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PDBsum entry 1bf2

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protein metals links
Hydrolase PDB id
1bf2
Jmol
Contents
Protein chain
750 a.a. *
Metals
_CA
Waters ×407
* Residue conservation analysis
PDB id:
1bf2
Name: Hydrolase
Title: Structure of pseudomonas isoamylase
Structure: Isoamylase. Chain: a. Synonym: glycogen 6-glucanohydrolase. Ec: 3.2.1.68
Source: Pseudomonas amyloderamosa. Organism_taxid: 32043
Resolution:
2.00Å     R-factor:   0.161     R-free:   0.214
Authors: Y.Katsuya,Y.Mezaki,M.Kubota,Y.Matsuura
Key ref:
Y.Katsuya et al. (1998). Three-dimensional structure of Pseudomonas isoamylase at 2.2 A resolution. J Mol Biol, 281, 885-897. PubMed id: 9719642 DOI: 10.1006/jmbi.1998.1992
Date:
26-May-98     Release date:   12-Aug-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P10342  (ISOA_PSEAY) -  Isoamylase
Seq:
Struc:
 
Seq:
Struc:
776 a.a.
750 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.68  - Isoamylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of alpha-(1,6)-D-glucosidic branch linkages in glycogen, amylopectin and their beta-limits dextrins.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
DOI no: 10.1006/jmbi.1998.1992 J Mol Biol 281:885-897 (1998)
PubMed id: 9719642  
 
 
Three-dimensional structure of Pseudomonas isoamylase at 2.2 A resolution.
Y.Katsuya, Y.Mezaki, M.Kubota, Y.Matsuura.
 
  ABSTRACT  
 
The three-dimensional structure of isoamylase from Pseudomonas amyloderamosa, which hydrolyzes alpha-1,6-glucosidic linkages of amylopectin and glycogen, has been determined by X-ray structure analysis. The enzyme has 750 amino acid residues and a molecular mass of 80 kDa, and it can be crystallized from ammonium sulfate solution. The structure was elucidated by the multiple isomorphous replacement method and refined at 2.2 A resolution, resulting in a final R-factor of 0.161 for significant reflections with a root-mean-square deviation from ideality in bond lengths of 0.009 A. The analysis revealed that in the N-terminal region, isoamylase has a novel extra domain that we call domain N, whose three-dimensional structure has not so far been reported. It has a (beta/alpha)8-barrel-type supersecondary structure in the catalytic domain common to the alpha-amylase family enzymes, though the barrel is incomplete, with a deletion of an alpha-helix between the fifth and sixth beta-strands. A long excursed region is present between the third beta-strand and the third alpha-helix of the barrel but, in contrast to the so-called domain B that has been identified in the other enzymes of alpha-amylase family, it cannot be considered to be an independent domain, because this loop forms a globular cluster together with the loop between the fourth beta-strand and the fourth alpha-helix. Isoamylase contains a bound calcium ion, but this is not in the same position as the conserved calcium ion that has been reported in other alpha-amylase family enzymes.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. A representation of Pseudomonas isoamylase viewed along the axis of the pseudo (b/a)[8]barrel, using the program MOLSCRIPT [Kraulis 1991]. The filled circle represents the calcium ion. The catalytic residues Asp375, Glu435 and Asp510 are shown as a ball-and-stick model.
Figure 6.
Figure 6. Close-up views of the region around the conserved calcium ion in various enzymes of the a-amylase family. The models are colored green, blue, red, yellow, purple and orange for isoamylase, TAA, PPA, BA2, G4A and CGT, respectively. The calcium ions are represented by balls. This picture was produced using the program
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 281, 885-897) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20957707 K.Hamacher (2011).
Efficient quantification of the importance of contacts for the dynamical stability of proteins.
  J Comput Chem, 32, 810-815.  
20812985 K.Yamamoto, H.Miyake, M.Kusunoki, and S.Osaki (2010).
Crystal structures of isomaltase from Saccharomyces cerevisiae and in complex with its competitive inhibitor maltose.
  FEBS J, 277, 4205-4214.
PDB codes: 3a4a 3aj7
20939100 S.Kalkhof, S.Haehn, M.Paulsson, N.Smyth, J.Meiler, and A.Sinz (2010).
Computational modeling of laminin N-terminal domains using sparse distance constraints from disulfide bonds and chemical cross-linking.
  Proteins, 78, 3409-3427.  
19139240 M.Palomo, S.Kralj, M.J.van der Maarel, and L.Dijkhuizen (2009).
The unique branching patterns of Deinococcus glycogen branching enzymes are determined by their N-terminal domains.
  Appl Environ Microbiol, 75, 1355-1362.  
17827690 Y.Takashima, T.Senoura, T.Yoshizaki, S.Hamada, H.Ito, and H.Matsui (2007).
Differential chain-length specificities of two isoamylase-type starch-debranching enzymes from developing seeds of kidney bean.
  Biosci Biotechnol Biochem, 71, 2308-2312.  
16703471 L.L.Lin, P.J.Chen, J.S.Liu, W.C.Wang, and H.F.Lo (2006).
Identification of glutamate residues important for catalytic activity or thermostability of a truncated Bacillus sp. strain TS-23 alpha-amylase by site-directed mutagenesis.
  Protein J, 25, 232-239.  
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
15184138 C.Bertoldo, M.Armbrecht, F.Becker, T.Schäfer, G.Antranikian, and W.Liebl (2004).
Cloning, sequencing, and characterization of a heat- and alkali-stable type I pullulanase from Anaerobranca gottschalkii.
  Appl Environ Microbiol, 70, 3407-3416.  
12747837 G.Polekhina, A.Gupta, B.J.Michell, B.van Denderen, S.Murthy, S.C.Feil, I.G.Jennings, D.J.Campbell, L.A.Witters, M.W.Parker, B.E.Kemp, and D.Stapleton (2003).
AMPK beta subunit targets metabolic stress sensing to glycogen.
  Curr Biol, 13, 867-871.  
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
12618437 H.Imamura, S.Fushinobu, M.Yamamoto, T.Kumasaka, B.S.Jeon, T.Wakagi, and H.Matsuzawa (2003).
Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor.
  J Biol Chem, 278, 19378-19386.
PDB codes: 1k1w 1k1x 1k1y
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.  
12196524 M.C.Abad, K.Binderup, J.Rios-Steiner, R.K.Arni, J.Preiss, and J.H.Geiger (2002).
The X-ray crystallographic structure of Escherichia coli branching enzyme.
  J Biol Chem, 277, 42164-42170.
PDB code: 1m7x
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.  
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.  
11094287 M.A.Teste, B.Enjalbert, J.L.Parrou, and J.M.François (2000).
The Saccharomyces cerevisiae YPR184w gene encodes the glycogen debranching enzyme.
  FEMS Microbiol Lett, 193, 105-110.  
  10473430 J.Abe, C.Ushijima, and S.Hizukuri (1999).
Expression of the isoamylase gene of Flavobacterium odoratum KU in Escherichia coli and identification of essential residues of the enzyme by site-directed mutagenesis.
  Appl Environ Microbiol, 65, 4163-4170.  
10574960 J.C.Uitdehaag, K.H.Kalk, B.A.van Der Veen, L.Dijkhuizen, and B.W.Dijkstra (1999).
The cyclization mechanism of cyclodextrin glycosyltransferase (CGTase) as revealed by a gamma-cyclodextrin-CGTase complex at 1.8-A resolution.
  J Biol Chem, 274, 34868-34876.
PDB code: 1d3c
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.