S00210
type: Enzyme
rlcp: p972
cath: TIM Barrel
ec: https://purl.uniprot.org/enzyme/3.2.1.78
uniprot: Q8L5J1
uniprot: Q99036
kegg enzyme: Mannan endo-1,4-beta-mannosidase
kegg enzyme: Endo-1,4-beta-mannanase
kegg enzyme: Endo-beta-1,4-mannase
kegg enzyme: Beta-mannanase B
kegg enzyme: Beta-1, 4-mannan 4-mannanohydrolase
kegg enzyme: Endo-beta-mannanase
kegg enzyme: Beta-D-mannanase
kegg enzyme: 1,4-beta-D-mannan mannanohydrolase
kegg pathway: Fructose and mannose metabolism
kegg substrate: 1,4-beta-D-Mannan
kegg substrate: Galactomannan
kegg substrate: Glucomannan
kegg substrate: H2O
kegg product: 1,4-beta-D-Mannan
kegg product: Galactomannan
kegg product: Glucomannan
kegg intermediate: Peptidyl-Glu-D-mannan
pdb: 1rh9A00
pdb: 1qnoA00
pdb: 1qnpA00
pdb: 1qnqA00
pdb: 1qnrA00
pdb: 1qnsA00
pdb bound state: Unbound
  compound: 1,4-beta-D-Mannan
  pdb: 1rh9A00
pdb bound state: Unbound
  compound: 1,4-beta-D-Mannan
  pdb: 1qnoA00
pdb bound state: Unbound
  compound: 1,4-beta-D-Mannan
  pdb: 1qnpA00
pdb bound state: Unbound
  compound: 1,4-beta-D-Mannan
  pdb: 1qnqA00
pdb bound state: Unbound
  compound: 1,4-beta-D-Mannan
  pdb: 1qnrA00
pdb bound state: Unbound
  compound: 1,4-beta-D-Mannan
  pdb: 1qnsA00
pdb bound state: Unbound
  compound: Galactomannan
  pdb: 1rh9A00
pdb bound state: Unbound
  compound: Galactomannan
  pdb: 1qnoA00
pdb bound state: Unbound
  compound: Galactomannan
  pdb: 1qnpA00
pdb bound state: Unbound
  compound: Galactomannan
  pdb: 1qnqA00
pdb bound state: Unbound
  compound: Galactomannan
  pdb: 1qnrA00
pdb bound state: Unbound
  compound: Galactomannan
  pdb: 1qnsA00
pdb bound state: Unbound
  compound: Glucomannan
  pdb: 1rh9A00
pdb bound state: Unbound
  compound: Glucomannan
  pdb: 1qnoA00
pdb bound state: Unbound
  compound: Glucomannan
  pdb: 1qnpA00
pdb bound state: Unbound
  compound: Glucomannan
  pdb: 1qnqA00
pdb bound state: Unbound
  compound: Glucomannan
  pdb: 1qnrA00
pdb bound state: Unbound
  compound: Glucomannan
  pdb: 1qnsA00
pdb bound state: Unbound
  compound: 1,4-beta-D-Mannan
  pdb: 1rh9A00
pdb bound state: Unbound
  compound: 1,4-beta-D-Mannan
  pdb: 1qnoA00
pdb bound state: Unbound
  compound: 1,4-beta-D-Mannan
  pdb: 1qnpA00
pdb bound state: Unbound
  compound: 1,4-beta-D-Mannan
  pdb: 1qnqA00
pdb bound state: Unbound
  compound: 1,4-beta-D-Mannan
  pdb: 1qnsA00
pdb bound state: Unbound
  compound: Galactomannan
  pdb: 1rh9A00
pdb bound state: Unbound
  compound: Galactomannan
  pdb: 1qnoA00
pdb bound state: Unbound
  compound: Galactomannan
  pdb: 1qnpA00
pdb bound state: Unbound
  compound: Galactomannan
  pdb: 1qnqA00
pdb bound state: Unbound
  compound: Galactomannan
  pdb: 1qnrA00
pdb bound state: Unbound
  compound: Galactomannan
  pdb: 1qnsA00
pdb bound state: Unbound
  compound: Glucomannan
  pdb: 1rh9A00
pdb bound state: Unbound
  compound: Glucomannan
  pdb: 1qnoA00
pdb bound state: Unbound
  compound: Glucomannan
  pdb: 1qnpA00
pdb bound state: Unbound
  compound: Glucomannan
  pdb: 1qnqA00
active site residues resources: Characterisation of an endo-(1,4)-beta-mannanase (LeMAN4) expressed in ripening tomato fruit
active site residues resources: Substrate distortion by a lichenase highlights the different conformational itineraries harnessed by related glycoside hydrolases.
active site residues resources: Q8L5J1
references: Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases.
references: High-resolution native and complex structures of thermostable beta-mannanase from Thermomonospora fusca - substrate specificity in glycosyl hydrolase family 5.
references: A comparative study of two retaining enzymes of Trichoderma reesei: transglycosylation of oligosaccharides catalysed by the cellobiohydrolase I, Cel7A, and the beta-mannanase, Man5A.
references: The three-dimensional structure of a Trichoderma reesei beta-mannanase from glycoside hydrolase family 5.
references: Characterisation of an endo-(1,4)-beta-mannanase (LeMAN4) expressed in ripening tomato fruit
references: Crystallization and preliminary X-ray study of alkaline mannanase from an alkaliphilic Bacillus isolate.
references: An elaboration on the syn-anti proton donor concept of glycoside hydrolases: electrostatic stabilisation of the transition state as a general strategy.
references: Three-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit.
references: Substrate distortion by a lichenase highlights the different conformational itineraries harnessed by related glycoside hydrolases.
references: Investigations into the role of oxacarbenium ions in glycosylation reactions by ab initio molecular dynamics.
references: Three-dimensional crystal structure and enzymic characterization of beta-mannanase Man5A from blue mussel Mytilus edulis.
references: Microbial mannanases: an overview of production and applications.
references: Mechanistic insights into glycosidase chemistry.
references: Understanding how diverse beta-mannanases recognize heterogeneous substrates.
comment: This enzyme belongs to the glycosidase family-5. According to the literature [11], beta-mannanase belonging to the glycosidase family-5 can be divided into three subfamilies. This enzyme, which is from eukaryote, belongs to subfamily-7. On the other hand, another enzyme group from eukaryote (S00907 in EzCatDB) belongs to subfamily-10, whereas an enzyme group from bacteria (S00906 and D00861 in EzCatDB) belongs to subfamily-8. However, the catalytic site seems to be conserved among these three subfamilies. Thus, according to the literature [8] and [11], the reaction proceeds as follows: (0) His277 (of 1rh9) may modulate the activity of acid/base, Glu04, whereas Tyr279 may modulate the activity of nucleophile, Glu318. Moreover, Arg86 may modulate the nucleophile, Glu318, as well. (1) Glu204 acts as a general acid to protonate the leaving oxygen in mannan, whereas Glu318 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 Asn203 (and probably Tyr279). (2) Glu318 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) Glu204 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.

TIM Barrel
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.20.20.80
catalytic domain: index.html

Fructose and mannose metabolism
type: KeggPathway
references: KEGG:MAP00051

1,4-beta-D-Mannan
type: KeggSubstrate
references: KEGG:C02492
compound type: polysaccharide
type: KeggProduct

Galactomannan
type: KeggSubstrate
references: KEGG:C00883
compound type: polysaccharide
references: CHEBI:27680
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi
type: KeggProduct

Glucomannan
type: KeggSubstrate
references: KEGG:C01810
compound type: polysaccharide
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi
type: KeggProduct

H2O
type: KeggSubstrate
references: KEGG:C00001
compound type: H2O
references: CHEBI:15377
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Peptidyl-Glu-D-mannan
type: KeggIntermediate
references: KEGG:I00118

1rh9A00
type: Pdb
references: 1rh9
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1rh9
catalytic residue: ARG 86;ASN 203;GLU 204;HIS 277;TYR 279;GLU 318

1qnoA00
type: Pdb
references: 1qno
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1qno
catalytic residue: ARG 54;ASN 168;GLU 169;HIS 241;TYR 243;GLU 276

1qnpA00
type: Pdb
references: 1qnp
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1qnp
catalytic residue: ARG 54;ASN 168;GLU 169;HIS 241;TYR 243;GLU 276

1qnqA00
type: Pdb
references: 1qnq
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1qnq
catalytic residue: ARG 54;ASN 168;GLU 169;HIS 241;TYR 243;GLU 276

1qnrA00
type: Pdb
references: 1qnr
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1qnr
catalytic residue: ARG 54;ASN 168;GLU 169;HIS 241;TYR 243;GLU 276

1qnsA00
type: Pdb
references: 1qns
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1qns
catalytic residue: ARG 54;ASN 168;GLU 169;HIS 241;TYR 243;GLU 276

Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7624375
journal: Proc Natl Acad Sci U S A
volume: 92
pages: 7090-4
published year: 1995
authors:
  item: Henrissat B
  item: Callebaut I
  item: Fabrega S
  item: Lehn P
  item: Mornon JP
  item: Davies G

High-resolution native and complex structures of thermostable beta-mannanase from Thermomonospora fusca - substrate specificity in glycosyl hydrolase family 5.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/9817845
journal: Structure
volume: 6
pages: 1433-44
published year: 1998
authors:
  item: Hilge M
  item: Gloor SM
  item: Rypniewski W
  item: Sauer O
  item: Heightman TD
  item: Zimmermann W
  item: Winterhalter K
  item: Piontek K
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q9ZF13

A comparative study of two retaining enzymes of Trichoderma reesei: transglycosylation of oligosaccharides catalysed by the cellobiohydrolase I, Cel7A, and the beta-mannanase, Man5A.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9989594
journal: FEBS Lett
volume: 443
pages: 149-53
published year: 1999
authors:
  item: Harjunpaa V
  item: Helin J
  item: Koivula A
  item: Siika-aho M
  item: Drakenberg T

The three-dimensional structure of a Trichoderma reesei beta-mannanase from glycoside hydrolase family 5.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) OF 28-371.
references: http://www.ncbi.nlm.nih.gov/pubmed/10666621
journal: Acta Crystallogr D Biol Crystallogr
volume: 56
pages: 3-13
published year: 2000
authors:
  item: Sabini E
  item: Schubert H
  item: Murshudov G
  item: Wilson KS
  item: Siika-Aho M
  item: Penttila M
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q99036

Characterisation of an endo-(1,4)-beta-mannanase (LeMAN4) expressed in ripening tomato fruit
type: BibliographicResource
comment: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
journal: Plant Sci
volume: 163
pages: 599-606
published year: 2002
authors:
  item: Carrington CMS
  item: Vendrell M
  item: Domi'nguez-Puigjaner E

Crystallization and preliminary X-ray study of alkaline mannanase from an alkaliphilic Bacillus isolate.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/15272186
journal: Acta Crystallogr D Biol Crystallogr
volume: 60
pages: 1490-2
published year: 2004
authors:
  item: Akita M
  item: Takeda N
  item: Hirasawa K
  item: Sakai H
  item: Kawamoto M
  item: Yamamoto M
  item: Grant WD
  item: Hatada Y
  item: Ito S
  item: Horikoshi K
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q4W8M3

An elaboration on the syn-anti proton donor concept of glycoside hydrolases: electrostatic stabilisation of the transition state as a general strategy.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/15642336
journal: FEBS Lett
volume: 579
pages: 302-12
published year: 2005
authors:
  item: Nerinckx W
  item: Desmet T
  item: Piens K
  item: Claeyssens M

Three-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 27-399.
references: http://www.ncbi.nlm.nih.gov/pubmed/15840830
journal: Protein Sci
volume: 14
pages: 1233-41
published year: 2005
authors:
  item: Bourgault R
  item: Oakley AJ
  item: Bewley JD
  item: Wilce MC
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q8L5J1

Substrate distortion by a lichenase highlights the different conformational itineraries harnessed by related glycoside hydrolases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/16823793
journal: Angew Chem Int Ed Engl
volume: 45
pages: 5136-40
published year: 2006
authors:
  item: Money VA
  item: Smith NL
  item: Scaffidi A
  item: Stick RV
  item: Gilbert HJ
  item: Davies GJ

Investigations into the role of oxacarbenium ions in glycosylation reactions by ab initio molecular dynamics.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/17069777
journal: Carbohydr Res
volume: 341
pages: 2912-20
published year: 2006
authors:
  item: Ionescu AR
  item: Whitfield DM
  item: Zgierski MZ
  item: Nukada T

Three-dimensional crystal structure and enzymic characterization of beta-mannanase Man5A from blue mussel Mytilus edulis.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/16487541
journal: J Mol Biol
volume: 357
pages: 1500-10
published year: 2006
authors:
  item: Larsson AM
  item: Anderson L
  item: Xu B
  item: Munoz IG
  item: Uson I
  item: Janson JC
  item: Stalbrand H
  item: Stahlberg J
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q8WPJ2

Microbial mannanases: an overview of production and applications.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/18085462
journal: Crit Rev Biotechnol
volume: 27
pages: 197-216
published year: 2007
authors:
  item: Dhawan S
  item: Kaur J

Mechanistic insights into glycosidase chemistry.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/18558099
journal: Curr Opin Chem Biol
volume: 12
pages: 539-55
published year: 2008
authors:
  item: Vocadlo DJ
  item: Davies GJ

Understanding how diverse beta-mannanases recognize heterogeneous substrates.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/19441796
journal: Biochemistry
volume: 48
pages: 7009-18
published year: 2009
authors:
  item: Tailford LE
  item: Ducros VM
  item: Flint JE
  item: Roberts SM
  item: Morland C
  item: Zechel DL
  item: Smith N
  item: Bjornvad ME
  item: Borchert TV
  item: Wilson KS
  item: Davies GJ
  item: Gilbert HJ
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q5YEX6

ReferenceForCatalyticMechanism
reference index: 2
reference section: p.1439-1440

ReferenceForCatalyticMechanism
reference index: 4
reference section: p.9-10

ReferenceForCatalyticMechanism
reference index: 8
reference section: Figure 1, p.1234, p.1238-1239

ReferenceForCatalyticMechanism
reference index: 11
reference section: p.1502-1504