EzCatDB: S00915
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DB codeS00915
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,S00911,S00912,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

B3PGI1
Protein 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
SynonymsEndo-1, 4-beta mannanase, putative, man26C
EC 3.2.1.78
RefSeqYP_001980760.1 (Protein)
NC_010995.1 (DNA/RNA sequence)
PfamPF02156 (Glyco_hydro_26)
[Graphical view]
CAZyGH26 (Glycoside Hydrolase Family)

KEGG pathways
MAP codePathways
MAP00051Fructose and mannose metabolism

UniProtKB:Accession NumberB3PGI1
Entry nameB3PGI1_CELJU
Activity
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC02492C00883C00001C01728L00074C02492C00883I00129I00130
Compound1,4-beta-D-MannanGalactomannanH2OMannobioseGalactomannobiose1,4-beta-D-MannanGalactomannanPeptidyl-Glu-D-mannobiosePeptidyl-Glu-D-galactomannobiose
TypepolysaccharidepolysaccharideH2Opolysaccharidepolysaccharidepolysaccharidepolysaccharide

ChEBI
27680
15377
62357
27680

27680


PubChem
439336
962
22247451
439557
439336

439336


                 
2vx4A00UnboundUnbound UnboundUnboundUnboundUnboundUnboundUnbound
2vx5A00UnboundUnbound Analogue:BMAUnboundUnboundUnboundUnboundUnbound
2vx6A00UnboundBound:GLA-BMA-BMA-BMA-BMA UnboundUnboundUnboundUnboundUnboundUnbound
2vx7A00UnboundUnbound Bound:MABUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Literature [2]
pdbCatalytic residuescomment
          
2vx4A00ARG 217;HIS 220;GLU 221;TRP 226;TYR 297;GLU 338;TRP 373
 
2vx5A00ARG 217;HIS 220;GLU 221;TRP 226;TYR 297;GLU 338;TRP 373
 
2vx6A00ARG 217;HIS 220;GLU 221;TRP 226;TYR 297;GLU 338;TRP 373
 
2vx7A00ARG 217;HIS 220;GLU 221;TRP 226;TYR 297;       ;TRP 373
mutant E338A

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], this enzyme is an exo-acting mannanase, producing disaccharide, mannobiose, or galactomannobiose, from the non-reducing end of mannan or galactomannan, whereas most of homologous enzymes (S00911 and M00346 in EzCatDB) are endo-mannanases.
According to the literature [2], [3] and [5], this enzyme catalyzes the following reaction:
(0) Arg217, Tyr297 and His220 modulate the nucleophilic residue, Glu338, whereas the sidechain of Trp226 modulates Acid-base, Glu221. The mannopyranoside at -1 subsite adopts a 1S5 Skew boat conformation.
(1) Glu221 acts as a general acid to protonate the leaving oxygen in mannan, whereas Glu338 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 His220 and Trp373.
(2) Glu338 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) Glu221 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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