Journal of Computer-Aided Molecular Design

, Volume 28, Issue 6, pp 685–698 | Cite as

Structural and functional analysis of a novel psychrophilic β-mannanase from Glaciozyma antarctica PI12

  • Sepideh Parvizpour
  • Jafar Razmara
  • Aizi Nor Mazila Ramli
  • Rosli Md Illias
  • Mohd Shahir Shamsir


The structure of a novel psychrophilic β-mannanase enzyme from Glaciozyma antarctica PI12 yeast has been modelled and analysed in detail. To our knowledge, this is the first attempt to model a psychrophilic β-mannanase from yeast. To this end, a 3D structure of the enzyme was first predicted using a threading method because of the low sequence identity (<30 %) using MODELLER9v12 and simulated using GROMACS at varying low temperatures for structure refinement. Comparisons with mesophilic and thermophilic mannanases revealed that the psychrophilic mannanase contains longer loops and shorter helices, increases in the number of aromatic and hydrophobic residues, reductions in the number of hydrogen bonds and salt bridges and numerous amino acid substitutions on the surface that increased the flexibility and its efficiency for catalytic reactions at low temperatures.


Mannanase Psychrophiles Cold adaptation Structure prediction Flexibility 


  1. 1.
    Kokkinidis M, Glykos NM, Fadouloglou VE (2012) Protein flexibility and enzymatic catalysis. Adv Protein Chem Struct Biol 87:181–218CrossRefGoogle Scholar
  2. 2.
    Metpally RPR, Reddy BVB (2009) Comparative proteome analysis of psychrophilic versus mesophilic bacterial species: insights into the molecular basis of cold adaptation of proteins. BMC Genomics 10:11CrossRefGoogle Scholar
  3. 3.
    Liu Z, Qi W, He Z (2008) Optimization of beta-mannanase production from Bacillus licheniformis TJ-101 using response surface methodology. Chem Biochem Eng Q 22:355–362Google Scholar
  4. 4.
    Wang M, You S, Zhang S, Qi W, Liu Z, Wu W, Su R, He Z (2013) Purification, characterization, and production of β-mannanase from Bacillus subtilis TJ-102 and its application in gluco-mannooligosaccharides preparation. Eur Food Res Technol 237:399–408CrossRefGoogle Scholar
  5. 5.
    Haiqiang L, Huitu Z, Pengjun S, Huiying L (2013) A family 5 β-mannanase from the thermophilic fungus Thielavia arenaria XZ7 with typical thermophilic enzyme features. Appl Microb Biotechnol 97:8121–8128CrossRefGoogle Scholar
  6. 6.
    Chantorn ST, Buengsrisawat K, Pokaseam A, Sombat T, Dangpram P, Jantawon K, Nitisinprasert S (2013) Optimization of extracellular mannanase production from Penicillium oxalicum KUB-SN2-1 and application for hydrolysis property. J Sci Technol 35(1):17–22Google Scholar
  7. 7.
    Ourgault R, Bewley JD (2002) Variation in its C-terminal amino acids determines whether endo-beta-mannanase is active or inactive in ripening tomato fruits of different cultivars. Plant Physiol 130(3):1254–1262CrossRefGoogle Scholar
  8. 8.
    Xu B et al (2002) Endo-β-1,4-Mannanases from blue mussel, Mytilus edulis: purification, characterization, and mode of action. J Biotechnol 92(3):267–277CrossRefGoogle Scholar
  9. 9.
    Davies G, Henrissat B (1995) Structures and mechanisms of glycosyl hydrolases. Structure 3:853–859CrossRefGoogle Scholar
  10. 10.
    El-Naggar MY et al (2006) Extracellular β-Mannanase production by the immobilization of the locally isolated Aspergillus niger. Int J Agric Biol 8(1):57–62Google Scholar
  11. 11.
    Ehsani M, Torki M (2010) Effects of dietary inclusion of guar meal supplemented by β-Mannanase on performance of laying hens. Egg Qual Charact Diacritical Count White Blood Cells 5(4):237–243Google Scholar
  12. 12.
    Zhou H, Yang Y, Nie X, Yang W, Wu Y (2013) Comparison of expression systems for the extracellular production of mannanase Man23 originated from Bacillus subtilis B23. Microb Cell Fact 12:78CrossRefGoogle Scholar
  13. 13.
    Lee JT, Bailey CA, Cartwright AL (2003) Beta-Mannanase ameliorates viscosity-associated depression of growth in broiler chickens fed guar germ and hull fractions. Poult Sci 82(12):1925–1931CrossRefGoogle Scholar
  14. 14.
    Chandra M et al (2011) Isolation, purification and characterization of a thermostable β-Mannanase from Paenibacillus sp. DZ3. J Korean Soc Appl Biol Chem 54(3):325–331CrossRefGoogle Scholar
  15. 15.
    Tailford LE, Ducros VM-A, Flint JE, Roberts SM, Morland C, Zechel DL, Smith N, Bjørnvad ME, Borchert TV, Wilson KS, Davies GJ, Gilbert HJ (2009) Understanding how diverse beta-mannanases recognize heterogeneous substrates. Biochemistry 48:7009–7018CrossRefGoogle Scholar
  16. 16.
    Park SH, Park KH, Oh BC, Alli I, Lee BH (2011) Expression and characterization of an extremely thermostable B-glycosidase (mannosidase) from the hyperthermophillic archaeon Pyrococcus furiosus DSM 3638. N Biotechnol 28:639–648CrossRefGoogle Scholar
  17. 17.
    Goncalves AM, Silva C, Madeira T, Coelho R, Sanctis D, Romao MV, Bento I (2012) Endo-β-D-1,4-mannanase from Chrysonilia sitophila displays a novel loop arrangement for substrate selectivity. Acta Cryst D68:1468–1478Google Scholar
  18. 18.
    Zhao Y, Zhang Y, Cao Y, Qi J, Mao L, Xue Y, Gao F, Peng H, Wang X, Gao G, Ma Y (2011) Structural analysis of alkaline β-Mannanase from alkaliphilic Bacillus sp. N16-5: implications for adaptation to alkaline conditions. PLoS ONE 6(1):e14608CrossRefGoogle Scholar
  19. 19.
    Santos CR, Squina FM, Navarro AM, Ruller R, Prade R, Murakami MT (2010) Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of the catalytic domain of a hyperthermostable endo-1,4-β-D-mannanase from Thermotoga petrophila RKU-1. Acta Cryst F66:1078–1081Google Scholar
  20. 20.
    Akita M, Takeda N, Hirasawa K, Sakai H, Kawamoto M, Yamamoto M, Grant WD, Hatada Y, Ito S, Horikoshi K (2004) Crystallization and preliminary X-ray study of alkaline mannanase from an alkaliphilic Bacillus isolate. Acta Cryst D60:1490–1492Google Scholar
  21. 21.
    Sabini E, Schubert H, Murshudov G, Wilson KS, Siika-Aho M, Penttila M (2000) The three-dimensional structure of a Trichoderma reesei beta-mannanase from glycoside hydrolase family 5. Acta Cryst D56:3–13Google Scholar
  22. 22.
    Larsson AM, Anderson L, Xu B, Munoz IG, Uson I, Janson JC, Stalbrand H, Stahlberg J (2006) Three-dimensional crystal structure and enzymic characterization of β-mannanase Man5A from blue mussel Mytilus edulis. J Mol Biol 357:1500–1510CrossRefGoogle Scholar
  23. 23.
    Bourgault R et al (2005) Three-dimensional structure of (1,4)-β-D-mannan mannanohydrolase from tomato fruit. Protein Sci 14:1233–1241CrossRefGoogle Scholar
  24. 24.
    Zakaria MM, Yamamoto S, Yagi T (1998) Purification and characterization of an endo-1,4-β-mannanase from Bacillus subtilis KU-1. FEMS Microbiol Lett 158:25–31Google Scholar
  25. 25.
    Huang JW, Chen CC, Huang CH, Huang TY, Wu TH, Cheng YS, Ko TP, Lin CY, Liu JR, Guo RT (2014) Improving the specific activity of β-mannanase from Aspergillus niger BK01 by structure-based rational design. Biochimica et Biophysica Acta (BBA) Proteins and Proteomics 1844(3):663–669Google Scholar
  26. 26.
    Ramli ANM et al (2011) Molecular cloning, expression and biochemical characterisation of a cold-adapted novel recombinant chitinase from Glaciozyma antarctica PI12. Microb Cell Fact 10(1):94CrossRefGoogle Scholar
  27. 27.
    Altschul SF et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res 25(17):3389–3402CrossRefGoogle Scholar
  28. 28.
    Altschul SF et al (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410CrossRefGoogle Scholar
  29. 29.
    Gough J et al (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 313(4):903–919CrossRefGoogle Scholar
  30. 30.
    Fornes O et al (2009) ModLink+: improving fold recognition by using protein–protein interactions. Bioinformatics 25(12):1506–1512CrossRefGoogle Scholar
  31. 31.
    Söding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acid Res 33(2):W244–W248CrossRefGoogle Scholar
  32. 32.
    Jones DT (1999) An efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 287(4):797–815CrossRefGoogle Scholar
  33. 33.
    Kelley LA, Sternberg MJE (2009) Protein structure prediction on the web: a case study using the Phyre server. Nat Protoc 4(3):363–371CrossRefGoogle Scholar
  34. 34.
    Eswar N et al (2007) Comparative protein structure modeling using MODELLER. Curr Protoc Bioinformatics 2(1):1–30CrossRefGoogle Scholar
  35. 35.
    Zhang Y, Skolnick J (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acid Res 33(7):2302–2309CrossRefGoogle Scholar
  36. 36.
    Luthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356(6364):83–85CrossRefGoogle Scholar
  37. 37.
    Laskowski RA et al (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26(2):283–291CrossRefGoogle Scholar
  38. 38.
    Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2(9):1511–1519CrossRefGoogle Scholar
  39. 39.
    Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acid Res 35(2):W407–W410CrossRefGoogle Scholar
  40. 40.
    Hess B et al (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4(3):435–447CrossRefGoogle Scholar
  41. 41.
    Couturier M, Roussel A, Rosengren A, Leone P, Stalbrand H, Berrin JG (2013) Structural and biochemical analyses of glycoside hydrolase families 5 and 26 β-(1,4)-mannanases from Podospora anserina reveal differences upon manno-oligosaccharide catalysis. J Biol Chem 288:14624CrossRefGoogle Scholar
  42. 42.
    Costantini S, Colonna G, Facchiano AM (2008) ESBRI: a web server for evaluating salt bridges in proteins. Bioinformation 3(1):137–138CrossRefGoogle Scholar
  43. 43.
    Pettersen E et al (2004) UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612CrossRefGoogle Scholar
  44. 44.
    Chaitanya M et al (2010) Exploring the molecular basis for selective binding of Mycobacterium tuberculosis Asp kinase toward its natural substrates and feedback inhibitors: a docking and molecular dynamics study. J Mol Model 16(8):1357–1367CrossRefGoogle Scholar
  45. 45.
    Geralt M, Alimenti C, Vallesi A, Luporini P, Wuthrich K (2013) Thermodynamic stability of psychrophilic and mesophilic pheromones of the protozoan ciliate euplotes. Biology 2:142–150CrossRefGoogle Scholar
  46. 46.
    Alvarez M et al (1998) Triose phosphate isomerase (TIM) of the psychrophilic Bacterium Vibrio marinus. J Biol Chem 273:2199–2206CrossRefGoogle Scholar
  47. 47.
    Wallon G et al (1997) Sequence and homology model of 3-isopropylmalate dehydrogenase from the psychrotrophic bacterium Vibrio sp. I5 suggest reasons for thermal instability. Protein Eng 10(6):665–672CrossRefGoogle Scholar
  48. 48.
    Davail S et al (1994) Cold adaptation of proteins. Purification, characterization, and sequence of the heatlabile subtilisin from the antarctic psychrophile Bacillus TA41. J Biol Chem 269(26):17448–17453Google Scholar
  49. 49.
    Herning T et al (1992) Role of proline residues in human lysozyme stability: a scanning calorimetric study combined with X-ray structure analysis of proline mutants. Biochemistry 31(31):7077–7085CrossRefGoogle Scholar
  50. 50.
    Kumar S, Nussinov R (2004) Different roles of electrostatics in heat and in cold: adaptation by citrate synthase. Chem Biochem 5(3):280–290Google Scholar
  51. 51.
    Alimenti C et al (2009) Molecular cold-adaptation: comparative analysis of two homologous families of psychrophilic and mesophilic signal proteins of the protozoan ciliate, Euplotes. IUBMB Life 61(8):838–845CrossRefGoogle Scholar
  52. 52.
    Galkin A et al (1999) Coldadapted alanine dehydrogenases from two Antarctic bacterial strains: gene cloning, protein characterization, and comparison with mesophilic and thermophilic counterparts. Appl Environ Microbiol 65(9):4014–4020Google Scholar
  53. 53.
    Kim SY et al (1999) Structural basis for cold adaptation. J Biol Chem 274(17):11761–11767CrossRefGoogle Scholar
  54. 54.
    Zuber H (1988) Temperature adaptation of lactate dehydrogenase Structural, functional and genetic aspects. Biophys Chem 29(1–2):171–179CrossRefGoogle Scholar
  55. 55.
    Saunders N et al (2003) Mechanisms of thermal adaptation revealed from the genomes of the antarctic archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res 13(7):1241–1255CrossRefGoogle Scholar
  56. 56.
    Kundu S, Roy D (2009) Comparative structural studies of psychrophilic and mesophilic protein homologues by molecular dynamics simulation. J Mol Graph Model 27(8):871–880CrossRefGoogle Scholar
  57. 57.
    Kumar S, Nussinov R (1999) Salt bridge stability in monomeric proteins. J Mol Biol 293(5):1241–1255CrossRefGoogle Scholar
  58. 58.
    Ramli ANM, Mahadi NM, Shamsir MH (2012) Structural prediction of a novel chitinase from the psychrophilic G. antarctica PI12 and an analysis of its structural properties and function. J Comput Aided Mol Des 26:947–961CrossRefGoogle Scholar
  59. 59.
    Bae E, Phillips G (2004) Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases. 279(27):28202–28208Google Scholar
  60. 60.
    Tronelli D et al (2007) Structural adaptation to low temperatures—analysis of the subunit interface of oligomeric psychrophilic enzymes. FEBS J 274(17):4595–4608CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Sepideh Parvizpour
    • 1
  • Jafar Razmara
    • 2
  • Aizi Nor Mazila Ramli
    • 4
  • Rosli Md Illias
    • 3
  • Mohd Shahir Shamsir
    • 1
  1. 1.Bioinformatics Research Group, Faculty of Bioscience and Medical EngineeringUniversiti Teknologi MalaysiaJohor BahruMalaysia
  2. 2.Department of Computer Science, Faculty of Mathematical SciencesUniversity of TabrizTabrizIran
  3. 3.Department of Bioprocess Engineering, Faculty of Chemical EngineeringUniversiti Teknologi MalaysiaJohor BahruMalaysia
  4. 4.Faculty of Industrial Sciences & TechnologyUniversiti Malaysia PahangKuantan Malaysia

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