DB code: D00861

RLCP classification 1.30.35885.972 : Hydrolysis
CATH domain 3.20.20.80 : TIM Barrel Catalytic domain
2.60.120.- : Jelly Rolls
E.C. 3.2.1.78
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.20.20.80 : TIM Barrel S00202 S00210 S00748 S00906 S00907 S00911 S00912 S00915 M00134 M00160 D00479 S00204 S00205 S00206 S00207 S00203 S00208 S00209 S00211 S00213 S00214 M00113 T00307 D00165 D00166 D00169 D00176 D00501 D00502 D00503 D00844 D00864 M00026 M00112 M00193 M00346 T00057 T00062 T00063 T00066 T00067

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam
Q4W8M3
Mannanase
CBM59 (Carbohydrate-Binding Module Family 59)
GH5 (Glycoside Hydrolase Family 5)
PF00150 (Cellulase)
[Graphical View]
Q5YEX6
Beta-mannanase
EC 3.2.1.78
CBM59 (Carbohydrate-Binding Module Family 59)
GH5 (Glycoside Hydrolase Family 5)
PF00150 (Cellulase)
[Graphical View]

KEGG enzyme name
Mannan endo-1,4-beta-mannosidase
Endo-1,4-beta-mannanase
Endo-beta-1,4-mannase
Beta-mannanase B
Beta-1, 4-mannan 4-mannanohydrolase
Endo-beta-mannanase
Beta-D-mannanase
1,4-beta-D-mannan mannanohydrolase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q5YEX6 Q5YEX6_9BACI
Q4W8M3 Q4W8M3_9BACI

KEGG Pathways
Map code Pathways E.C.
MAP00051 Fructose and mannose metabolism

Compound table
Substrates Products Intermediates
KEGG-id C02492 C00883 C01810 C00001 C02492 C00883 C01810 I00118
E.C.
Compound 1,4-beta-D-Mannan Galactomannan Glucomannan H2O 1,4-beta-D-Mannan Galactomannan Glucomannan Peptidyl-Glu-D-mannan
Type polysaccharide polysaccharide polysaccharide H2O polysaccharide polysaccharide polysaccharide
ChEBI 27680
15377
27680
PubChem 439336
24892726
22247451
962
439336
24892726
1wkyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2whjA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2whlA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:MAN-BMA-BMA Unbound Unbound Unbound
1wkyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [2]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1wkyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 83;ASN 157;GLU 158;HIS 223;TYR 225;GLU 253
2whjA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 52;ASN 126;GLU 127;HIS 192;TYR 194;GLU 222
2whlA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 52;ASN 126;GLU 127;HIS 192;TYR 194;GLU 222
1wkyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
p.1439-1440
[4]
p.9-10
[8]
Figure 1, p.1234, p.1238-1239
[11]
p.1502-1504

References
[1]
Resource
Comments
Medline ID
PubMed ID 7624375
Journal Proc Natl Acad Sci U S A
Year 1995
Volume 92
Pages 7090-4
Authors Henrissat B, Callebaut I, Fabrega S, Lehn P, Mornon JP, Davies G
Title Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS).
Medline ID
PubMed ID 9817845
Journal Structure
Year 1998
Volume 6
Pages 1433-44
Authors Hilge M, Gloor SM, Rypniewski W, Sauer O, Heightman TD, Zimmermann W, Winterhalter K, Piontek K
Title High-resolution native and complex structures of thermostable beta-mannanase from Thermomonospora fusca - substrate specificity in glycosyl hydrolase family 5.
Related PDB 1bqc 2man 3man
Related UniProtKB Q9ZF13
[3]
Resource
Comments
Medline ID
PubMed ID 9989594
Journal FEBS Lett
Year 1999
Volume 443
Pages 149-53
Authors Harjunpaa V, Helin J, Koivula A, Siika-aho M, Drakenberg T
Title A comparative study of two retaining enzymes of Trichoderma reesei: transglycosylation of oligosaccharides catalysed by the cellobiohydrolase I, Cel7A, and the beta-mannanase, Man5A.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) OF 28-371.
Medline ID
PubMed ID 10666621
Journal Acta Crystallogr D Biol Crystallogr
Year 2000
Volume 56
Pages 3-13
Authors Sabini E, Schubert H, Murshudov G, Wilson KS, Siika-Aho M, Penttila M
Title The three-dimensional structure of a Trichoderma reesei beta-mannanase from glycoside hydrolase family 5.
Related PDB 1qno 1qnp 1qnq 1qnr 1qns
Related UniProtKB Q99036
[5]
Resource
Comments NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
Medline ID
PubMed ID
Journal Plant Sci
Year 2002
Volume 163
Pages 599-606
Authors Carrington CMS, Vendrell M, Domi'nguez-Puigjaner E
Title Characterisation of an endo-(1,4)-beta-mannanase (LeMAN4) expressed in ripening tomato fruit
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS).
Medline ID
PubMed ID 15272186
Journal Acta Crystallogr D Biol Crystallogr
Year 2004
Volume 60
Pages 1490-2
Authors Akita M, Takeda N, Hirasawa K, Sakai H, Kawamoto M, Yamamoto M, Grant WD, Hatada Y, Ito S, Horikoshi K
Title Crystallization and preliminary X-ray study of alkaline mannanase from an alkaliphilic Bacillus isolate.
Related PDB 1wky
Related UniProtKB Q4W8M3
[7]
Resource
Comments
Medline ID
PubMed ID 15642336
Journal FEBS Lett
Year 2005
Volume 579
Pages 302-12
Authors Nerinckx W, Desmet T, Piens K, Claeyssens M
Title An elaboration on the syn-anti proton donor concept of glycoside hydrolases: electrostatic stabilisation of the transition state as a general strategy.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 27-399.
Medline ID
PubMed ID 15840830
Journal Protein Sci
Year 2005
Volume 14
Pages 1233-41
Authors Bourgault R, Oakley AJ, Bewley JD, Wilce MC
Title Three-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit.
Related PDB 1rh9
Related UniProtKB Q8L5J1
[9]
Resource
Comments
Medline ID
PubMed ID 16823793
Journal Angew Chem Int Ed Engl
Year 2006
Volume 45
Pages 5136-40
Authors Money VA, Smith NL, Scaffidi A, Stick RV, Gilbert HJ, Davies GJ
Title Substrate distortion by a lichenase highlights the different conformational itineraries harnessed by related glycoside hydrolases.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 17069777
Journal Carbohydr Res
Year 2006
Volume 341
Pages 2912-20
Authors Ionescu AR, Whitfield DM, Zgierski MZ, Nukada T
Title Investigations into the role of oxacarbenium ions in glycosylation reactions by ab initio molecular dynamics.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
Medline ID
PubMed ID 16487541
Journal J Mol Biol
Year 2006
Volume 357
Pages 1500-10
Authors Larsson AM, Anderson L, Xu B, Munoz IG, Uson I, Janson JC, Stalbrand H, Stahlberg J
Title Three-dimensional crystal structure and enzymic characterization of beta-mannanase Man5A from blue mussel Mytilus edulis.
Related PDB 2c0h
Related UniProtKB Q8WPJ2
[12]
Resource
Comments
Medline ID
PubMed ID 18558099
Journal Curr Opin Chem Biol
Year 2008
Volume 12
Pages 539-55
Authors Vocadlo DJ, Davies GJ
Title Mechanistic insights into glycosidase chemistry.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 18579426
Journal Comp Biochem Physiol B Biochem Mol Biol
Year 2008
Volume 151
Pages 32-40
Authors Song JM, Nam KW, Kang SG, Kim CG, Kwon ST, Lee YH
Title Molecular cloning and characterization of a novel cold-active beta-1,4-D-mannanase from the Antarctic springtail, Cryptopygus antarcticus.
Related PDB
Related UniProtKB
[14]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS).
Medline ID
PubMed ID 19441796
Journal Biochemistry
Year 2009
Volume 48
Pages 7009-18
Authors Tailford LE, Ducros VM, Flint JE, Roberts SM, Morland C, Zechel DL, Smith N, Bjornvad ME, Borchert TV, Wilson KS, Davies GJ, Gilbert HJ
Title Understanding how diverse beta-mannanases recognize heterogeneous substrates.
Related PDB 2whj 2whl
Related UniProtKB Q5YEX6

Comments
This enzyme belongs to the glycosidase family-5.
This enzyme is composed of N-terminal catalytic domain and C-terminal carbohydrate binding module.
According to the literature [11] and [13], beta-mannanase belonging to the glycosidase family-5 can be divided into three subfamilies. This enzyme and a counterpart enzyme (S00906 in EzCatDB), which are from bacteria, belong to subfamily-8. On the other hand, an enzyme group from plant and fungi (eukaryote) (S00210 in EzCatDB) belongs to subfamily-7, whereas another enzyme group from mollusc (eukaryote) (S00907 in EzCatDB) belongs to subfamily-10. However, the catalytic site seems to be conserved among these three subfamilies and other related enzymes in family-5.
Thus, the reaction proceeds as follows (see [8] and [11]):
(0) His223 (of 1wky) may modulate the activity of acid/base, Glu158, whereas Tyr225 may modulate the activity of nucleophile, Glu253. Moreover, Arg83 may modulate the nucleophile, Glu253, as well.
(1) Glu158 acts as a general acid to protonate the leaving oxygen in mannan, whereas Glu253 approaches the C1 atom of substrate mannan as a nucleophile. This process leads to an oxocarbenium-like transition-state (half-chair conformation; 4H3). The transition-state is stabilized by Asn157 (and probably Tyr225).
(2) Glu253 makes a nucleophilic attack on the C1 atom of mannosyl group, to form a covalent intermediate, whereas the leaving group is cleaved from mannosyl group at subsite -1.
(3) Glu158 acts as a general base to deprotonate a water molecule, to activate it.
(4) The activated water makes a nucleophilic attack on the C1 atom of the covalent intermediate. Finally, the reaction completes.

Created Updated
2010-05-20 2012-02-14