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PDBsum entry 1bqc

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protein links
Hydrolase PDB id
1bqc
Jmol
Contents
Protein chain
302 a.a. *
Waters ×434
* Residue conservation analysis
PDB id:
1bqc
Name: Hydrolase
Title: Beta-mannanase from thermomonospora fusca
Structure: Protein (beta-mannanase). Chain: a. Ec: 3.2.1.78
Source: Thermobifida fusca. Organism_taxid: 2021. Strain: kw3. Other_details: german collection of microorganisms (dsm)
Resolution:
1.50Å     R-factor:   0.119     R-free:   0.176
Authors: M.Hilge,S.M.Gloor,K.Piontek
Key ref:
M.Hilge et al. (1998). High-resolution native and complex structures of thermostable beta-mannanase from Thermomonospora fusca - substrate specificity in glycosyl hydrolase family 5. Structure, 6, 1433-1444. PubMed id: 9817845 DOI: 10.1016/S0969-2126(98)00142-7
Date:
12-Aug-98     Release date:   13-Aug-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9ZF13  (Q9ZF13_THEFU) -  Beta-mannanase (Fragment)
Seq:
Struc:
279 a.a.
302 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.78  - Mannan endo-1,4-beta-mannosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Random hydrolysis of 1,4-beta-D-mannosidic linkages in mannans, galactomannans, glucomannans, and galactoglucomannans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1016/S0969-2126(98)00142-7 Structure 6:1433-1444 (1998)
PubMed id: 9817845  
 
 
High-resolution native and complex structures of thermostable beta-mannanase from Thermomonospora fusca - substrate specificity in glycosyl hydrolase family 5.
M.Hilge, S.M.Gloor, W.Rypniewski, O.Sauer, T.D.Heightman, W.Zimmermann, K.Winterhalter, K.Piontek.
 
  ABSTRACT  
 
Background:. beta-Mannanases hydrolyse the O-glycosidic bonds in mannan, a hemicellulose constituent of plants. These enzymes have potential use in pulp and paper production and are of significant biotechnological interest. Thermostable beta-mannanases would be particularly useful due to their high temperature optimum and broad pH tolerance. The thermophilic actinomycete Thermomonospora fusca secretes at least one beta-mannanase (molecular mass 38 kDa) with a temperature optimum of 80 degreesC. No three-dimensional structure of a mannan-degrading enzyme has been reported until now. Results:. The crystal structure of the thermostable beta-mannanase from T. fusca has been determined by the multiple isomorphous replacement method and refined to 1.5 A resolution. In addition to the native enzyme, the structures of the mannotriose- and mannohexaose-bound forms of the enzyme have been determined to resolutions of 1.9 A and 1.6 A, respectively. Conclusions:. Analysis of the -1 subsite of T. fusca mannanase reveals neither a favourable interaction towards the axial HO-C(2) nor a discrimination against the equatorial hydroxyl group of gluco-configurated substrates. We propose that selectivity arises from two possible mechanisms: a hydrophobic interaction of the substrate with Val263, conserved in family 5 bacterial mannanases, which discriminates between the different conformations of the hydroxymethyl group in native mannan and cellulose; and/or a specific interaction between Asp259 and the axial hydroxyl group at the C(2) of the substrate in the -2 subsite. Compared with the catalytic clefts of family 5 cellulases, the groove of T. fusca mannanase has a strongly reduced number of aromatic residues providing platforms for stacking with the substrate. This deletion of every second platform is in good agreement with the orientation of the axial hydroxyl groups in mannan.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The reaction catalysed by b-mannanase. (a) The nomenclature for sugar-binding subsites in glycosyl hydrolases [15]. (b) The retaining mechanism for T. fusca mannanase, in which the glycosidic oxygen is protonated by Glu128 (proton donor) and the anomeric carbon atom is attacked by Glu225 (nucleophile). The resulting mannosyl-mannanase intermediate is then hydrolysed by a water molecule, generating a product with the same anomeric configuration as the substrate [17].
 
  The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 1433-1444) copyright 1998.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20686915 P.Shi, T.Yuan, J.Zhao, H.Huang, H.Luo, K.Meng, Y.Wang, and B.Yao (2011).
Genetic and biochemical characterization of a protease-resistant mesophilic β-mannanase from Streptomyces sp. S27.
  J Ind Microbiol Biotechnol, 38, 451-458.  
20562312 Y.Han, D.Dodd, C.W.Hespen, S.Ohene-Adjei, C.M.Schroeder, R.I.Mackie, and I.K.Cann (2010).
Comparative analyses of two thermophilic enzymes exhibiting both beta-1,4 mannosidic and beta-1,4 glucosidic cleavage activities from Caldanaerobius polysaccharolyticus.
  J Bacteriol, 192, 4111-4121.  
19912637 B.C.Do, T.T.Dang, J.G.Berrin, D.Haltrich, K.A.To, J.C.Sigoillot, and M.Yamabhai (2009).
Cloning, expression in Pichia pastoris, and characterization of a thermostable GH5 mannan endo-1,4-beta-mannosidase from Aspergillus niger BK01.
  Microb Cell Fact, 8, 59.  
18832174 E.J.Dimise, P.F.Widboom, and S.D.Bruner (2008).
Structure elucidation and biosynthesis of fuscachelins, peptide siderophores from the moderate thermophile Thermobifida fusca.
  Proc Natl Acad Sci U S A, 105, 15311-15316.  
18310439 H.Ichinose, T.Kotake, Y.Tsumuraya, and S.Kaneko (2008).
Characterization of an endo-beta-1,6-Galactanase from Streptomyces avermitilis NBRC14893.
  Appl Environ Microbiol, 74, 2379-2383.  
  18323611 Y.Zhang, F.Gao, Y.Xue, Y.Zeng, H.Peng, J.Qi, and Y.Ma (2008).
Crystallization and preliminary X-ray study of native and selenomethionyl beta-1,4-mannanase AaManA from Alicyclobacillus acidocaldariusTc-12-31.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 209-212.  
18755688 Y.Zhang, J.Ju, H.Peng, F.Gao, C.Zhou, Y.Zeng, Y.Xue, Y.Li, B.Henrissat, G.F.Gao, and Y.Ma (2008).
Biochemical and Structural Characterization of the Intracellular Mannanase AaManA of Alicyclobacillus acidocaldarius Reveals a Novel Glycoside Hydrolase Family Belonging to Clan GH-A.
  J Biol Chem, 283, 31551-31558.
PDB code: 3civ
17209016 A.Lykidis, K.Mavromatis, N.Ivanova, I.Anderson, M.Land, G.DiBartolo, M.Martinez, A.Lapidus, S.Lucas, A.Copeland, P.Richardson, D.B.Wilson, and N.Kyrpides (2007).
Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX.
  J Bacteriol, 189, 2477-2486.  
17329247 M.E.Caines, M.D.Vaughan, C.A.Tarling, S.M.Hancock, R.A.Warren, S.G.Withers, and N.C.Strynadka (2007).
Structural and mechanistic analyses of endo-glycoceramidase II, a membrane-associated family 5 glycosidase in the Apo and GM3 ganglioside-bound forms.
  J Biol Chem, 282, 14300-14308.
PDB codes: 2osw 2osx 2osy
18085462 S.Dhawan, and J.Kaur (2007).
Microbial mannanases: an overview of production and applications.
  Crit Rev Biotechnol, 27, 197-216.  
17351093 T.Sakamoto, Y.Taniguchi, S.Suzuki, H.Ihara, and H.Kawasaki (2007).
Characterization of Fusarium oxysporum beta-1,6-galactanase, an enzyme that hydrolyzes larch wood arabinogalactan.
  Appl Environ Microbiol, 73, 3109-3112.  
16240096 E.Papaleo, P.Fantucci, M.Vai, and L.De Gioia (2006).
Three-dimensional structure of the catalytic domain of the yeast beta-(1,3)-glucan transferase Gas1: a molecular modeling investigation.
  J Mol Model, 12, 237-248.  
15014076 F.M.Dias, F.Vincent, G.Pell, J.A.Prates, M.S.Centeno, L.E.Tailford, L.M.Ferreira, C.M.Fontes, G.J.Davies, and H.J.Gilbert (2004).
Insights into the molecular determinants of substrate specificity in glycoside hydrolase family 5 revealed by the crystal structure and kinetics of Cellvibrio mixtus mannosidase 5A.
  J Biol Chem, 279, 25517-25526.
PDB code: 1uuq
15316858 Y.Ma, Y.Xue, Y.Dou, Z.Xu, W.Tao, and P.Zhou (2004).
Characterization and gene cloning of a novel beta-mannanase from alkaliphilic Bacillus sp. N16-5.
  Extremophiles, 8, 447-454.  
12676668 E.Béki, I.Nagy, J.Vanderleyden, S.Jäger, L.Kiss, L.Fülöp, L.Hornok, and J.Kukolya (2003).
Cloning and heterologous expression of a beta-D-mannosidase (EC 3.2.1.25)-encoding gene from Thermobifida fusca TM51.
  Appl Environ Microbiol, 69, 1944-1952.  
11856850 B.Xu, I.G.Muñoz I, J.C.Janson, and J.Ståhlberg (2002).
Crystallization and X-ray analysis of native and selenomethionyl beta-mannanase Man5A from blue mussel, Mytilus edulis, expressed in Pichia pastoris.
  Acta Crystallogr D Biol Crystallogr, 58, 542-545.  
11222610 J.C.Hurlbert, and J.F.Preston (2001).
Functional characterization of a novel xylanase from a corn strain of Erwinia chrysanthemi.
  J Bacteriol, 183, 2093-2100.  
11134925 M.Hilge, A.Perrakis, J.P.Abrahams, K.Winterhalter, K.Piontek, and S.M.Gloor (2001).
Structure elucidation of beta-mannanase: from the electron-density map to the DNA sequence.
  Acta Crystallogr D Biol Crystallogr, 57, 37-43.  
10653733 A.Sunna, M.D.Gibbs, C.W.Chin, P.J.Nelson, and P.L.Bergquist (2000).
A gene encoding a novel multidomain beta-1,4-mannanase from Caldibacillus cellulovorans and action of the recombinant enzyme on kraft pulp.
  Appl Environ Microbiol, 66, 664-670.  
10666621 E.Sabini, H.Schubert, G.Murshudov, K.S.Wilson, M.Siika-Aho, and M.Penttilä (2000).
The three-dimensional structure of a Trichoderma reesei beta-mannanase from glycoside hydrolase family 5.
  Acta Crystallogr D Biol Crystallogr, 56, 3.
PDB codes: 1qno 1qnp 1qnq 1qnr 1qns
11018131 T.Y.Wong, L.A.Preston, and N.L.Schiller (2000).
ALGINATE LYASE: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications.
  Annu Rev Microbiol, 54, 289-340.  
  10347049 D.Stoll, H.Stålbrand, and R.A.Warren (1999).
Mannan-degrading enzymes from Cellulomonas fimi.
  Appl Environ Microbiol, 65, 2598-2605.  
10508763 J.Jiménez-Barbero, J.L.Asensio, F.J.Cañada, and A.Poveda (1999).
Free and protein-bound carbohydrate structures.
  Curr Opin Struct Biol, 9, 549-555.  
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.