EzCatDB: D00861
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DB codeD00861
RLCP classification1.30.35885.972 : Hydrolysis
CATH domainDomain 13.20.20.80 : TIM BarrelCatalytic domain
Domain 22.60.120.- : Jelly Rolls
E.C.3.2.1.78

CATH domainRelated DB codes (homologues)
3.20.20.80 : TIM BarrelS00202,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

Enzyme Name
UniProtKBKEGG

Q4W8M3Q5YEX6
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
SynonymsMannanase
Beta-mannanase
EC 3.2.1.78
PfamPF00150 (Cellulase)
[Graphical view]
PF00150 (Cellulase)
[Graphical view]
CAZyGH5 (Glycoside Hydrolase Family)
GH5 (Glycoside Hydrolase Family)

KEGG pathways
MAP codePathways
MAP00051Fructose and mannose metabolism

UniProtKB:Accession NumberQ4W8M3Q5YEX6
Entry nameQ4W8M3_9BACIQ5YEX6_9BACI
Activity

Subunit

Subcellular location

Cofactor


Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC02492C00883C01810C00001C02492C00883C01810I00118
Compound1,4-beta-D-MannanGalactomannanGlucomannanH2O1,4-beta-D-MannanGalactomannanGlucomannanPeptidyl-Glu-D-mannan
TypepolysaccharidepolysaccharidepolysaccharideH2Opolysaccharidepolysaccharidepolysaccharide
ChEBI
27680

15377

27680


PubChem
439336
24892726
962
22247451

439336
24892726

                
1wkyA01UnboundUnboundUnbound UnboundUnboundUnboundUnbound
2whjA00UnboundUnboundUnbound UnboundUnboundUnboundUnbound
2whlA00UnboundUnboundUnbound Analogue:MAN-BMA-BMAUnboundUnboundUnbound
1wkyA02UnboundUnboundUnbound UnboundUnboundUnboundUnbound

Active-site residues
resource
literature [2]
pdbCatalytic residues
         
1wkyA01ARG 83;ASN 157;GLU 158;HIS 223;TYR 225;GLU 253
2whjA00ARG 52;ASN 126;GLU 127;HIS 192;TYR 194;GLU 222
2whlA00ARG 52;ASN 126;GLU 127;HIS 192;TYR 194;GLU 222
1wkyA02 

References for Catalytic Mechanism
ReferencesSectionsNo. 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]
PubMed ID7624375
JournalProc Natl Acad Sci U S A
Year1995
Volume92
Pages7090-4
AuthorsHenrissat B, Callebaut I, Fabrega S, Lehn P, Mornon JP, Davies G
TitleConserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS).
PubMed ID9817845
JournalStructure
Year1998
Volume6
Pages1433-44
AuthorsHilge M, Gloor SM, Rypniewski W, Sauer O, Heightman TD, Zimmermann W, Winterhalter K, Piontek K
TitleHigh-resolution native and complex structures of thermostable beta-mannanase from Thermomonospora fusca - substrate specificity in glycosyl hydrolase family 5.
Related PDB1bqc,2man,3man
Related UniProtKBQ9ZF13
[3]
PubMed ID9989594
JournalFEBS Lett
Year1999
Volume443
Pages149-53
AuthorsHarjunpaa V, Helin J, Koivula A, Siika-aho M, Drakenberg T
TitleA comparative study of two retaining enzymes of Trichoderma reesei: transglycosylation of oligosaccharides catalysed by the cellobiohydrolase I, Cel7A, and the beta-mannanase, Man5A.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) OF 28-371.
PubMed ID10666621
JournalActa Crystallogr D Biol Crystallogr
Year2000
Volume56
Pages3-13
AuthorsSabini E, Schubert H, Murshudov G, Wilson KS, Siika-Aho M, Penttila M
TitleThe three-dimensional structure of a Trichoderma reesei beta-mannanase from glycoside hydrolase family 5.
Related PDB1qno,1qnp,1qnq,1qnr,1qns
Related UniProtKBQ99036
[5]
CommentsNUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
JournalPlant Sci
Year2002
Volume163
Pages599-606
AuthorsCarrington CMS, Vendrell M, Domi'nguez-Puigjaner E
TitleCharacterisation of an endo-(1,4)-beta-mannanase (LeMAN4) expressed in ripening tomato fruit
[6]
CommentsX-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS).
PubMed ID15272186
JournalActa Crystallogr D Biol Crystallogr
Year2004
Volume60
Pages1490-2
AuthorsAkita M, Takeda N, Hirasawa K, Sakai H, Kawamoto M, Yamamoto M, Grant WD, Hatada Y, Ito S, Horikoshi K
TitleCrystallization and preliminary X-ray study of alkaline mannanase from an alkaliphilic Bacillus isolate.
Related PDB1wky
Related UniProtKBQ4W8M3
[7]
PubMed ID15642336
JournalFEBS Lett
Year2005
Volume579
Pages302-12
AuthorsNerinckx W, Desmet T, Piens K, Claeyssens M
TitleAn elaboration on the syn-anti proton donor concept of glycoside hydrolases: electrostatic stabilisation of the transition state as a general strategy.
[8]
CommentsX-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 27-399.
PubMed ID15840830
JournalProtein Sci
Year2005
Volume14
Pages1233-41
AuthorsBourgault R, Oakley AJ, Bewley JD, Wilce MC
TitleThree-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit.
Related PDB1rh9
Related UniProtKBQ8L5J1
[9]
PubMed ID16823793
JournalAngew Chem Int Ed Engl
Year2006
Volume45
Pages5136-40
AuthorsMoney VA, Smith NL, Scaffidi A, Stick RV, Gilbert HJ, Davies GJ
TitleSubstrate distortion by a lichenase highlights the different conformational itineraries harnessed by related glycoside hydrolases.
[10]
PubMed ID17069777
JournalCarbohydr Res
Year2006
Volume341
Pages2912-20
AuthorsIonescu AR, Whitfield DM, Zgierski MZ, Nukada T
TitleInvestigations into the role of oxacarbenium ions in glycosylation reactions by ab initio molecular dynamics.
[11]
CommentsX-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
PubMed ID16487541
JournalJ Mol Biol
Year2006
Volume357
Pages1500-10
AuthorsLarsson AM, Anderson L, Xu B, Munoz IG, Uson I, Janson JC, Stalbrand H, Stahlberg J
TitleThree-dimensional crystal structure and enzymic characterization of beta-mannanase Man5A from blue mussel Mytilus edulis.
Related PDB2c0h
Related UniProtKBQ8WPJ2
[12]
PubMed ID18558099
JournalCurr Opin Chem Biol
Year2008
Volume12
Pages539-55
AuthorsVocadlo DJ, Davies GJ
TitleMechanistic insights into glycosidase chemistry.
[13]
PubMed ID18579426
JournalComp Biochem Physiol B Biochem Mol Biol
Year2008
Volume151
Pages32-40
AuthorsSong JM, Nam KW, Kang SG, Kim CG, Kwon ST, Lee YH
TitleMolecular cloning and characterization of a novel cold-active beta-1,4-D-mannanase from the Antarctic springtail, Cryptopygus antarcticus.
[14]
CommentsX-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS).
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 PDB2whj,2whl
Related UniProtKBQ5YEX6

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.

createdupdated
2010-05-202012-02-14


Copyright: Nozomi Nagano, JST & CBRC-AIST
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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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