EzCatDB: S00911
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DB codeS00911
RLCP classification1.30.36027.984 : Hydrolysis
CATH domainDomain 13.20.20.80 : TIM BarrelCatalytic domain
E.C.3.2.1.78

CATH domainRelated DB codes (homologues)
3.20.20.80 : TIM BarrelS00202,S00210,S00748,S00906,S00907,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,D00861,D00864,M00026,M00112,M00193,M00346,T00057,T00062,T00063,T00066,T00067

Enzyme Name
UniProtKBKEGG

Q5PSP8O05512P49424
Protein name
Mannan endo-1,4-beta-mannosidaseMannan endo-1,4-beta-mannosidaseMannan 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
SynonymsBeta-1,4-mannanase
EC 3.2.1.78
EC 3.2.1.78
Beta-mannanase
1,4-beta-D-mannan mannanohydrolase
EC 3.2.1.78
Mannanase A
RefSeq
NP_388469.2 (Protein)
NC_000964.3 (DNA/RNA sequence)
YP_001983229.1 (Protein)
NC_010995.1 (DNA/RNA sequence)
PfamPF02156 (Glyco_hydro_26)
[Graphical view]
PF02156 (Glyco_hydro_26)
[Graphical view]
PF02156 (Glyco_hydro_26)
[Graphical view]
CAZyGH26 (Glycoside Hydrolase Family)
GH26 (Glycoside Hydrolase Family)
GH26 (Glycoside Hydrolase Family)

KEGG pathways
MAP codePathways
MAP00051Fructose and mannose metabolism

UniProtKB:Accession NumberQ5PSP8O05512P49424
Entry nameQ5PSP8_BACSUMANB1_BACSUMANA_CELJU
Activity
Random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans.Random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans.
Subunit


Subcellular location
Secreted (Potential).
Cofactor



Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC02492C00883C00001C02492C00883I00118
Compound1,4-beta-D-MannanGalactomannanH2O1,4-beta-D-MannanGalactomannanPeptidyl-Glu-D-mannan
TypepolysaccharidepolysaccharideH2Opolysaccharidepolysaccharide
ChEBI
27680
15377

27680

PubChem
439336
962
22247451

439336

              
2qhaA00UnboundUnbound UnboundUnboundUnbound
2qhaB00UnboundUnbound UnboundUnboundUnbound
2whkA00UnboundUnbound UnboundUnboundUnbound
3cbwA00UnboundUnbound UnboundUnboundUnbound
3cbwB00UnboundUnbound UnboundUnboundUnbound
1gvyA00Analogue:BMA-BMA-MBF-NINUnbound UnboundUnboundUnbound
1gw1A00Analogue:BMA-BMA-MBF-NINUnbound UnboundUnboundIntermediate-analogue:BMA-BMA-MAF
1j9yA00UnboundUnbound UnboundUnboundUnbound
1odzA00UnboundUnbound Analogue:MAN-BMAUnboundUnbound
1odzB00UnboundUnbound Analogue:MAN-BMAUnboundUnbound
1r7oA00UnboundUnbound UnboundUnboundUnbound
2whmA00UnboundUnbound Analogue:MAN-BMAUnboundUnbound

Active-site residues
resource
Literature [2]
pdbCatalytic residuescomment
          
2qhaA00ARG 163;HIS 166;GLU 167;TRP 172;TYR 242;GLU 266;TRP 298
 
2qhaB00ARG 163;HIS 166;GLU 167;TRP 172;TYR 242;GLU 266;TRP 298
 
2whkA00ARG 163;HIS 166;GLU 167;TRP 172;TYR 242;GLU 266;TRP 298
 
3cbwA00ARG 189;HIS 192;GLU 193;TRP 198;TYR 268;GLU 292;TRP 324
 
3cbwB00ARG 189;HIS 192;GLU 193;TRP 198;TYR 268;GLU 292;TRP 324
 
1gvyA00ARG 208;HIS 211;       ;TRP 217;TYR 285;GLU 320;TRP 360
mutant E212A
1gw1A00ARG 208;HIS 211;       ;TRP 217;TYR 285;GLU 320;TRP 360
mutant E212A
1j9yA00ARG 208;HIS 211;GLU 212;TRP 217;TYR 285;GLU 320;TRP 360
 
1odzA00ARG 208;HIS 211;GLU 212;TRP 217;TYR 285;       ;TRP 360
mutant E320G
1odzB00ARG 208;HIS 211;GLU 212;TRP 217;TYR 285;       ;TRP 360
mutant E320G
1r7oA00ARG 208;HIS 211;GLU 212;TRP 217;TYR 285;GLU 320;TRP 360
 
2whmA00ARG 208;HIS 211;GLU 212;TRP 217;TYR 285;       ;TRP 360
mutant E320G

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]FIGURE 1b
[2]p.31187, p.31190-31191
[3]Scheme 3
[5]Figure 4, p.34405-34409
[8]Fig. 2

references
[1]
PubMed ID10639071
JournalAcc Chem Res
Year2000
Volume33
Pages11-8
AuthorsZechel DL, Withers SG
TitleGlycosidase mechanisms: anatomy of a finely tuned catalyst.
[2]
PubMed ID11382747
JournalJ Biol Chem
Year2001
Volume276
Pages31186-92
AuthorsHogg D, Woo EJ, Bolam DN, McKie VA, Gilbert HJ, Pickersgill RW
TitleCrystal structure of mannanase 26A from Pseudomonas cellulosa and analysis of residues involved in substrate binding.
Related PDB1j9y
Related UniProtKBP49424
[3]
PubMed ID12203498
JournalAngew Chem Int Ed Engl
Year2002
Volume41
Pages2824-7
AuthorsDucros VM, Zechel DL, Murshudov GN, Gilbert HJ, Szabo L, Stoll D, Withers SG, Davies GJ
TitleSubstrate distortion by a beta-mannanase: snapshots of the Michaelis and covalent-intermediate complexes suggest a B(2,5) conformation for the transition state.
Related PDB1gvy,1gw1
Related UniProtKBP49424
[4]
PubMed ID12841226
JournalChem Commun (Camb)
Year2003
Volume(12)
Pages1327-9
AuthorsJahn M, Stoll D, Warren RA, Szabo L, Singh P, Gilbert HJ, Ducros VM, Davies GJ, Withers SG
TitleExpansion of the glycosynthase repertoire to produce defined manno-oligosaccharides.
Related PDB1odz
Related UniProtKBP49424
[5]
PubMed ID18799462
JournalJ Biol Chem
Year2008
Volume283
Pages34403-13
AuthorsCartmell A, Topakas E, Ducros VM, Suits MD, Davies GJ, Gilbert HJ
TitleThe Cellvibrio japonicus mannanase CjMan26C displays a unique exo-mode of action that is conferred by subtle changes to the distal region of the active site.
Related PDB2vx4,2vx5,2vx6,2vx7
Related UniProtKBB3PGI1
[6]
CommentsX-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) OF 27-362 IN COMPLEX WITH ZINC.
PubMed ID18455734
JournalJ Mol Biol
Year2008
Volume379
Pages535-44
AuthorsYan XX, An XM, Gui LL, Liang DC
TitleFrom structure to function: insights into the catalytic substrate specificity and thermostability displayed by Bacillus subtilis mannanase BCman.
Related PDB2qha
Related UniProtKBQ5PSP8
[7]
PubMed ID19441796
JournalBiochemistry
Year2009
Volume48
Pages7009-18
AuthorsTailford LE, Ducros VM, Flint JE, Roberts SM, Morland C, Zechel DL, Smith N, Bjornvad ME, Borchert TV, Wilson KS, Davies GJ, Gilbert HJ
TitleUnderstanding how diverse beta-mannanases recognize heterogeneous substrates.
Related PDB2whk,2whm
Related UniProtKBO05512,P49424
[8]
JournalProcess Biochem
Year2010
Volume45
Pages1203-13
Authorsvan Zyl WH, Rose SH, Trollope K, Gorgens JF
TitleFungal beta-mannanases: Mannan hydrolysis, heterologous production and biotechnological applications.

comments
This enzyme belongs to the glycosidase family-26, which adopts (alpha/beta)8 barrel structure.
According to the literature [7], this enzyme in family-26 hydrolyzes only mannan and galactomannan, whereas the counterpart enzymes from family-5 hydrolyze glucomannan as well as mannnan and galactomannan.
Moreover, according to the literature [5], a homologous enzyme (S00915 in EzCatDB) is an exo-acting mannanase, producing disaccharide, mannobiose, or galactomannobiose, from the non-reducing end of mannan or galactomannan, whereas this enzyme and other homologous enzyme (M00346 in EzCatDB) are endo-mannanases.
According to the literature [2], [3] and [5], this enzyme catalyzes the following reaction:
(0) Arg163, Tyr242 and His166 (of 2qha) modulate the nucleophilic residue, Glu266, whereas the sidechain of Trp172 modulates Acid-base, Glu167. The mannopyranoside at -1 subsite adopts a 1S5 Skew boat conformation.
(1) Glu167 acts as a general acid to protonate the leaving oxygen in mannan, whereas Glu266 approaches the C1 atom of substrate mannan as a nucleophile. This process leads to an oxocarbenium-like transition-state (Boat conformation; B2,5). The -1 subsite in the transition-state is stabilized by His166 and Trp298.
(2) Glu266 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) Glu167 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.

createdupdated
2012-02-082012-05-14


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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