Toward a structural understanding of the dehydratase mechanism

Simon T.M. Allard; Konstantinos Beis; Marie France Giraud; Adrian D. Hegeman; Jeffrey W. Gross; Rupert C. Wilmouth; Chris Whitfield; Michael Graninger; Paul Messner; Andrew G. Allen; Duncan J. Maskell; James H. Naismith

doi:10.1016/S0969-2126(01)00694-3

Toward a structural understanding of the dehydratase mechanism

Simon T.M. Allard, Konstantinos Beis, Marie France Giraud, Adrian D. Hegeman, Jeffrey W. Gross, Rupert C. Wilmouth, Chris Whitfield, Michael Graninger, Paul Messner, Andrew G. Allen, Duncan J. Maskell, James H. Naismith

Horticultural Science

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Abstract

dTDP-D-glucose 4,6-dehydratase (RmlB) was first identified in the L-rhamnose biosynthetic pathway, where it catalyzes the conversion of dTDP-D-glucose into dTDP-4-keto-6-deoxy-D-glucose. The structures of RmlB from Salmonella enterica serovar Typhimurium in complex with substrate deoxythymidine 5′-diphospho-D-glucose (dTDP-D-glucose) and deoxythymidine 5′-diphosphate (dTDP), and RmlB from Streptococcus suis serotype 2 in complex with dTDP-D-glucose, dTDP, and deoxythymidine 5′-diphospho-D-pyrano-xylose (dTDP-xylose) have all been solved at resolutions between 1.8 Å and 2.4 Å. The structures show that the active sites are highly conserved. Importantly, the structures show that the active site tyrosine functions directly as the active site base, and an aspartic and glutamic acid pairing accomplishes the dehydration step of the enzyme mechanism. We conclude that the substrate is required to move within the active site to complete the catalytic cycle and that this movement is driven by the elimination of water. The results provide insight into members of the SDR superfamily.

Original language	English (US)
Pages (from-to)	81-92
Number of pages	12
Journal	Structure
Volume	10
Issue number	1
DOIs	https://doi.org/10.1016/S0969-2126(01)00694-3
State	Published - 2002

Bibliographical note

Funding Information:
This project is supported by a grant from the Wellcome trust (J.H.N., 056851), a Wellcome Trust International Travel grant (J.H.N. and C.W.), and funding from the Natural Sciences and Engineering Research Council of Canada (C.W.). J.H.N. is a BBSRC career development fellow, C.W. is the recipient of a Canadian Research Chair, and A.G.A. is a Wellcome Research Career Development Fellow. The use of beamlines 9.6 at the CCLRC Daresbury Laboratory, UK and 14.2 at the ESRF, Grenoble is gratefully acknowledged. We are grateful to H.M. Holden, W.W. Cleland, and P.A. Frey for useful discussions.

Keywords

Crystallography
Dehydratase
L-rhamnose
Mechanism
RmlB
dTDP-D-glucose 4,6-dehydratase

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@article{c4e1fca7d8bd4020b7fa737e775c062c,

title = "Toward a structural understanding of the dehydratase mechanism",

abstract = "dTDP-D-glucose 4,6-dehydratase (RmlB) was first identified in the L-rhamnose biosynthetic pathway, where it catalyzes the conversion of dTDP-D-glucose into dTDP-4-keto-6-deoxy-D-glucose. The structures of RmlB from Salmonella enterica serovar Typhimurium in complex with substrate deoxythymidine 5′-diphospho-D-glucose (dTDP-D-glucose) and deoxythymidine 5′-diphosphate (dTDP), and RmlB from Streptococcus suis serotype 2 in complex with dTDP-D-glucose, dTDP, and deoxythymidine 5′-diphospho-D-pyrano-xylose (dTDP-xylose) have all been solved at resolutions between 1.8 {\AA} and 2.4 {\AA}. The structures show that the active sites are highly conserved. Importantly, the structures show that the active site tyrosine functions directly as the active site base, and an aspartic and glutamic acid pairing accomplishes the dehydration step of the enzyme mechanism. We conclude that the substrate is required to move within the active site to complete the catalytic cycle and that this movement is driven by the elimination of water. The results provide insight into members of the SDR superfamily.",

keywords = "Crystallography, Dehydratase, L-rhamnose, Mechanism, RmlB, dTDP-D-glucose 4,6-dehydratase",

author = "Allard, {Simon T.M.} and Konstantinos Beis and Giraud, {Marie France} and Hegeman, {Adrian D.} and Gross, {Jeffrey W.} and Wilmouth, {Rupert C.} and Chris Whitfield and Michael Graninger and Paul Messner and Allen, {Andrew G.} and Maskell, {Duncan J.} and Naismith, {James H.}",

note = "Funding Information: This project is supported by a grant from the Wellcome trust (J.H.N., 056851), a Wellcome Trust International Travel grant (J.H.N. and C.W.), and funding from the Natural Sciences and Engineering Research Council of Canada (C.W.). J.H.N. is a BBSRC career development fellow, C.W. is the recipient of a Canadian Research Chair, and A.G.A. is a Wellcome Research Career Development Fellow. The use of beamlines 9.6 at the CCLRC Daresbury Laboratory, UK and 14.2 at the ESRF, Grenoble is gratefully acknowledged. We are grateful to H.M. Holden, W.W. Cleland, and P.A. Frey for useful discussions. ",

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doi = "10.1016/S0969-2126(01)00694-3",

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AU - Allard, Simon T.M.

AU - Beis, Konstantinos

AU - Giraud, Marie France

AU - Hegeman, Adrian D.

AU - Gross, Jeffrey W.

AU - Wilmouth, Rupert C.

AU - Whitfield, Chris

AU - Graninger, Michael

AU - Messner, Paul

AU - Allen, Andrew G.

AU - Maskell, Duncan J.

AU - Naismith, James H.

N1 - Funding Information: This project is supported by a grant from the Wellcome trust (J.H.N., 056851), a Wellcome Trust International Travel grant (J.H.N. and C.W.), and funding from the Natural Sciences and Engineering Research Council of Canada (C.W.). J.H.N. is a BBSRC career development fellow, C.W. is the recipient of a Canadian Research Chair, and A.G.A. is a Wellcome Research Career Development Fellow. The use of beamlines 9.6 at the CCLRC Daresbury Laboratory, UK and 14.2 at the ESRF, Grenoble is gratefully acknowledged. We are grateful to H.M. Holden, W.W. Cleland, and P.A. Frey for useful discussions.

PY - 2002

Y1 - 2002

N2 - dTDP-D-glucose 4,6-dehydratase (RmlB) was first identified in the L-rhamnose biosynthetic pathway, where it catalyzes the conversion of dTDP-D-glucose into dTDP-4-keto-6-deoxy-D-glucose. The structures of RmlB from Salmonella enterica serovar Typhimurium in complex with substrate deoxythymidine 5′-diphospho-D-glucose (dTDP-D-glucose) and deoxythymidine 5′-diphosphate (dTDP), and RmlB from Streptococcus suis serotype 2 in complex with dTDP-D-glucose, dTDP, and deoxythymidine 5′-diphospho-D-pyrano-xylose (dTDP-xylose) have all been solved at resolutions between 1.8 Å and 2.4 Å. The structures show that the active sites are highly conserved. Importantly, the structures show that the active site tyrosine functions directly as the active site base, and an aspartic and glutamic acid pairing accomplishes the dehydration step of the enzyme mechanism. We conclude that the substrate is required to move within the active site to complete the catalytic cycle and that this movement is driven by the elimination of water. The results provide insight into members of the SDR superfamily.

AB - dTDP-D-glucose 4,6-dehydratase (RmlB) was first identified in the L-rhamnose biosynthetic pathway, where it catalyzes the conversion of dTDP-D-glucose into dTDP-4-keto-6-deoxy-D-glucose. The structures of RmlB from Salmonella enterica serovar Typhimurium in complex with substrate deoxythymidine 5′-diphospho-D-glucose (dTDP-D-glucose) and deoxythymidine 5′-diphosphate (dTDP), and RmlB from Streptococcus suis serotype 2 in complex with dTDP-D-glucose, dTDP, and deoxythymidine 5′-diphospho-D-pyrano-xylose (dTDP-xylose) have all been solved at resolutions between 1.8 Å and 2.4 Å. The structures show that the active sites are highly conserved. Importantly, the structures show that the active site tyrosine functions directly as the active site base, and an aspartic and glutamic acid pairing accomplishes the dehydration step of the enzyme mechanism. We conclude that the substrate is required to move within the active site to complete the catalytic cycle and that this movement is driven by the elimination of water. The results provide insight into members of the SDR superfamily.

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KW - Mechanism

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Toward a structural understanding of the dehydratase mechanism

Abstract

Bibliographical note

Keywords

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