuka (2009).
Crystal structures of open and closed forms of cyclo/maltodextrin-binding protein.
  FEBS J, 276, 3008-3019.
PDB codes: 2zym 2zyn 2zyo
18223106 A.Labes, E.N.Karlsson, O.H.Fridjonsson, P.Turner, G.O.Hreggvidson, J.K.Kristjansson, O.Holst, and P.Schönheit (2008).
Novel members of glycoside hydrolase family 13 derived from environmental DNA.
  Appl Environ Microbiol, 74, 1914-1921.  
18004751 J.W.Torrance, M.W.Macarthur, and J.M.Thornton (2008).
Evolution of binding sites for zinc and calcium ions playing structural roles.
  Proteins, 71, 813-830.  
18049800 S.B.Mabrouk, E.B.Messaoud, D.Ayadi, S.Jemli, A.Roy, M.Mezghani, and S.Bejar (2008).
Cloning and sequencing of an original gene encoding a maltogenic amylase from Bacillus sp. US149 strain and characterization of the recombinant activity.
  Mol Biotechnol, 38, 211-219.  
17630303 S.J.Yang, B.C.Min, Y.W.Kim, S.M.Jang, B.H.Lee, and K.H.Park (2007).
Changes in the catalytic properties of Pyrococcus furiosus thermostable amylase by mutagenesis of the substrate binding sites.
  Appl Environ Microbiol, 73, 5607-5612.  
16302977 A.Abe, H.Yoshida, T.Tonozuka, Y.Sakano, and S.Kamitori (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.
PDB codes: 2d0f 2d0g 2d0h
16310726 P.Turner, A.Labes, O.H.Fridjonsson, G.O.Hreggvidson, P.Schönheit, J.K.Kristjansson, O.Holst, and E.N.Karlsson (2005).
Two novel cyclodextrin-degrading enzymes isolated from thermophilic bacteria have similar domain structures but differ in oligomeric state and activity profile.
  J Biosci Bioeng, 100, 380-390.  
15138257 A.Ohtaki, M.Mizuno, T.Tonozuka, Y.Sakano, and S.Kamitori (2004).
Complex structures of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with acarbose and cyclodextrins demonstrate the multiple substrate recognition mechanism.
  J Biol Chem, 279, 31033-31040.
PDB codes: 1vfk 1vfm 1vfo 1vfu 3a6o
15182368 M.Mizuno, T.Tonozuka, A.Uechi, A.Ohtaki, K.Ichikawa, S.Kamitori, A.Nishikawa, and Y.Sakano (2004).
The crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) complexed with transglycosylated product.
  Eur J Biochem, 271, 2530-2538.
PDB code: 1vb9
12752453 H.B.Fritzsche, T.Schwede, and G.E.Schulz (2003).
Covalent and three-dimensional structure of the cyclodextrinase from Flavobacterium sp. no. 92.
  Eur J Biochem, 270, 2332-2341.
PDB code: 1h3g
12719434 T.Nonaka, M.Fujihashi, A.Kita, H.Hagihara, K.Ozaki, S.Ito, and K.Miki (2003).
Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites.
  J Biol Chem, 278, 24818-24824.
PDB codes: 1ud2 1ud3 1ud4 1ud5 1ud6 1ud8
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.