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PDBsum entry 2amg

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protein metals links
Hydrolase PDB id
2amg
Jmol
Contents
Protein chain
415 a.a. *
Metals
_CA ×2
Waters ×178
* Residue conservation analysis
PDB id:
2amg
Name: Hydrolase
Title: Structure of hydrolase (glycosidase)
Structure: 1,4-alpha-d-glucan maltotetrahydrolase. Chain: a. Ec: 3.2.1.60
Source: Pseudomonas stutzeri. Organism_taxid: 316
Resolution:
2.00Å     R-factor:   0.178    
Authors: Y.Morishita,K.Hasegawa,Y.Matsuura,M.Kubota,S.Sakai,Y.Katsube
Key ref:
Y.Morishita et al. (1997). Crystal structure of a maltotetraose-forming exo-amylase from Pseudomonas stutzeri. J Mol Biol, 267, 661-672. PubMed id: 9126844 DOI: 10.1006/jmbi.1996.0887
Date:
23-Dec-96     Release date:   01-Apr-97    
Supersedes: 1amg
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P13507  (AMT4_PSEST) -  Glucan 1,4-alpha-maltotetraohydrolase
Seq:
Struc:
 
Seq:
Struc:
548 a.a.
415 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.60  - Glucan 1,4-alpha-maltotetraohydrolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of 1,4-alpha-D-glucosidic linkages in amylaceous polysaccharides so as to remove successive maltotetraose residues from the non-reducing chain ends.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
DOI no: 10.1006/jmbi.1996.0887 J Mol Biol 267:661-672 (1997)
PubMed id: 9126844  
 
 
Crystal structure of a maltotetraose-forming exo-amylase from Pseudomonas stutzeri.
Y.Morishita, K.Hasegawa, Y.Matsuura, Y.Katsube, M.Kubota, S.Sakai.
 
  ABSTRACT  
 
The three-dimensional structure of an exo-type alpha-amylase from Pseudomonas stutzeri which degrades starch from its non-reducing end to produce maltotetraose has been determined by X-ray structure analysis. The catalytic domain of this enzyme (G4-2), whose structure was determined, is a product of spontaneous limited proteolysis in culture broth. It has 429 amino acid residues and a molecular mass of 47,200, and crystallizes in ammonium sulfate solution at pH 7.5. The structure was elucidated by the multiple isomorphous replacement method and refined at 2.0 A resolution, resulting in a final R-factor of 0.178 for significant reflections with a root-mean-square deviation from ideality in bond distances of 0.013 A. The polypeptide chain of this molecule folds into three domains; the first with a (beta/alpha)8 barrel structure, the second with an excursed part from the first one, and the third with five-stranded antiparallel beta-sheets. The active cleft is formed on the C-terminal side of the beta-sheets in the (beta/alpha)8 barrel as in the known endo-type alpha-amylases. A histidine side-chain nitrogen ND1 is coordinated to one of the bound calcium ion. The recognition site of the non-reducing end of the amylose that determines exo-wise degradation is presumed to be at one end of this cleft where there is a disordered loop consisting of the 66th to 72nd residues, and a loop carrying an aspartic acid (Asp160). These structural features may be responsible for the binding of the non-reducing end of the substrate amylose.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Stereo plots of the coordination around the calcium sites: (a) calcium site 1, WAT designates a liganded water molecule WAT553; (b) calcium site 2.
Figure 8.
Figure 8. Stereo pair of a section of the MIR-map at 2.5 Å resolution superimposed on the rnal model in the region of the β-sheets in the (β/α)[8] barrel, at residues Ile19 to Phe23 and Pro329 to Tyr332.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 267, 661-672) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
15583388 M.Momma, and Z.Fujimoto (2004).
Expression, crystallization and preliminary X-ray crystallographic studies of Klebsiella pneumoniae maltohexaose-producing alpha-amylase.
  Acta Crystallogr D Biol Crystallogr, 60, 2352-2354.  
14501113 J.Koepke, E.I.Scharff, C.Lücke, H.Rüterjans, and G.Fritzsch (2003).
Statistical analysis of crystallographic data obtained from squid ganglion DFPase at 0.85 A resolution.
  Acta Crystallogr D Biol Crystallogr, 59, 1744-1754.
PDB code: 1pjx
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.  
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.  
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.  
11272837 Y.Mezaki, Y.Katsuya, M.Kubota, and Y.Matsuura (2001).
Crystallization and structural analysis of intact maltotetraose-forming exo-amylase from Pseudomonas stutzeri.
  Biosci Biotechnol Biochem, 65, 222-225.
PDB code: 1gcy
9558324 A.K.Schmidt, S.Cottaz, H.Driguez, and G.E.Schulz (1998).
Structure of cyclodextrin glycosyltransferase complexed with a derivative of its main product beta-cyclodextrin.
  Biochemistry, 37, 5909-5915.
PDB code: 3cgt
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.