PDBsum entry: 2man

Hydrolase

PDB-id

2man

Contents

Description

Header details

Protein chain

Ligands

BMA-MAN

Waters ×182

* Residue conservation analysis

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PDB id:

2man

Name:

Hydrolase

Title:

Mannotriose complex of thermomonospora fusca beta-mannanase

Structure:

Protein (beta-mannanase). Chain: a. Other_details: mannotriose complex

Source:

Thermobifida fusca. Organism_taxid: 2021. Strain: kw3. Other_details: german collection of microorganisms (dsm)

UniProt:

Q9ZF13 (Q9ZF13_THEFU)

Seq:

Struc:

Seq:

279 a.a.

Struc:

298 a.a.*

Key:		PfamA domain
		Secondary structure			CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme class:

E.C.3.2.1.78 [IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Random hydrolysis of 1,4-beta-D-mannosidic linkages in mannans, galactomannans, glucomannans, and galactoglucomannans.

Resolution:

1.90Å

R-factor:

0.178

R-free:

0.217

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

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CATH

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Clefts

Surface

Key reference

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

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.

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

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.

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.