Catalysis and specificity in enzymatic glycoside hydrolysis: a B-2,B-5 conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase

E  Sabini; G  Sulzenbacher; M  Dauter; Z  Dauter; P L  Jorgensen; M  Schulein; C  Dupont; G J  Davies; K S  Wilson

Catalysis and specificity in enzymatic glycoside hydrolysis: a B-2,B-5 conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase

E Sabini, G Sulzenbacher, M Dauter, Z Dauter, P L Jorgensen, M Schulein, C Dupont, G J Davies, K S Wilson

Chemistry

Research output: Contribution to journal › Article › peer-review

Abstract

Background: The enzymatic hydrolysis of glycosides involves the formation and subsequent breakdown of a covalent glycosyl-enzyme intermediate via oxocarbenium-ion-like transition states. The covalent intermediate may be trapped on-enzyme using 2-fluoro-substituted glycosides, which provide details of the intermediate conformation and noncovalent interactions between enzyme and oligosaccharide. Xylanases are important in industrial applications - in the pulp and paper industry, pretreating wood with xylanases decreases the amount of chlorine-containing chemicals used. Xylanases are structurally similar to cellulases but differ in their specificity for xylose-based, versus glucose-based, substrates.

Results: The structure of the family 11 xylanase, Xyl11, from Bacillus agaradhaerens has been solved using X-ray crystallography in both native and xylobiosyl-enzyme intermediate forms at 1.78 Angstrom and 2.0 Angstrom resolution, respectively The covalent glycosyl-enzyme intermediate has been trapped using a 2-fluoro-2-deoxy substrate with a good leaving group. Unlike covalent intermediate structures for glycoside hydrolases from other families, the covalent glycosyl-enzyme intermediate in family 11 adopts an unusual B-2,B-5 conformation.

Conclusions: The 2,5B conformation found for the a-linked xylobiosyl-enzyme intermediate of Xyl11, unlike the C-4(1) chair conformation observed for other systems, is consistent with the stereochemical constraints required of the oxocarbenium-ion-like transition state. Comparison of the Xyl11 covalent glycosyl-enzyme intermediate with the equivalent structure for the related family 12 endoglucanase, CelB, from Streptomyces lividans reveals the likely determinants for substrate specificity in this dan of glycoside hydrolases.

Original language	English
Pages (from-to)	483-492
Number of pages	10
Journal	Chemistry & Biology
Volume	6
Issue number	7
Publication status	Published - Jul 1999

Keywords

boat conformation
enzyme specificity
transition state
xylanase
ACID-SEQUENCE SIMILARITIES
X-RAY STRUCTURE
ACTIVE-SITE
MACROMOLECULAR STRUCTURES
MOLECULAR REPLACEMENT
ANGSTROM RESOLUTION
FUSARIUM-OXYSPORUM
CRYSTAL-STRUCTURES
ENDOGLUCANASE-I
LEAVING GROUP

Cite this

@article{acfff969df564fc9a4aac7bc5817364e,

title = "Catalysis and specificity in enzymatic glycoside hydrolysis: a B-2,B-5 conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase",

abstract = "Background: The enzymatic hydrolysis of glycosides involves the formation and subsequent breakdown of a covalent glycosyl-enzyme intermediate via oxocarbenium-ion-like transition states. The covalent intermediate may be trapped on-enzyme using 2-fluoro-substituted glycosides, which provide details of the intermediate conformation and noncovalent interactions between enzyme and oligosaccharide. Xylanases are important in industrial applications - in the pulp and paper industry, pretreating wood with xylanases decreases the amount of chlorine-containing chemicals used. Xylanases are structurally similar to cellulases but differ in their specificity for xylose-based, versus glucose-based, substrates.Results: The structure of the family 11 xylanase, Xyl11, from Bacillus agaradhaerens has been solved using X-ray crystallography in both native and xylobiosyl-enzyme intermediate forms at 1.78 Angstrom and 2.0 Angstrom resolution, respectively The covalent glycosyl-enzyme intermediate has been trapped using a 2-fluoro-2-deoxy substrate with a good leaving group. Unlike covalent intermediate structures for glycoside hydrolases from other families, the covalent glycosyl-enzyme intermediate in family 11 adopts an unusual B-2,B-5 conformation.Conclusions: The 2,5B conformation found for the a-linked xylobiosyl-enzyme intermediate of Xyl11, unlike the C-4(1) chair conformation observed for other systems, is consistent with the stereochemical constraints required of the oxocarbenium-ion-like transition state. Comparison of the Xyl11 covalent glycosyl-enzyme intermediate with the equivalent structure for the related family 12 endoglucanase, CelB, from Streptomyces lividans reveals the likely determinants for substrate specificity in this dan of glycoside hydrolases.",

keywords = "boat conformation, enzyme specificity, transition state, xylanase, ACID-SEQUENCE SIMILARITIES, X-RAY STRUCTURE, ACTIVE-SITE, MACROMOLECULAR STRUCTURES, MOLECULAR REPLACEMENT, ANGSTROM RESOLUTION, FUSARIUM-OXYSPORUM, CRYSTAL-STRUCTURES, ENDOGLUCANASE-I, LEAVING GROUP",

author = "E Sabini and G Sulzenbacher and M Dauter and Z Dauter and Jorgensen, {P L} and M Schulein and C Dupont and Davies, {G J} and Wilson, {K S}",

year = "1999",

month = jul,

language = "English",

volume = "6",

pages = "483--492",

journal = "Chemistry & Biology",

issn = "1074-5521",

publisher = "Elsevier",

number = "7",

}

Catalysis and specificity in enzymatic glycoside hydrolysis: a B-2,B-5 conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase. / Sabini, E ; Sulzenbacher, G ; Dauter, M et al.
In: Chemistry & Biology, Vol. 6, No. 7, 07.1999, p. 483-492.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Catalysis and specificity in enzymatic glycoside hydrolysis: a B-2,B-5 conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase

AU - Sabini, E

AU - Sulzenbacher, G

AU - Dauter, M

AU - Dauter, Z

AU - Jorgensen, P L

AU - Schulein, M

AU - Dupont, C

AU - Davies, G J

AU - Wilson, K S

PY - 1999/7

Y1 - 1999/7

N2 - Background: The enzymatic hydrolysis of glycosides involves the formation and subsequent breakdown of a covalent glycosyl-enzyme intermediate via oxocarbenium-ion-like transition states. The covalent intermediate may be trapped on-enzyme using 2-fluoro-substituted glycosides, which provide details of the intermediate conformation and noncovalent interactions between enzyme and oligosaccharide. Xylanases are important in industrial applications - in the pulp and paper industry, pretreating wood with xylanases decreases the amount of chlorine-containing chemicals used. Xylanases are structurally similar to cellulases but differ in their specificity for xylose-based, versus glucose-based, substrates.Results: The structure of the family 11 xylanase, Xyl11, from Bacillus agaradhaerens has been solved using X-ray crystallography in both native and xylobiosyl-enzyme intermediate forms at 1.78 Angstrom and 2.0 Angstrom resolution, respectively The covalent glycosyl-enzyme intermediate has been trapped using a 2-fluoro-2-deoxy substrate with a good leaving group. Unlike covalent intermediate structures for glycoside hydrolases from other families, the covalent glycosyl-enzyme intermediate in family 11 adopts an unusual B-2,B-5 conformation.Conclusions: The 2,5B conformation found for the a-linked xylobiosyl-enzyme intermediate of Xyl11, unlike the C-4(1) chair conformation observed for other systems, is consistent with the stereochemical constraints required of the oxocarbenium-ion-like transition state. Comparison of the Xyl11 covalent glycosyl-enzyme intermediate with the equivalent structure for the related family 12 endoglucanase, CelB, from Streptomyces lividans reveals the likely determinants for substrate specificity in this dan of glycoside hydrolases.

AB - Background: The enzymatic hydrolysis of glycosides involves the formation and subsequent breakdown of a covalent glycosyl-enzyme intermediate via oxocarbenium-ion-like transition states. The covalent intermediate may be trapped on-enzyme using 2-fluoro-substituted glycosides, which provide details of the intermediate conformation and noncovalent interactions between enzyme and oligosaccharide. Xylanases are important in industrial applications - in the pulp and paper industry, pretreating wood with xylanases decreases the amount of chlorine-containing chemicals used. Xylanases are structurally similar to cellulases but differ in their specificity for xylose-based, versus glucose-based, substrates.Results: The structure of the family 11 xylanase, Xyl11, from Bacillus agaradhaerens has been solved using X-ray crystallography in both native and xylobiosyl-enzyme intermediate forms at 1.78 Angstrom and 2.0 Angstrom resolution, respectively The covalent glycosyl-enzyme intermediate has been trapped using a 2-fluoro-2-deoxy substrate with a good leaving group. Unlike covalent intermediate structures for glycoside hydrolases from other families, the covalent glycosyl-enzyme intermediate in family 11 adopts an unusual B-2,B-5 conformation.Conclusions: The 2,5B conformation found for the a-linked xylobiosyl-enzyme intermediate of Xyl11, unlike the C-4(1) chair conformation observed for other systems, is consistent with the stereochemical constraints required of the oxocarbenium-ion-like transition state. Comparison of the Xyl11 covalent glycosyl-enzyme intermediate with the equivalent structure for the related family 12 endoglucanase, CelB, from Streptomyces lividans reveals the likely determinants for substrate specificity in this dan of glycoside hydrolases.

KW - boat conformation

KW - enzyme specificity

KW - transition state

KW - xylanase

KW - ACID-SEQUENCE SIMILARITIES

KW - X-RAY STRUCTURE

KW - ACTIVE-SITE

KW - MACROMOLECULAR STRUCTURES

KW - MOLECULAR REPLACEMENT

KW - ANGSTROM RESOLUTION

KW - FUSARIUM-OXYSPORUM

KW - CRYSTAL-STRUCTURES

KW - ENDOGLUCANASE-I

KW - LEAVING GROUP

M3 - Article

SN - 1074-5521

VL - 6

SP - 483

EP - 492

JO - Chemistry & Biology

JF - Chemistry & Biology

IS - 7

ER -