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PDBsum entry 6taa

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protein metals links
Hydrolase(o-glycosyl) PDB id
6taa
Jmol
Contents
Protein chain
476 a.a. *
Metals
_CA ×2
Waters ×239
* Residue conservation analysis
PDB id:
6taa
Name: Hydrolase(o-glycosyl)
Title: Structure and molecular model refinement of aspergillus oryzae (taka) alpha-amylase: an application of the simulated-annealing method
Structure: Alpha-amylase. Chain: a. Engineered: yes
Source: Aspergillus oryzae. Organism_taxid: 5062
Resolution:
2.10Å     R-factor:   0.198    
Authors: H.J.Swift,L.Brady,Z.S.Derewenda,E.J.Dodson,J.P.Turkenburg, A.J.Wilkinson
Key ref: H.J.Swift et al. (1991). Structure and molecular model refinement of Aspergillus oryzae (TAKA) alpha-amylase: an application of the simulated-annealing method. Acta Crystallogr B, 47, 535-544. PubMed id: 1930835
Date:
21-Aug-92     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0C1B3  (AMYA1_ASPOR) -  Alpha-amylase A type-1/2
Seq:
Struc:
499 a.a.
476 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.1  - Alpha-amylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-alpha-glucosidic linkages in oligosaccharides and polysaccharides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cellular_component   6 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
Acta Crystallogr B 47:535-544 (1991)
PubMed id: 1930835  
 
 
Structure and molecular model refinement of Aspergillus oryzae (TAKA) alpha-amylase: an application of the simulated-annealing method.
H.J.Swift, L.Brady, Z.S.Derewenda, E.J.Dodson, G.G.Dodson, J.P.Turkenburg, A.J.Wilkinson.
 
  ABSTRACT  
 
Monoclinic crystals of a neutral alpha-amylase from Aspergillus oryzae, containing three molecules in the asymmetric unit, have been reported previously and studied at 3 A resolution [Matsuura, Kunusoki, Harada & Kakudo (1984). J. Biochem. 95, 697-702]. Here we report the solution of the structure of this enzyme in a different crystal form (space group P2(1)2(1)2(1), a = 50.9, b = 67.2, c = 132.7 A), with only one molecule in the asymmetric unit. The structure was solved by the molecular replacement method, using a model of acid alpha-amylase from a related fungus A. niger [Brady, Brzozowski, Derewenda, Dodson & Dodson (1991). Acta Cryst. B47, 527-535]. Conventional least-squares crystallographic refinement failed to converge in a satisfactory manner, and the technique of molecular dynamics in the form of the XPLOR package [Brunger (1988). XPLOR Manual. Yale Univ., USA] was used to overcome the problem. A large rigid-body type movement of the C-terminal domain was identified and accounted for. The final round of restrained least-squares refinement (at 2.1 A resolution) including 3675 protein atoms and 247 water molecules resulted in a conventional crystallographic R factor of 0.183 and an atomic model which conforms well to standard stereochemical parameters (standard deviation of bond lengths from their expected values is 0.028 A, while that for planar groups is 0.029 A).
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  16880540 A.Vujicić-Zagar, and B.W.Dijkstra (2006).
Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 angstroms resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 716-721.
PDB codes: 2guy 2gvy
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
15722449 R.Maurus, A.Begum, H.H.Kuo, A.Racaza, S.Numao, C.Andersen, J.W.Tams, J.Vind, C.M.Overall, S.G.Withers, and G.D.Brayer (2005).
Structural and mechanistic studies of chloride induced activation of human pancreatic alpha-amylase.
  Protein Sci, 14, 743-755.
PDB codes: 1xgz 1xh0 1xh1 1xh2
12906828 X.Robert, R.Haser, T.E.Gottschalk, F.Ratajczak, H.Driguez, B.Svensson, and N.Aghajari (2003).
The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs.
  Structure, 11, 973-984.
PDB codes: 1ht6 1p6w
11676021 K.Watanabe, K.Miyake, and Y.Suzuki (2001).
Identification of catalytic and substrate-binding site residues in Bacillus cereus ATCC7064 oligo-1,6-glucosidase.
  Biosci Biotechnol Biochem, 65, 2058-2064.  
12483584 H.Kambe-Honjoh, K.Ohsumi, H.Shimoi, H.Nakajima, and K.Kitamoto (2000).
Molecular breeding of yeast with higher metal-adsorption capacity by expression of histidine-repeat insertion in the protein anchored to the cell wall.
  J Gen Appl Microbiol, 46, 113-117.  
10792537 L.Janda, J.Damborský, M.Petrícek, J.Spízek, and P.Tichý (2000).
Molecular characterization of the Thermomonospora curvata aglA gene encoding a thermotolerant alpha-1,4-glucosidase.
  J Appl Microbiol, 88, 773-783.  
  10091666 E.H.Rydberg, G.Sidhu, H.C.Vo, J.Hewitt, H.C.Côte, Y.Wang, S.Numao, R.T.MacGillivray, C.M.Overall, G.D.Brayer, and S.G.Withers (1999).
Cloning, mutagenesis, and structural analysis of human pancreatic alpha-amylase expressed in Pichia pastoris.
  Protein Sci, 8, 635-643.
PDB code: 1bsi
  10508102 K.Ohdan, T.Kuriki, H.Kaneko, J.Shimada, T.Takada, Z.Fujimoto, H.Mizuno, and S.Okada (1999).
Characteristics of two forms of alpha-amylases and structural implication.
  Appl Environ Microbiol, 65, 4652-4658.  
9634702 F.Vallée, A.Kadziola, Y.Bourne, M.Juy, K.W.Rodenburg, B.Svensson, and R.Haser (1998).
Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution.
  Structure, 6, 649-659.
PDB code: 1ava
  9541387 N.Aghajari, G.Feller, C.Gerday, and R.Haser (1998).
Crystal structures of the psychrophilic alpha-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor.
  Protein Sci, 7, 564-572.
PDB codes: 1aqh 1aqm
9862804 N.Aghajari, G.Feller, C.Gerday, and R.Haser (1998).
Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level.
  Structure, 6, 1503-1516.
PDB code: 1b0i
9689337 X.Baur, and A.Posch (1998).
Characterized allergens causing bakers' asthma.
  Allergy, 53, 562-566.  
8681972 C.Gilles, J.P.Astier, G.Marchis-Mouren, C.Cambillau, and F.Payan (1996).
Crystal structure of pig pancreatic alpha-amylase isoenzyme II, in complex with the carbohydrate inhibitor acarbose.
  Eur J Biochem, 238, 561-569.
PDB code: 1ose
8735862 V.Liebers, I.Sander, V.Van Kampen, M.Raulf-Heimsoth, P.Rozynek, and X.Baur (1996).
Overview on denominated allergens.
  Clin Exp Allergy, 26, 494-516.  
7556163 F.Casset, A.Imberty, R.Haser, F.Payan, and S.Perez (1995).
Molecular modelling of the interaction between the catalytic site of pig pancreatic alpha-amylase and amylose fragments.
  Eur J Biochem, 232, 284-293.  
  8528071 G.D.Brayer, Y.Luo, and S.G.Withers (1995).
The structure of human pancreatic alpha-amylase at 1.8 A resolution and comparisons with related enzymes.
  Protein Sci, 4, 1730-1742.
PDB code: 1hny
  7613472 M.Qian, R.Haser, and F.Payan (1995).
Carbohydrate binding sites in a pancreatic alpha-amylase-substrate complex, derived from X-ray structure analysis at 2.1 A resolution.
  Protein Sci, 4, 747-755.  
7813489 B.Schwermann, K.Pfau, B.Liliensiek, M.Schleyer, T.Fischer, and E.P.Bakker (1994).
Purification, properties and structural aspects of a thermoacidophilic alpha-amylase from Alicyclobacillus acidocaldarius atcc 27009. Insight into acidostability of proteins.
  Eur J Biochem, 226, 981-991.  
8020481 G.Feller, F.Payan, F.Theys, M.Qian, R.Haser, and C.Gerday (1994).
Stability and structural analysis of alpha-amylase from the antarctic psychrophile Alteromonas haloplanctis A23.
  Eur J Biochem, 222, 441-447.  
8087658 X.Baur, Z.Chen, and I.Sander (1994).
Isolation and denomination of an important allergen in baking additives: alpha-amylase from Aspergillus oryzae (Asp o II).
  Clin Exp Allergy, 24, 465-470.  
7922041 Y.Harpaz, M.Gerstein, and C.Chothia (1994).
Volume changes on protein folding.
  Structure, 2, 641-649.  
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.