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Hydrolase PDB id
1aqm
Jmol
Contents
Protein chain
448 a.a. *
Ligands
TRS
Metals
_CA
_CL
Waters ×693
* Residue conservation analysis
PDB id:
1aqm
Name: Hydrolase
Title: Alpha-amylase from alteromonas haloplanctis complexed with tris
Structure: Alpha-amylase. Chain: a. Engineered: yes
Source: Pseudoalteromonas haloplanktis. Organism_taxid: 228. Strain: a23. Cell_line: rr1. Organ: pancreas. Gene: amy. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: rr1
Resolution:
1.85Å     R-factor:   0.157     R-free:   0.186
Authors: N.Aghajari,R.Haser
Key ref: N.Aghajari et al. (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. PubMed id: 9541387 Ref: Full text
Date:
31-Jul-97     Release date:   02-Mar-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P29957  (AMY_PSEHA) -  Alpha-amylase
Seq:
Struc: 		 
Seq:
Struc: 		669 a.a.
448 a.a.
Key:    PfamA domain  PfamB 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!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
Full text Protein Sci 7:564-572 (1998)
PubMed id: 9541387  
 
 
Crystal structures of the psychrophilic alpha-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor.
N.Aghajari, G.Feller, C.Gerday, R.Haser.
 
  ABSTRACT  
 
Alteromonas haloplanctis is a bacterium that flourishes in Antarctic sea-water and it is considered as an extreme psychrophile. We have determined the crystal structures of the alpha-amylase (AHA) secreted by this bacterium, in its native state to 2.0 angstroms resolution as well as in complex with Tris to 1.85 angstroms resolution. The structure of AHA, which is the first experimentally determined three-dimensional structure of a psychrophilic enzyme, resembles those of other known alpha-amylases of various origins with a surprisingly greatest similarity to mammalian alpha-amylases. AHA contains a chloride ion which activates the hydrolytic cleavage of substrate alpha-1,4-glycosidic bonds. The chloride binding site is situated approximately 5 angstroms from the active site which is characterized by a triad of acid residues (Asp 174, Glu 200, Asp 264). These are all involved in firm binding of the Tris moiety. A reaction mechanism for substrate hydrolysis is proposed on the basis of the Tris inhibitor binding and the chloride activation. A trio of residues (Ser 303, His 337, Glu 19) having a striking spatial resemblance with serine-protease like catalytic triads was found approximately 22 angstroms from the active site. We found that this triad is equally present in other chloride dependent alpha-amylases, and suggest that it could be responsible for autoproteolytic events observed in solution for this cold adapted alpha-amylase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19763902 O.Prakash, and N.Jaiswal (2010).
alpha-Amylase: an ideal representative of thermostable enzymes.
  Appl Biochem Biotechnol, 160, 2401-2414.  
19329633 L.J.Gourlay, I.Santi, A.Pezzicoli, G.Grandi, M.Soriani, and M.Bolognesi (2009).
Group B streptococcus pullulanase crystal structures in the context of a novel strategy for vaccine development.
  J Bacteriol, 191, 3544-3552.
PDB codes: 3faw 3fax
18494783 A.Godány, B.Vidová, and S.Janecek (2008).
The unique glycoside hydrolase family 77 amylomaltase from Borrelia burgdorferi with only catalytic triad conserved.
  FEMS Microbiol Lett, 284, 84-91.  
17729287 J.C.Marx, J.Poncin, J.P.Simorre, P.W.Ramteke, and G.Feller (2008).
The noncatalytic triad of alpha-amylases: a novel structural motif involved in conformational stability.
  Proteins, 70, 320-328.  
17937401 O.Almog, A.Kogan, M.Leeuw, G.Y.Gdalevsky, R.Cohen-Luria, and A.H.Parola (2008).
Structural insights into cold inactivation of tryptophanase and cold adaptation of subtilisin S41.
  Biopolymers, 89, 354-359.  
18759222 W.C.Too, Y.C.Liew, and L.L.Few (2008).
Cloning of glyceraldehyde-3-phosphate dehydrogenase from an Antarctic psychrophilic bacterium by inverse and splinkerette PCR.
  J Basic Microbiol, 48, 430-435.  
17697122 D.Tronelli, E.Maugini, F.Bossa, and S.Pascarella (2007).
Structural adaptation to low temperatures--analysis of the subunit interface of oligomeric psychrophilic enzymes.
  FEBS J, 274, 4595-4608.  
16630257 A.M.Cusano, E.Parrilli, A.Duilio, G.Sannia, G.Marino, and M.L.Tutino (2006).
Secretion of psychrophilic alpha-amylase deletion mutants in Pseudoalteromonas haloplanktis TAC125.
  FEMS Microbiol Lett, 258, 67-71.  
17169153 A.M.Cusano, E.Parrilli, G.Marino, and M.L.Tutino (2006).
A novel genetic system for recombinant protein secretion in the Antarctic Pseudoalteromonas haloplanktis TAC125.
  Microb Cell Fact, 5, 40.  
16705665 K.S.Siddiqui, A.Poljak, M.Guilhaus, D.De Francisci, P.M.Curmi, G.Feller, S.D'Amico, C.Gerday, V.N.Uversky, and R.Cavicchioli (2006).
Role of lysine versus arginine in enzyme cold-adaptation: modifying lysine to homo-arginine stabilizes the cold-adapted alpha-amylase from Pseudoalteramonas haloplanktis.
  Proteins, 64, 486-501.  
16756497 K.S.Siddiqui, and R.Cavicchioli (2006).
Cold-adapted enzymes.
  Annu Rev Biochem, 75, 403-433.  
16294337 O.A.Adekoya, R.Helland, N.P.Willassen, and I.Sylte (2006).
Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family.
  Proteins, 62, 435-449.  
16416448 P.B.Pelegrini, A.M.Murad, M.F.Grossi-de-Sá, L.V.Mello, L.A.Romeiro, E.F.Noronha, R.A.Caldas, and O.L.Franco (2006).
Structure and enzyme properties of Zabrotes subfasciatus alpha-amylase.
  Arch Insect Biochem Physiol, 61, 77-86.  
  16511027 D.Dong, T.Ihara, H.Motoshima, and K.Watanabe (2005).
Crystallization and preliminary X-ray crystallographic studies of a psychrophilic subtilisin-like protease Apa1 from Antarctic Pseudoalteromonas sp. strain AS-11.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 308-311.  
16109962 K.S.Siddiqui, A.Poljak, M.Guilhaus, G.Feller, S.D'Amico, C.Gerday, and R.Cavicchioli (2005).
Role of disulfide bridges in the activity and stability of a cold-active alpha-amylase.
  J Bacteriol, 187, 6206-6212.  
16109961 K.S.Siddiqui, G.Feller, S.D'Amico, C.Gerday, L.Giaquinto, and R.Cavicchioli (2005).
The active site is the least stable structure in the unfolding pathway of a multidomain cold-adapted alpha-amylase.
  J Bacteriol, 187, 6197-6205.  
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
  16233714 A.Hoyoux, V.Blaise, T.Collins, S.D'Amico, E.Gratia, A.L.Huston, J.C.Marx, G.Sonan, Y.Zeng, G.Feller, and C.Gerday (2004).
Extreme catalysts from low-temperature environments.
  J Biosci Bioeng, 98, 317-330.  
14975528 D.Georlette, V.Blaise, T.Collins, S.D'Amico, E.Gratia, A.Hoyoux, J.C.Marx, G.Sonan, G.Feller, and C.Gerday (2004).
Some like it cold: biocatalysis at low temperatures.
  FEMS Microbiol Rev, 28, 25-42.  
15356864 G.André, and V.Tran (2004).
Putative implication of alpha-amylase loop 7 in the mechanism of substrate binding and reaction products release.
  Biopolymers, 75, 95.  
15182367 N.Ramasubbu, C.Ragunath, P.J.Mishra, L.M.Thomas, G.Gyémánt, and L.Kandra (2004).
Human salivary alpha-amylase Trp58 situated at subsite -2 is critical for enzyme activity.
  Eur J Biochem, 271, 2517-2529.
PDB codes: 1jxj 1nm9
12876336 I.Leiros, E.Moe, O.Lanes, A.O.Smalås, and N.P.Willassen (2003).
The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features.
  Acta Crystallogr D Biol Crystallogr, 59, 1357-1365.
PDB code: 1okb
12577270 N.Aghajari, F.Van Petegem, V.Villeret, J.P.Chessa, C.Gerday, R.Haser, and J.Van Beeumen (2003).
Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases.
  Proteins, 50, 636-647.
PDB codes: 1g9k 1h71
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.  
12423352 J.Arnórsdottir, R.B.Smáradóttir, O.T.Magnússon, S.H.Thorbjarnardóttir, G.Eggertsson, and M.M.Kristjánsson (2002).
Characterization of a cloned subtilisin-like serine proteinase from a psychrotrophic Vibrio species.
  Eur J Biochem, 269, 5536-5546.  
11985615 K.Mavromatis, I.Tsigos, M.Tzanodaskalaki, M.Kokkinidis, and V.Bouriotis (2002).
Exploring the role of a glycine cluster in cold adaptation of an alkaline phosphatase.
  Eur J Biochem, 269, 2330-2335.  
12021442 N.Aghajari, G.Feller, C.Gerday, and R.Haser (2002).
Structural basis of alpha-amylase activation by chloride.
  Protein Sci, 11, 1435-1441.
PDB codes: 1jd7 1jd9 1l0p
12171655 S.D'Amico, P.Claverie, T.Collins, D.Georlette, E.Gratia, A.Hoyoux, M.A.Meuwis, G.Feller, and C.Gerday (2002).
Molecular basis of cold adaptation.
  Philos Trans R Soc Lond B Biol Sci, 357, 917-925.  
11589698 I.Tsigos, K.Mavromatis, M.Tzanodaskalaki, C.Pozidis, M.Kokkinidis, and V.Bouriotis (2001).
Engineering the properties of a cold active enzyme through rational redesign of the active site.
  Eur J Biochem, 268, 5074-5080.  
11160110 T.Lonhienne, K.Mavromatis, C.E.Vorgias, L.Buchon, C.Gerday, and V.Bouriotis (2001).
Cloning, sequences, and characterization of two chitinase genes from the Antarctic Arthrobacter sp. strain TAD20: isolation and partial characterization of the enzymes.
  J Bacteriol, 183, 1773-1779.  
10924103 A.M.Brzozowski, D.M.Lawson, J.P.Turkenburg, H.Bisgaard-Frantzen, A.Svendsen, T.V.Borchert, Z.Dauter, K.S.Wilson, and G.J.Davies (2000).
Structural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes.
  Biochemistry, 39, 9099-9107.
PDB codes: 1e3x 1e3z 1e40 1e43
10672012 H.K.Leiros, N.P.Willassen, and A.O.Smalås (2000).
Structural comparison of psychrophilic and mesophilic trypsins. Elucidating the molecular basis of cold-adaptation.
  Eur J Biochem, 267, 1039-1049.  
10672010 K.W.Rodenburg, F.Vallée, N.Juge, N.Aghajari, X.Guo, R.Haser, and B.Svensson (2000).
Specific inhibition of barley alpha-amylase 2 by barley alpha-amylase/subtilisin inhibitor depends on charge interactions and can be conferred to isozyme 1 by mutation.
  Eur J Biochem, 267, 1019-1029.  
  11064190 Y.Okubo, K.Yokoigawa, N.Esaki, K.Soda, and H.Misono (2000).
High catalytic activity of alanine racemase from psychrophilic Bacillus psychrosaccharolyticus at high temperatures in the presence of pyridoxal 5'-phosphate.
  FEMS Microbiol Lett, 192, 169-173.  
10491128 J.E.Nielsen, L.Beier, D.Otzen, T.V.Borchert, H.B.Frantzen, K.V.Andersen, and A.Svendsen (1999).
Electrostatics in the active site of an alpha-amylase.
  Eur J Biochem, 264, 816-824.  
10103004 M.M.Kristjánsson, O.T.Magnússon, H.M.Gudmundsson, G.A.Alfredsson, and H.Matsuzawa (1999).
Properties of a subtilisin-like proteinase from a psychrotrophic Vibrio species comparison with proteinase K and aqualysin I.
  Eur J Biochem, 260, 752-760.  
9755156 G.Parsiegla, M.Juy, C.Reverbel-Leroy, C.Tardif, J.P.Belaïch, H.Driguez, and R.Haser (1998).
The crystal structure of the processive endocellulase CelF of Clostridium cellulolyticum in complex with a thiooligosaccharide inhibitor at 2.0 A resolution.
  EMBO J, 17, 5551-5562.
PDB code: 1fce
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.