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Hydrolase PDB id
1bvz
Jmol
Contents
Protein chains
585 a.a. *
Waters ×478
* Residue conservation analysis
PDB id:
1bvz
Name: Hydrolase
Title: Alpha-amylase ii (tvaii) from thermoactinomyces vulgaris r- 47
Structure: Protein (alpha-amylase ii). Chain: a, b. Fragment: n,a,b.C. Engineered: yes
Source: Thermoactinomyces vulgaris. Organism_taxid: 2026. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.60Å     R-factor:   0.196     R-free:   0.272
Authors: S.Kamitori,S.Kondo,K.Okuyama,T.Yokota,Y.Shimura,T.Tonozuka, Y.Sakano
Key ref:
S.Kamitori et al. (1999). Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution. J Mol Biol, 287, 907-921. PubMed id: 10222200 DOI: 10.1006/jmbi.1999.2647
Date:
22-Sep-98     Release date:   02-Mar-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q08751  (NEPU2_THEVU) -  Neopullulanase 2
Seq:
Struc: 		 
Seq:
Struc: 		585 a.a.
585 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!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
DOI no: 10.1006/jmbi.1999.2647 J Mol Biol 287:907-921 (1999)
PubMed id: 10222200  
 
 
Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution.
S.Kamitori, S.Kondo, K.Okuyama, T.Yokota, Y.Shimura, T.Tonozuka, Y.Sakano.
 
  ABSTRACT  
 
The crystal structure of Thermoactinomyces vulgaris R-47 alpha-Amylase II (TVAII) has been determined by multiple isomorphous replacement at 2.6 A resolution. TVAII was crystallized in an orthorhombic system with the space group P212121 and the cell dimensions a=118.5 A, b=119.5 A, c=114.5 A. There are two molecules in an asymmetric unit, related by the non-crystallographic 2-fold symmetry. Diffraction data were collected at 113 K and the cell dimensions reduced to a=114.6 A, b=117.9 A, c=114.2 A, and the model was refined against 7.0-2.6 A resolution data giving an R-factor of 0.204 (Rfree=0.272). The final model consists of 1170 amino acid residues (two molecules) and 478 water molecules with good chemical geometry. TVAII has three domains, A, B, and C, like other alpha-amylases. Domain A with a (beta/alpha)8 barrel structure and domain C with a beta-sandwich structure are very similar to those found in other alpha-amylases. Additionally, TVAII has an extra domain N composed of 121 amino acid residues at the N-terminal site, which has a beta-barrel-like structure consisting of seven antiparallel beta-strands. Domain N is one of the driving forces in the formation of the dimer structure of TVAII, but its role in the enzyme activity is still not clear. TVAII does not have the Ca2+ binding site that connects domains A and B in other alpha-amylases, rather the NZ atom of Lys299 of TVAII serves as the connector between these domains. TVAII can hydrolyze cyclodextrins and pullulan as well as starch. Based on a structural comparison with the complex between a mutant cyclodextrin glucanotransferase and a beta-cyclodextrin derivative, Phe286 located at domain B is considered the residue most likely to recognize the hydrophobic cavity of cyclodextrins. The active-site cleft of TVAII is wider and shallower than that of other alpha-amylases, and seems to be suitable for the binding of pullulan which is expected not to adopt the helical structure of amylose.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. Stereoviews of the active site structures of (a) TVAII and (b) CGT8. Superimposed b-CD moieties are shown by broken lines in (a), and a binding b-CD moiety is shown by thin lines in (b). 		Figure 8.
Figure 8. Stereoview of the dimer structure of TVAII viewed from the non-crystallographic 2-fold axis as illustrated by the program MOLSCRIPT. Mol-2 is shown in the light colors.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 287, 907-921) copyright 1999.  
  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
20190251 W.Y.Chou, W.I.Chou, T.W.Pai, S.C.Lin, T.Y.Jiang, C.Y.Tang, and M.D.Chang (2010).
Feature-incorporated alignment based ligand-binding residue prediction for carbohydrate-binding modules.
  Bioinformatics, 26, 1022-1028.  
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
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
17459873 M.Nagae, A.Tsuchiya, T.Katayama, K.Yamamoto, S.Wakatsuki, and R.Kato (2007).
Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum.
  J Biol Chem, 282, 18497-18509.
PDB codes: 2eab 2eac 2ead 2eae
17371546 T.Tonozuka, A.Sogawa, M.Yamada, N.Matsumoto, H.Yoshida, S.Kamitori, K.Ichikawa, M.Mizuno, A.Nishikawa, and Y.Sakano (2007).
Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein.
  FEBS J, 274, 2109-2120.
PDB codes: 2dfz 2zyk
16230347 A.B.Boraston, M.Healey, J.Klassen, E.Ficko-Blean, A.Lammerts van Bueren, and V.Law (2006).
A structural and functional analysis of alpha-glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition.
  J Biol Chem, 281, 587-598.
PDB codes: 2c3g 2c3h 2c3v 2c3w 2c3x
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
15501829 A.L.Lovering, S.S.Lee, Y.W.Kim, S.G.Withers, and N.C.Strynadka (2005).
Mechanistic and structural analysis of a family 31 alpha-glycosidase and its glycosyl-enzyme intermediate.
  J Biol Chem, 280, 2105-2115.
PDB codes: 1xsi 1xsj 1xsk
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
14660599 K.S.Bak-Jensen, G.André, T.E.Gottschalk, G.Paës, V.Tran, and B.Svensson (2004).
Tyrosine 105 and threonine 212 at outermost substrate binding subsites -6 and +4 control substrate specificity, oligosaccharide cleavage patterns, and multiple binding modes of barley alpha-amylase 1.
  J Biol Chem, 279, 10093-10102.  
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
14517232 K.Hövel, D.Shallom, K.Niefind, V.Belakhov, G.Shoham, T.Baasov, Y.Shoham, and D.Schomburg (2003).
Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase.
  EMBO J, 22, 4922-4932.
PDB codes: 1pz2 1pz3 1qw8 1qw9
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.  
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
12423336 H.Mori, K.S.Bak-Jensen, and B.Svensson (2002).
Barley alpha-amylase Met53 situated at the high-affinity subsite -2 belongs to a substrate binding motif in the beta-->alpha loop 2 of the catalytic (beta/alpha)8-barrel and is critical for activity and substrate specificity.
  Eur J Biochem, 269, 5377-5390.  
11856298 O.L.Franco, D.J.Rigden, F.R.Melo, and M.F.Grossi-De-Sá (2002).
Plant alpha-amylase inhibitors and their interaction with insect alpha-amylases.
  Eur J Biochem, 269, 397-412.  
  12005440 S.C.Garman, L.Hannick, A.Zhu, and D.N.Garboczi (2002).
The 1.9 A structure of alpha-N-acetylgalactosaminidase: molecular basis of glycosidase deficiency diseases.
  Structure, 10, 425-434.
PDB codes: 1ktb 1ktc
11257505 E.A.MacGregor, S.Janecek, and B.Svensson (2001).
Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes.
  Biochim Biophys Acta, 1546, 1.  
11737209 H.Mori, K.S.Bak-Jensen, T.E.Gottschalk, M.S.Motawia, I.Damager, B.L.Møller, and B.Svensson (2001).
Modulation of activity and substrate binding modes by mutation of single and double subsites +1/+2 and -5/-6 of barley alpha-amylase 1.
  Eur J Biochem, 268, 6545-6558.  
11168426 R.Koukiekolo, V.Desseaux, Y.Moreau, G.Marchis-Mouren, and M.Santimone (2001).
Mechanism of porcine pancreatic alpha-amylase. Inhibition of amylose and maltopentaose hydrolysis by alpha-, beta- and gamma-cyclodextrins.
  Eur J Biochem, 268, 841-848.  
11302176 T.Yokota, T.Tonozuka, S.Kamitori, and Y.Sakano (2001).
The deletion of amino-terminal domain in Thermoactinomyces vulgaris R-47 alpha-amylases: effects of domain N on activity, specificity, stability and dimerization.
  Biosci Biotechnol Biochem, 65, 401-408.  
11330677 T.Yokota, T.Tonozuka, Y.Shimura, K.Ichikawa, S.Kamitori, and Y.Sakano (2001).
Structures of Thermoactinomyces vulgaris R-47 alpha-amylase II complexed with substrate analogues.
  Biosci Biotechnol Biochem, 65, 619-626.
PDB codes: 1jib 1jl8
11053856 J.H.Lebbink, C.Bertoldo, G.Tibbelin, J.T.Andersen, F.Duffner, G.Antranikian, and R.Ladenstein (2000).
Crystallization and preliminary X-ray crystallographic studies of the thermoactive pullulanase type I, hydrolyzing alpha-1,6 glycosidic linkages, from Fervidobacterium pennivorans Ven5.
  Acta Crystallogr D Biol Crystallogr, 56, 1470-1472.  
10650202 J.Matzke, A.Herrmann, E.Schneider, and E.P.Bakker (2000).
Gene cloning, nucleotide sequence and biochemical properties of a cytoplasmic cyclomaltodextrinase (neopullulanase) from Alicyclobacillus acidocaldarius, reclassification of a group of enzymes.
  FEMS Microbiol Lett, 183, 55-61.  
10705452 N.Ichikawa, R.Fujisaka, and R.Kuribayashi (2000).
Requirement for lysine-19 of the yeast mitochondrial ATPase inhibitor for the stability of the inactivated inhibitor-F1Fo complex at higher pH.
  Biosci Biotechnol Biochem, 64, 89-95.  
10473583 J.S.Kim, S.S.Cha, H.J.Kim, T.J.Kim, N.C.Ha, S.T.Oh, H.S.Cho, M.J.Cho, M.J.Kim, H.S.Lee, J.W.Kim, K.Y.Choi, K.H.Park, and B.H.Oh (1999).
Crystal structure of a maltogenic amylase provides insights into a catalytic versatility.
  J Biol Chem, 274, 26279-26286.
PDB code: 1sma
10586502 S.Kashiwabara, S.Ogawa, N.Miyoshi, M.Oda, and Y.Suzuki (1999).
Three domains comprised in thermostable molecular weight 54,000 pullulanase of type I from Bacillus flavocaldarius KP1228.
  Biosci Biotechnol Biochem, 63, 1736-1748.  
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.