DB code: D00861

RLCP classification	1.30.35885.972 : Hydrolysis
CATH domain	3.20.20.80 : TIM Barrel	Catalytic domain
CATH 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
Q4W8M3	Q4W8M3_9BACI
Q5YEX6	Q5YEX6_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 27680		15377 15377		27680 27680
PubChem		439336 439336	24892726 24892726	22247451 962 22247451 962		439336 439336	24892726 24892726

1wkyA01	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound
2whjA00	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound
2whlA00	Unbound	Unbound	Unbound		Analogue:MAN-BMA-BMA	Unbound	Unbound	Unbound
1wkyA02	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	ARG 83;ASN 157;GLU 158;HIS 223;TYR 225;GLU 253
2whjA00	ARG 52;ASN 126;GLU 127;HIS 192;TYR 194;GLU 222
2whlA00	ARG 52;ASN 126;GLU 127;HIS 192;TYR 194;GLU 222
1wkyA02

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.

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