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PDBsum entry 1qbd
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Glycosyl hydrolase
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PDB id
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1qbd
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Nat Struct Biol
3:638-648
(1996)
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PubMed id:
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Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay-Sachs disease.
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I.Tews,
A.Perrakis,
A.Oppenheim,
Z.Dauter,
K.S.Wilson,
C.E.Vorgias.
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ABSTRACT
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Chitin, the second most abundant polysaccharide on earth, is degraded by
chitinases and chitobiases. The structure of Serratia marcescens chitobiase has
been refined at 1.9 A resolution. The mature protein is folded into four domains
and its active site is situated at the C-terminal end of the central (beta
alpha)8-barrel. Based on the structure of the complex with the substrate
disaccharide chitobiose, we propose an acid-base reaction mechanism, in which
only one protein carboxylate acts as catalytic acid, while the nucleophile is
the polar acetamido group of the sugar in a substrate-assisted reaction. The
structural data lead to the hypothesis that the reaction proceeds with retention
of anomeric configuration. The structure allows us to model the catalytic domain
of the homologous hexosaminidases to give a structural rationale to pathogenic
mutations that underlie Tay-Sachs and Sandhoff disease.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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H.Usuki,
Y.Yamamoto,
Y.Kumagai,
T.Nitoda,
H.Kanzaki,
and
T.Hatanaka
(2011).
MS/MS fragmentation-guided search of TMG-chitooligomycins and their structure-activity relationship in specific β-N-acetylglucosaminidase inhibition.
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Org Biomol Chem,
9,
2943-2951.
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S.Ghosh,
V.S.Meli,
A.Kumar,
A.Thakur,
N.Chakraborty,
S.Chakraborty,
and
A.Datta
(2011).
The N-glycan processing enzymes {alpha}-mannosidase and {beta}-D-N-acetylhexosaminidase are involved in ripening-associated softening in the non-climacteric fruits of capsicum.
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J Exp Bot,
62,
571-582.
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Y.Yang,
T.Liu,
Y.Yang,
Q.Wu,
Q.Yang,
and
B.Yu
(2011).
Synthesis, Evaluation, and Mechanism of N,N,N-Trimethyl-D-glucosamine-(1→4)-chitooligosaccharides as Selective Inhibitors of Glycosyl Hydrolase Family 20 β-N-Acetyl-D-hexosaminidases.
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Chembiochem,
12,
457-467.
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D.B.Jordan,
and
J.D.Braker
(2010).
beta-D-Xylosidase from Selenomonas ruminantium: role of glutamate 186 in catalysis revealed by site-directed mutagenesis, alternate substrates, and active-site inhibitor.
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Appl Biochem Biotechnol,
161,
395-410.
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S.Kalkhof,
S.Haehn,
M.Paulsson,
N.Smyth,
J.Meiler,
and
A.Sinz
(2010).
Computational modeling of laminin N-terminal domains using sparse distance constraints from disulfide bonds and chemical cross-linking.
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Proteins,
78,
3409-3427.
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T.M.Gloster,
and
D.J.Vocadlo
(2010).
Mechanism, Structure, and Inhibition of O-GlcNAc Processing Enzymes.
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Curr Signal Transduct Ther,
5,
74-91.
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T.M.Gloster,
and
G.J.Davies
(2010).
Glycosidase inhibition: assessing mimicry of the transition state.
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Org Biomol Chem,
8,
305-320.
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W.Suginta,
D.Chuenark,
M.Mizuhara,
and
T.Fukamizo
(2010).
Novel β-N-acetylglucosaminidases from Vibrio harveyi 650: cloning, expression, enzymatic properties, and subsite identification.
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BMC Biochem,
11,
40.
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D.Dodd,
and
I.K.Cann
(2009).
Enzymatic deconstruction of xylan for biofuel production.
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Glob Change Biol Bioenergy,
1,
2.
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D.W.Abbott,
M.S.Macauley,
D.J.Vocadlo,
and
A.B.Boraston
(2009).
Streptococcus pneumoniae Endohexosaminidase D, Structural and Mechanistic Insight into Substrate-assisted Catalysis in Family 85 Glycoside Hydrolases.
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J Biol Chem,
284,
11676-11689.
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PDB codes:
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M.D.Balcewich,
K.A.Stubbs,
Y.He,
T.W.James,
G.J.Davies,
D.J.Vocadlo,
and
B.L.Mark
(2009).
Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: structural basis for selective inhibition of the glycoside hydrolase NagZ.
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Protein Sci,
18,
1541-1551.
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PDB codes:
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A.Cartmell,
E.Topakas,
V.M.Ducros,
M.D.Suits,
G.J.Davies,
and
H.J.Gilbert
(2008).
The 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.
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J Biol Chem,
283,
34403-34413.
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PDB codes:
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D.J.Vocadlo,
and
G.J.Davies
(2008).
Mechanistic insights into glycosidase chemistry.
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Curr Opin Chem Biol,
12,
539-555.
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T.Parkkinen,
A.Koivula,
J.Vehmaanperä,
and
J.Rouvinen
(2008).
Crystal structures of Melanocarpus albomyces cellobiohydrolase Cel7B in complex with cello-oligomers show high flexibility in the substrate binding.
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Protein Sci,
17,
1383-1394.
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PDB codes:
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X.Lan,
X.Zhang,
R.Kodaira,
Z.Zhou,
and
M.Shimosaka
(2008).
Gene cloning, expression, and characterization of a second beta-N-acetylglucosaminidase from the chitinolytic bacterium Aeromonas hydrophila strain SUWA-9.
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Biosci Biotechnol Biochem,
72,
492-498.
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A.Scaffidi,
K.A.Stubbs,
R.J.Dennis,
E.J.Taylor,
G.J.Davies,
D.J.Vocadlo,
and
R.V.Stick
(2007).
A 1-acetamido derivative of 6-epi-valienamine: an inhibitor of a diverse group of beta-N-acetylglucosaminidases.
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Org Biomol Chem,
5,
3013-3019.
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PDB code:
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K.L.Frank,
and
R.Patel
(2007).
Poly-N-acetylglucosamine is not a major component of the extracellular matrix in biofilms formed by icaADBC-positive Staphylococcus lugdunensis isolates.
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Infect Immun,
75,
4728-4742.
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M.B.Tropak,
J.E.Blanchard,
S.G.Withers,
E.D.Brown,
and
D.Mahuran
(2007).
High-throughput screening for human lysosomal beta-N-Acetyl hexosaminidase inhibitors acting as pharmacological chaperones.
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Chem Biol,
14,
153-164.
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R.Ettrich,
V.Kopecký,
K.Hofbauerová,
V.Baumruk,
P.Novák,
P.Pompach,
P.Man,
O.Plíhal,
M.Kutý,
N.Kulik,
J.Sklenár,
H.Ryslavá,
V.Kren,
and
K.Bezouska
(2007).
Structure of the dimeric N-glycosylated form of fungal beta-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies.
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BMC Struct Biol,
7,
32.
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S.G.Manuel,
C.Ragunath,
H.B.Sait,
E.A.Izano,
J.B.Kaplan,
and
N.Ramasubbu
(2007).
Role of active-site residues of dispersin B, a biofilm-releasing beta-hexosaminidase from a periodontal pathogen, in substrate hydrolysis.
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FEBS J,
274,
5987-5999.
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T.Okada,
S.Ishiyama,
H.Sezutsu,
A.Usami,
T.Tamura,
K.Mita,
K.Fujiyama,
and
T.Seki
(2007).
Molecular cloning and expression of two novel beta-N-acetylglucosaminidases from silkworm Bombyx mori.
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Biosci Biotechnol Biochem,
71,
1626-1635.
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C.Mayer,
D.J.Vocadlo,
M.Mah,
K.Rupitz,
D.Stoll,
R.A.Warren,
and
S.G.Withers
(2006).
Characterization of a beta-N-acetylhexosaminidase and a beta-N-acetylglucosaminidase/beta-glucosidase from Cellulomonas fimi.
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FEBS J,
273,
2929-2941.
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K.A.Miroshnikov,
N.M.Faizullina,
N.N.Sykilinda,
and
V.V.Mesyanzhinov
(2006).
Properties of the endolytic transglycosylase encoded by gene 144 of Pseudomonas aeruginosa bacteriophage phiKZ.
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Biochemistry (Mosc),
71,
300-305.
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K.A.Stubbs,
N.Zhang,
and
D.J.Vocadlo
(2006).
A divergent synthesis of 2-acyl derivatives of PUGNAc yields selective inhibitors of O-GlcNAcase.
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Org Biomol Chem,
4,
839-845.
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M.J.Lemieux,
B.L.Mark,
M.M.Cherney,
S.G.Withers,
D.J.Mahuran,
and
M.N.James
(2006).
Crystallographic structure of human beta-hexosaminidase A: interpretation of Tay-Sachs mutations and loss of GM2 ganglioside hydrolysis.
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J Mol Biol,
359,
913-929.
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PDB codes:
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R.J.Dennis,
E.J.Taylor,
M.S.Macauley,
K.A.Stubbs,
J.P.Turkenburg,
S.J.Hart,
G.N.Black,
D.J.Vocadlo,
and
G.J.Davies
(2006).
Structure and mechanism of a bacterial beta-glucosaminidase having O-GlcNAcase activity.
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Nat Struct Mol Biol,
13,
365-371.
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PDB codes:
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R.Stern,
and
M.J.Jedrzejas
(2006).
Hyaluronidases: their genomics, structures, and mechanisms of action.
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Chem Rev,
106,
818-839.
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S.Pyrpassopoulos,
M.Vlassi,
A.Tsortos,
Y.Papanikolau,
K.Petratos,
C.E.Vorgias,
and
G.Nounesis
(2006).
Equilibrium heat-induced denaturation of chitinase 40 from Streptomyces thermoviolaceus.
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Proteins,
64,
513-523.
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X.Biarnés,
J.Nieto,
A.Planas,
and
C.Rovira
(2006).
Substrate distortion in the Michaelis complex of Bacillus 1,3-1,4-beta-glucanase. Insight from first principles molecular dynamics simulations.
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J Biol Chem,
281,
1432-1441.
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A.L.Lovering,
S.S.Lee,
Y.W.Kim,
S.G.Withers,
and
N.C.Strynadka
(2005).
Mechanistic and structural analysis of a family 31 alpha-glycosidase and its glycosyl-enzyme intermediate.
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J Biol Chem,
280,
2105-2115.
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PDB codes:
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M.S.Macauley,
G.E.Whitworth,
A.W.Debowski,
D.Chin,
and
D.J.Vocadlo
(2005).
O-GlcNAcase uses substrate-assisted catalysis: kinetic analysis and development of highly selective mechanism-inspired inhibitors.
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J Biol Chem,
280,
25313-25322.
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O.A.Andersen,
M.J.Dixon,
I.M.Eggleston,
and
D.M.van Aalten
(2005).
Natural product family 18 chitinase inhibitors.
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Nat Prod Rep,
22,
563-579.
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R.Bourgault,
A.J.Oakley,
J.D.Bewley,
and
M.C.Wilce
(2005).
Three-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit.
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Protein Sci,
14,
1233-1241.
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PDB code:
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S.M.Hancock,
K.Corbett,
A.P.Fordham-Skelton,
J.A.Gatehouse,
and
B.G.Davis
(2005).
Developing promiscuous glycosidases for glycoside synthesis: residues W433 and E432 in Sulfolobus solfataricus beta-glycosidase are important glucoside- and galactoside-specificity determinants.
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Chembiochem,
6,
866-875.
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B.Synstad,
S.Gåseidnes,
D.M.Van Aalten,
G.Vriend,
J.E.Nielsen,
and
V.G.Eijsink
(2004).
Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase.
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Eur J Biochem,
271,
253-262.
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G.Golan,
D.Shallom,
A.Teplitsky,
G.Zaide,
S.Shulami,
T.Baasov,
V.Stojanoff,
A.Thompson,
Y.Shoham,
and
G.Shoham
(2004).
Crystal structures of Geobacillus stearothermophilus alpha-glucuronidase complexed with its substrate and products: mechanistic implications.
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J Biol Chem,
279,
3014-3024.
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PDB codes:
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L.Verdoucq,
J.Morinière,
D.R.Bevan,
A.Esen,
A.Vasella,
B.Henrissat,
and
M.Czjze
(2004).
Structural determinants of substrate specificity in family 1 beta-glucosidases: novel insights from the crystal structure of sorghum dhurrinase-1, a plant beta-glucosidase with strict specificity, in complex with its natural substrate.
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J Biol Chem,
279,
31796-31803.
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PDB codes:
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M.Hrmova,
R.De Gori,
B.J.Smith,
A.Vasella,
J.N.Varghese,
and
G.B.Fincher
(2004).
Three-dimensional structure of the barley beta-D-glucan glucohydrolase in complex with a transition state mimic.
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J Biol Chem,
279,
4970-4980.
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PDB code:
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R.P.Gibson,
C.A.Tarling,
S.Roberts,
S.G.Withers,
and
G.J.Davies
(2004).
The donor subsite of trehalose-6-phosphate synthase: binary complexes with UDP-glucose and UDP-2-deoxy-2-fluoro-glucose at 2 A resolution.
|
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J Biol Chem,
279,
1950-1955.
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PDB codes:
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X.Lan,
N.Ozawa,
N.Nishiwaki,
R.Kodaira,
M.Okazaki,
and
M.Shimosaka
(2004).
Purification, cloning, and sequence analysis of beta-N-acetylglucosaminidase from the chitinolytic bacterium Aeromonas hydrophila strain SUWA-9.
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Biosci Biotechnol Biochem,
68,
1082-1090.
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A.Vrielink,
and
N.Sampson
(2003).
Sub-Angstrom resolution enzyme X-ray structures: is seeing believing?
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Curr Opin Struct Biol,
13,
709-715.
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B.L.Mark,
D.J.Mahuran,
M.M.Cherney,
D.Zhao,
S.Knapp,
and
M.N.James
(2003).
Crystal structure of human beta-hexosaminidase B: understanding the molecular basis of Sandhoff and Tay-Sachs disease.
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J Mol Biol,
327,
1093-1109.
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PDB codes:
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G.Hofhaus,
J.E.Lee,
I.Tews,
B.Rosenberg,
and
T.Lisowsky
(2003).
The N-terminal cysteine pair of yeast sulfhydryl oxidase Erv1p is essential for in vivo activity and interacts with the primary redox centre.
|
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Eur J Biochem,
270,
1528-1535.
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J.B.Kaplan,
C.Ragunath,
N.Ramasubbu,
and
D.H.Fine
(2003).
Detachment of Actinobacillus actinomycetemcomitans biofilm cells by an endogenous beta-hexosaminidase activity.
|
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J Bacteriol,
185,
4693-4698.
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K.Hövel,
D.Shallom,
K.Niefind,
V.Belakhov,
G.Shoham,
T.Baasov,
Y.Shoham,
and
D.Schomburg
(2003).
Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase.
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| |
EMBO J,
22,
4922-4932.
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PDB codes:
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R.Koyanagi,
and
T.G.Honegger
(2003).
Molecular cloning and sequence analysis of an ascidian egg beta-N-acetylhexosaminidase with a potential role in fertilization.
|
| |
Dev Growth Differ,
45,
209-218.
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R.Sharma,
S.Bukovac,
J.Callahan,
and
D.Mahuran
(2003).
A single site in human beta-hexosaminidase A binds both 6-sulfate-groups on hexosamines and the sialic acid moiety of GM2 ganglioside.
|
| |
Biochim Biophys Acta,
1637,
113-118.
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A.Vasella,
G.J.Davies,
and
M.Böhm
(2002).
Glycosidase mechanisms.
|
| |
Curr Opin Chem Biol,
6,
619-629.
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H.Tsujibo,
K.Miyamoto,
M.Yoshimura,
M.Takata,
J.Miyamoto,
and
Y.Inamori
(2002).
Molecular cloning of the gene encoding a novel beta-N-acetylhexosaminidase from a marine bacterium, Alteromonas sp. strain O-7, and characterization of the cloned enzyme.
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| |
Biosci Biotechnol Biochem,
66,
471-475.
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M.J.McGinniss,
D.H.Brown,
A.Fulwiler,
M.Marten,
J.S.Lim-Steele,
and
M.M.Kaback
(2002).
Eight novel mutations in the HEXA gene.
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| |
Genet Med,
4,
158-161.
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S.J.Williams,
B.L.Mark,
D.J.Vocadlo,
M.N.James,
and
S.G.Withers
(2002).
Aspartate 313 in the Streptomyces plicatus hexosaminidase plays a critical role in substrate-assisted catalysis by orienting the 2-acetamido group and stabilizing the transition state.
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| |
J Biol Chem,
277,
40055-40065.
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PDB codes:
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V.B.Lokeshwar,
G.L.Schroeder,
R.I.Carey,
M.S.Soloway,
and
N.Iida
(2002).
Regulation of hyaluronidase activity by alternative mRNA splicing.
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| |
J Biol Chem,
277,
33654-33663.
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B.L.Mark,
D.J.Vocadlo,
D.Zhao,
S.Knapp,
S.G.Withers,
and
M.N.James
(2001).
Biochemical and structural assessment of the 1-N-azasugar GalNAc-isofagomine as a potent family 20 beta-N-acetylhexosaminidase inhibitor.
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| |
J Biol Chem,
276,
42131-42137.
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PDB code:
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D.M.van Aalten,
D.Komander,
B.Synstad,
S.Gåseidnes,
M.G.Peter,
and
V.G.Eijsink
(2001).
Structural insights into the catalytic mechanism of a family 18 exo-chitinase.
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| |
Proc Natl Acad Sci U S A,
98,
8979-8984.
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PDB codes:
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R.Sharma,
H.Deng,
A.Leung,
and
D.Mahuran
(2001).
Identification of the 6-sulfate binding site unique to alpha-subunit-containing isozymes of human beta-hexosaminidase.
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Biochemistry,
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Mixed-linkage cellooligosaccharides: a new class of glycoside hydrolase inhibitors.
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Chembiochem,
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PDB code:
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T.Lonhienne,
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C.E.Vorgias,
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Cloning, sequences, and characterization of two chitinase genes from the Antarctic Arthrobacter sp. strain TAD20: isolation and partial characterization of the enzymes.
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J Bacteriol,
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Characterization of the Glu and Asp residues in the active site of human beta-hexosaminidase B.
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Biochemistry,
40,
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A.J.Harvey,
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Comparative modeling of the three-dimensional structures of family 3 glycoside hydrolases.
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Proteins,
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C.S.Rye,
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Glycosidase mechanisms.
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Curr Opin Chem Biol,
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D.M.van Aalten,
B.Synstad,
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B.W.Riise,
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(2000).
Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9-A resolution.
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Proc Natl Acad Sci U S A,
97,
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PDB code:
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H.Tsujibo,
J.Miyamoto,
N.Kondo,
K.Miyamoto,
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Molecular cloning of the gene encoding an outer-membrane-associated beta-N-acetylglucosaminidase involved in chitin degradation system of Alteromonas sp. strain O-7.
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Biosci Biotechnol Biochem,
64,
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M.Czjzek,
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V.Zamboni,
D.R.Bevan,
B.Henrissat,
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The mechanism of substrate (aglycone) specificity in beta -glucosidases is revealed by crystal structures of mutant maize beta -glucosidase-DIMBOA, -DIMBOAGlc, and -dhurrin complexes.
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Proc Natl Acad Sci U S A,
97,
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PDB codes:
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P.Cordeiro,
P.Hechtman,
and
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(2000).
The GM2 gangliosidoses databases: allelic variation at the HEXA, HEXB, and GM2A gene loci.
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Genet Med,
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A fluorescence-quenched chitopentaose for the study of endo-chitinases and chitobiosidases.
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Eur J Biochem,
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Role of beta Arg211 in the active site of human beta-hexosaminidase B.
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Biochemistry,
39,
6219-6227.
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A.Varrot,
M.Schülein,
and
G.J.Davies
(1999).
Structural changes of the active site tunnel of Humicola insolens cellobiohydrolase, Cel6A, upon oligosaccharide binding.
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Biochemistry,
38,
8884-8891.
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PDB code:
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B.Amutha,
J.M.Khire,
and
M.I.Khan
(1999).
Active site characterization of the exo-N-acetyl-beta-D- glucosaminidase from thermotolerant Bacillus sp. NCIM 5120: involvement of tryptophan, histidine and carboxylate residues in catalytic activity.
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Biochim Biophys Acta,
1427,
121-132.
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D.H.Juers,
R.E.Huber,
and
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(1999).
Structural comparisons of TIM barrel proteins suggest functional and evolutionary relationships between beta-galactosidase and other glycohydrolases.
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Protein Sci,
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Biochemical consequences of mutations causing the GM2 gangliosidoses.
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Biochim Biophys Acta,
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G.Sidhu,
S.G.Withers,
N.T.Nguyen,
L.P.McIntosh,
L.Ziser,
and
G.D.Brayer
(1999).
Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase.
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| |
Biochemistry,
38,
5346-5354.
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PDB codes:
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H.D.Ly,
and
S.G.Withers
(1999).
Mutagenesis of glycosidases.
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Annu Rev Biochem,
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H.Tsujibo,
N.Kondo,
K.Tanaka,
K.Miyamoto,
N.Baba,
and
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(1999).
Molecular analysis of the gene encoding a novel transglycosylative enzyme from Alteromonas sp. strain O-7 and its physiological role in the chitinolytic system.
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J Bacteriol,
181,
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K.A.Watson,
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S.Geremia,
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H.Driguez,
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(1999).
Phosphorylase recognition and phosphorolysis of its oligosaccharide substrate: answers to a long outstanding question.
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| |
EMBO J,
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4619-4632.
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PDB codes:
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|
B.L.Mark,
G.A.Wasney,
T.J.Salo,
A.R.Khan,
Z.Cao,
P.W.Robbins,
M.N.James,
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Structural and functional characterization of Streptomyces plicatus beta-N-acetylhexosaminidase by comparative molecular modeling and site-directed mutagenesis.
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J Biol Chem,
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G.J.Davies,
L.Mackenzie,
A.Varrot,
M.Dauter,
A.M.Brzozowski,
M.Schülein,
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S.G.Withers
(1998).
Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase.
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| |
Biochemistry,
37,
11707-11713.
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PDB codes:
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M.P.Geimba,
A.Riffel,
and
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(1998).
Purification and characterization of beta-N-acetylhexosaminidase from the phytopathogenic fungus Bipolaris sorokiniana.
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J Appl Microbiol,
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Y.Hou,
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A Pro504 --> Ser substitution in the beta-subunit of beta-hexosaminidase A inhibits alpha-subunit hydrolysis of GM2 ganglioside, resulting in chronic Sandhoff disease.
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J Biol Chem,
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Mechanism of catalysis by retaining beta-glycosyl hydrolases.
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B.Henrissat,
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Structure of the endoglucanase I from Fusarium oxysporum: native, cellobiose, and 3,4-epoxybutyl beta-D-cellobioside-inhibited forms, at 2.3 A resolution.
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| |
Biochemistry,
36,
5902-5911.
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PDB codes:
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|
J.Sakon,
D.Irwin,
D.B.Wilson,
and
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(1997).
Structure and mechanism of endo/exocellulase E4 from Thermomonospora fusca.
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Nat Struct Biol,
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PDB codes:
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M.Horsch,
C.Mayer,
U.Sennhauser,
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Beta-N-acetylhexosaminidase: a target for the design of antifungal agents.
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M.J.Fernandes,
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B.Henrissat,
C.E.Vorgias,
R.A.Gravel,
P.Hechtman,
and
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(1997).
Identification of candidate active site residues in lysosomal beta-hexosaminidase A.
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J Biol Chem,
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R.Myerowitz
(1997).
Tay-Sachs disease-causing mutations and neutral polymorphisms in the Hex A gene.
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Hum Mutat,
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G.Sulzenbacher,
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M.Schülein,
and
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(1996).
Structure of the Fusarium oxysporum endoglucanase I with a nonhydrolyzable substrate analogue: substrate distortion gives rise to the preferred axial orientation for the leaving group.
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| |
Biochemistry,
35,
15280-15287.
|
|
|
PDB code:
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|
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|
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|
|
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Citation data come partly from CiteXplore and partly
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Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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|
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