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PDBsum entry 1b0i

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protein metals links
Hydrolase PDB id
1b0i
Jmol
Contents
Protein chain
448 a.a. *
Metals
_CL
_CA
Waters ×303
* Residue conservation analysis
PDB id:
1b0i
Name: Hydrolase
Title: Alpha-amylase from alteromonas haloplanctis
Structure: Protein (alpha-amylase). Chain: a. Engineered: yes
Source: Pseudoalteromonas haloplanktis. Organism_taxid: 228. Strain: alteromonas haloplanctis a23. Gene: amy. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.40Å     R-factor:   0.180     R-free:   0.217
Authors: N.Aghajari,R.Haser
Key ref:
N.Aghajari et al. (1998). Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level. Structure, 6, 1503-1516. PubMed id: 9862804 DOI: 10.1016/S0969-2126(98)00149-X
Date:
10-Nov-98     Release date:   17-Nov-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  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  

 

 
DOI no: 10.1016/S0969-2126(98)00149-X Structure 6:1503-1516 (1998)
PubMed id: 9862804  
 
 
Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level.
N.Aghajari, G.Feller, C.Gerday, R.Haser.
 
  ABSTRACT  
 
Background:. Enzymes from psychrophilic (cold-adapted) microorganisms operate at temperatures close to 0 degreesC, where the activity of their mesophilic and thermophilic counterparts is drastically reduced. It has generally been assumed that thermophily is associated with rigid proteins, whereas psychrophilic enzymes have a tendency to be more flexible. Results:. Insights into the cold adaptation of proteins are gained on the basis of a psychrophilic protein's molecular structure. To this end, we have determined the structure of the recombinant form of a psychrophilic alpha-amylase from Alteromonas haloplanctis at 2.4 A resolution. We have compared this with the structure of the wild-type enzyme, recently solved at 2.0 A resolution, and with available structures of their mesophilic counterparts. These comparative studies have enabled us to identify possible determinants of cold adaptation. Conclusions:. We propose that an increased resilience of the molecular surface and a less rigid protein core, with less interdomain interactions, are determining factors of the conformational flexibility that allows efficient enzyme catalysis in cold environments.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. A representation of charges at the surfaces of (a) AHA, (b) HPA and (c) BLA, displayed at the same potential range. Color codes are: red, aspartic and glutamic acids; blue, lysines and arginines. This figure was generated with the program GRASP [57].
 
  The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 1503-1516) copyright 1998.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20855205 S.Ben Mabrouk, N.Aghajari, M.Ben Ali, E.Ben Messaoud, M.Juy, R.Haser, and S.Bejar (2011).
Enhancement of the thermostability of the maltogenic amylase MAUS149 by Gly312Ala and Lys436Arg substitutions.
  Bioresour Technol, 102, 1740-1746.  
19966417 E.Champion, M.Remaud-Simeon, L.K.Skov, J.S.Kastrup, M.Gajhede, and O.Mirza (2009).
The apo structure of sucrose hydrolase from Xanthomonas campestris pv. campestris shows an open active-site groove.
  Acta Crystallogr D Biol Crystallogr, 65, 1309-1314.
PDB code: 2wpg
  19193992 H.L.Pedersen, N.P.Willassen, and I.Leiros (2009).
The first structure of a cold-adapted superoxide dismutase (SOD): biochemical and structural characterization of iron SOD from Aliivibrio salmonicida.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 84-92.
PDB code: 2w7w
19805185 T.P.Schrank, D.W.Bolen, and V.J.Hilser (2009).
Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins.
  Proc Natl Acad Sci U S A, 106, 16984-16989.
PDB codes: 3hpq 3hpr
18539590 C.Bauvois, L.Jacquamet, A.L.Huston, F.Borel, G.Feller, and J.L.Ferrer (2008).
Crystal structure of the cold-active aminopeptidase from Colwellia psychrerythraea, a close structural homologue of the human bifunctional leukotriene A4 hydrolase.
  J Biol Chem, 283, 23315-23325.
PDB code: 3cia
19011975 C.L.Goonasekara, and D.H.Heeley (2008).
Conformational properties of striated muscle tropomyosins from some salmonid fishes.
  J Muscle Res Cell Motil, 29, 135-143.  
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.  
17597061 S.Ravaud, X.Robert, H.Watzlawick, R.Haser, R.Mattes, and N.Aghajari (2007).
Trehalulose synthase native and carbohydrate complexed structures provide insights into sucrose isomerization.
  J Biol Chem, 282, 28126-28136.
PDB codes: 1zja 2pwd 2pwe 2pwf 2pwg 2pwh
17310272 S.Srimathi, G.Jayaraman, G.Feller, B.Danielsson, and P.R.Narayanan (2007).
Intrinsic halotolerance of the psychrophilic alpha-amylase from Pseudoalteromonas haloplanktis.
  Extremophiles, 11, 505-515.  
17235516 V.Spiwok, P.Lipovová, T.Skálová, J.Dusková, J.Dohnálek, J.Hasek, N.J.Russell, and B.Králová (2007).
Cold-active enzymes studied by comparative molecular dynamics simulation.
  J Mol Model, 13, 485-497.  
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.  
15670163 J.Arnórsdóttir, M.M.Kristjánsson, and R.Ficner (2005).
Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation.
  FEBS J, 272, 832-845.
PDB codes: 1s2n 1sh7
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.  
16133101 M.R.Smith, and J.C.Zahnley (2005).
Characteristics of the amylase of Arthrobacter psychrolactophilus.
  J Ind Microbiol Biotechnol, 32, 439-448.  
  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.  
14760745 A.Linden, and M.Wilmanns (2004).
Adaptation of class-13 alpha-amylases to diverse living conditions.
  Chembiochem, 5, 231-239.  
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.  
15100224 E.Bae, and G.N.Phillips (2004).
Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases.
  J Biol Chem, 279, 28202-28208.
PDB codes: 1p3j 1s3g
14981312 H.Tsuruta, J.Tamura, H.Yamagata, and Y.Aizono (2004).
Specification of amino acid residues essential for the catalytic reaction of cold-active protein-tyrosine phosphatase of a psychrophile, Shewanella sp.
  Biosci Biotechnol Biochem, 68, 440-443.  
14710189 M.Tehei, B.Franzetti, D.Madern, M.Ginzburg, B.Z.Ginzburg, M.T.Giudici-Orticoni, M.Bruschi, and G.Zaccai (2004).
Adaptation to extreme environments: macromolecular dynamics in bacteria compared in vivo by neutron scattering.
  EMBO Rep, 5, 66-70.  
12475991 F.Van Petegem, T.Collins, M.A.Meuwis, C.Gerday, G.Feller, and J.Van Beeumen (2003).
The structure of a cold-adapted family 8 xylanase at 1.3 A resolution. Structural adaptations to cold and investgation of the active site.
  J Biol Chem, 278, 7531-7539.
PDB codes: 1h12 1h13 1h14
15035024 G.Feller, and C.Gerday (2003).
Psychrophilic enzymes: hot topics in cold adaptation.
  Nat Rev Microbiol, 1, 200-208.  
12562783 H.Orikoshi, N.Baba, S.Nakayama, H.Kashu, K.Miyamoto, M.Yasuda, Y.Inamori, and H.Tsujibo (2003).
Molecular analysis of the gene encoding a novel cold-adapted chitinase (ChiB) from a marine bacterium, Alteromonas sp. strain O-7.
  J Bacteriol, 185, 1153-1160.  
12761390 J.Le Nours, C.Ryttersgaard, L.Lo Leggio, P.R.Østergaard, T.V.Borchert, L.L.Christensen, and S.Larsen (2003).
Structure of two fungal beta-1,4-galactanases: searching for the basis for temperature and pH optimum.
  Protein Sci, 12, 1195-1204.
PDB codes: 1hjq 1hjs 1hju
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
12511577 S.D'Amico, J.C.Marx, C.Gerday, and G.Feller (2003).
Activity-stability relationships in extremophilic enzymes.
  J Biol Chem, 278, 7891-7896.  
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
12084074 C.Alquati, L.De Gioia, G.Santarossa, L.Alberghina, P.Fantucci, and M.Lotti (2002).
The cold-active lipase of Pseudomonas fragi. Heterologous expression, biochemical characterization and molecular modeling.
  Eur J Biochem, 269, 3321-3328.  
11933070 G.Gianese, F.Bossa, and S.Pascarella (2002).
Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes.
  Proteins, 47, 236-249.  
12198303 H.Tsuruta, B.Mikami, C.Yamamoto, and Y.Aizono (2002).
Crystallization and preliminary X-ray studies of cold-active protein-tyrosine phosphatase of Shewanella sp.
  Acta Crystallogr D Biol Crystallogr, 58, 1465-1466.  
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.  
12364331 L.K.Skov, O.Mirza, D.Sprogøe, I.Dar, M.Remaud-Simeon, C.Albenne, P.Monsan, and M.Gajhede (2002).
Oligosaccharide and sucrose complexes of amylosucrase. Structural implications for the polymerase activity.
  J Biol Chem, 277, 47741-47747.
PDB codes: 1mvy 1mw0 1mw1 1mw2 1mw3
12270842 M.L.Tutino, E.Parrilli, L.Giaquinto, A.Duilio, G.Sannia, G.Feller, and G.Marino (2002).
Secretion of alpha-amylase from Pseudoalteromonas haloplanktis TAB23: two different pathways in different hosts.
  J Bacteriol, 184, 5814-5817.  
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
12324460 S.D'Amico, C.Gerday, and G.Feller (2002).
Dual effects of an extra disulfide bond on the activity and stability of a cold-adapted alpha-amylase.
  J Biol Chem, 277, 46110-46115.  
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.  
12036047 T.Murakawa, H.Yamagata, H.Tsuruta, and Y.Aizono (2002).
Cloning of cold-active alkaline phosphatase gene of a psychrophile, Shewanella sp., and expression of the recombinant enzyme.
  Biosci Biotechnol Biochem, 66, 754-761.  
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
10974127 A.T.Bull, A.C.Ward, and M.Goodfellow (2000).
Search and discovery strategies for biotechnology: the paradigm shift.
  Microbiol Mol Biol Rev, 64, 573-606.  
10675897 C.Gerday, M.Aittaleb, M.Bentahir, J.P.Chessa, P.Claverie, T.Collins, S.D'Amico, J.Dumont, G.Garsoux, D.Georlette, A.Hoyoux, T.Lonhienne, M.A.Meuwis, and G.Feller (2000).
Cold-adapted enzymes: from fundamentals to biotechnology.
  Trends Biotechnol, 18, 103-107.  
10848966 D.Georlette, Z.O.Jónsson, F.Van Petegem, J.Chessa, J.Van Beeumen, U.Hübscher, and C.Gerday (2000).
A DNA ligase from the psychrophile Pseudoalteromonas haloplanktis gives insights into the adaptation of proteins to low temperatures.
  Eur J Biochem, 267, 3502-3512.  
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.  
10672035 M.Rina, C.Pozidis, K.Mavromatis, M.Tzanodaskalaki, M.Kokkinidis, and V.Bouriotis (2000).
Alkaline phosphatase from the Antarctic strain TAB5. Properties and psychrophilic adaptations.
  Eur J Biochem, 267, 1230-1238.  
  10473410 A.Galkin, L.Kulakova, H.Ashida, Y.Sawa, and N.Esaki (1999).
Cold-adapted alanine dehydrogenases from two antarctic bacterial strains: gene cloning, protein characterization, and comparison with mesophilic and thermophilic counterparts.
  Appl Environ Microbiol, 65, 4014-4020.  
10591103 D.Maes, J.P.Zeelen, N.Thanki, N.Beaucamp, M.Alvarez, M.H.Thi, J.Backmann, J.A.Martial, L.Wyns, R.Jaenicke, and R.K.Wierenga (1999).
The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: a comparative thermostability structural analysis of ten different TIM structures.
  Proteins, 37, 441-453.
PDB code: 1b9b
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.