At the periphery of the amidohydrolase superfamily

Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate

Tinh T. Nguyen, Shoshana Brown, Alexander A. Fedorov, Elena V. Fedorov, Patricia C. Babbitt, Steven C. Almo, Frank M. Raushel

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

The amidohydrolase superfamily is a functionally diverse set of enzymes that catalyzes predominantly hydrolysis reactions involving sugars, nucleic acids, amino acids, and organophosphate esters. One of the most divergent members of this superfamily, uronate isomerase from Escherichia coli, catalyzes the isomerization of D-glucuronate to D-fructuronate and D-galacturonate to D-tagaturonate and is the only uronate isomerase in this organism. A gene encoding a putative uronate isomerase in Bacillus halodurans (Bh0705) was identified based on sequence similarity to uronate isomerases from other organisms. Kinetic evidence indicates that Bh0705 is relatively specific for the isomerization of D-glucuronate to D-fructuronate, confirming this functional assignment. Despite a low sequence identity to all other characterized uronate isomerases, phylogenetic and network-based analysis suggests that a second gene in this organism, Bh0493, is also a uronate isomerase, although it is an outlier in the group, with <20% sequence identity to any other characterized uronate isomerase from another species. The elucidation of the X-ray structure at a resolution of 2.0 Å confirms that Bh0493 is a member of the amidohydrolase superfamily with conserved residues common to other members of the uronate isomerase family. Functional characterization of this protein shows that unlike Bh0705, Bh0493 can utilize both D-glucuronate and D-galacturonate as substrates. In B. halodurans, Bh0705 is found in an operon for the metabolism of D-glucuronate, whereas Bh0493 is in an operon for the metabolism of D-galacturonate. These results provide the first identification of a uronate isomerase that operates in a pathway distinct from that for D-glucuronate. While most organisms that contain this pathway have only one gene for a uronate isomerase, sequence analysis and operon context show that five other organisms also appear to have two genes and one organism appears to have three genes for this activity.

Original languageEnglish (US)
Pages (from-to)1194-1206
Number of pages13
JournalBiochemistry
Volume47
Issue number4
DOIs
StatePublished - Jan 29 2008

Fingerprint

Amidohydrolases
Isomerases
Bacilli
Isomerization
Bacillus
Glucuronic Acid
Operon
Genes
Metabolism
Sugar Acids
Gene encoding
Organophosphates
Sugars
Escherichia coli
Nucleic Acids
Sequence Analysis
Hydrolysis
Esters

ASJC Scopus subject areas

  • Biochemistry

Cite this

At the periphery of the amidohydrolase superfamily : Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate. / Nguyen, Tinh T.; Brown, Shoshana; Fedorov, Alexander A.; Fedorov, Elena V.; Babbitt, Patricia C.; Almo, Steven C.; Raushel, Frank M.

In: Biochemistry, Vol. 47, No. 4, 29.01.2008, p. 1194-1206.

Research output: Contribution to journalArticle

Nguyen, Tinh T. ; Brown, Shoshana ; Fedorov, Alexander A. ; Fedorov, Elena V. ; Babbitt, Patricia C. ; Almo, Steven C. ; Raushel, Frank M. / At the periphery of the amidohydrolase superfamily : Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate. In: Biochemistry. 2008 ; Vol. 47, No. 4. pp. 1194-1206.
@article{87c9e8fb5b5449da87a463b806c0e59c,
title = "At the periphery of the amidohydrolase superfamily: Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate",
abstract = "The amidohydrolase superfamily is a functionally diverse set of enzymes that catalyzes predominantly hydrolysis reactions involving sugars, nucleic acids, amino acids, and organophosphate esters. One of the most divergent members of this superfamily, uronate isomerase from Escherichia coli, catalyzes the isomerization of D-glucuronate to D-fructuronate and D-galacturonate to D-tagaturonate and is the only uronate isomerase in this organism. A gene encoding a putative uronate isomerase in Bacillus halodurans (Bh0705) was identified based on sequence similarity to uronate isomerases from other organisms. Kinetic evidence indicates that Bh0705 is relatively specific for the isomerization of D-glucuronate to D-fructuronate, confirming this functional assignment. Despite a low sequence identity to all other characterized uronate isomerases, phylogenetic and network-based analysis suggests that a second gene in this organism, Bh0493, is also a uronate isomerase, although it is an outlier in the group, with <20{\%} sequence identity to any other characterized uronate isomerase from another species. The elucidation of the X-ray structure at a resolution of 2.0 {\AA} confirms that Bh0493 is a member of the amidohydrolase superfamily with conserved residues common to other members of the uronate isomerase family. Functional characterization of this protein shows that unlike Bh0705, Bh0493 can utilize both D-glucuronate and D-galacturonate as substrates. In B. halodurans, Bh0705 is found in an operon for the metabolism of D-glucuronate, whereas Bh0493 is in an operon for the metabolism of D-galacturonate. These results provide the first identification of a uronate isomerase that operates in a pathway distinct from that for D-glucuronate. While most organisms that contain this pathway have only one gene for a uronate isomerase, sequence analysis and operon context show that five other organisms also appear to have two genes and one organism appears to have three genes for this activity.",
author = "Nguyen, {Tinh T.} and Shoshana Brown and Fedorov, {Alexander A.} and Fedorov, {Elena V.} and Babbitt, {Patricia C.} and Almo, {Steven C.} and Raushel, {Frank M.}",
year = "2008",
month = "1",
day = "29",
doi = "10.1021/bi7017738",
language = "English (US)",
volume = "47",
pages = "1194--1206",
journal = "Biochemistry",
issn = "0006-2960",
publisher = "American Chemical Society",
number = "4",

}

TY - JOUR

T1 - At the periphery of the amidohydrolase superfamily

T2 - Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate

AU - Nguyen, Tinh T.

AU - Brown, Shoshana

AU - Fedorov, Alexander A.

AU - Fedorov, Elena V.

AU - Babbitt, Patricia C.

AU - Almo, Steven C.

AU - Raushel, Frank M.

PY - 2008/1/29

Y1 - 2008/1/29

N2 - The amidohydrolase superfamily is a functionally diverse set of enzymes that catalyzes predominantly hydrolysis reactions involving sugars, nucleic acids, amino acids, and organophosphate esters. One of the most divergent members of this superfamily, uronate isomerase from Escherichia coli, catalyzes the isomerization of D-glucuronate to D-fructuronate and D-galacturonate to D-tagaturonate and is the only uronate isomerase in this organism. A gene encoding a putative uronate isomerase in Bacillus halodurans (Bh0705) was identified based on sequence similarity to uronate isomerases from other organisms. Kinetic evidence indicates that Bh0705 is relatively specific for the isomerization of D-glucuronate to D-fructuronate, confirming this functional assignment. Despite a low sequence identity to all other characterized uronate isomerases, phylogenetic and network-based analysis suggests that a second gene in this organism, Bh0493, is also a uronate isomerase, although it is an outlier in the group, with <20% sequence identity to any other characterized uronate isomerase from another species. The elucidation of the X-ray structure at a resolution of 2.0 Å confirms that Bh0493 is a member of the amidohydrolase superfamily with conserved residues common to other members of the uronate isomerase family. Functional characterization of this protein shows that unlike Bh0705, Bh0493 can utilize both D-glucuronate and D-galacturonate as substrates. In B. halodurans, Bh0705 is found in an operon for the metabolism of D-glucuronate, whereas Bh0493 is in an operon for the metabolism of D-galacturonate. These results provide the first identification of a uronate isomerase that operates in a pathway distinct from that for D-glucuronate. While most organisms that contain this pathway have only one gene for a uronate isomerase, sequence analysis and operon context show that five other organisms also appear to have two genes and one organism appears to have three genes for this activity.

AB - The amidohydrolase superfamily is a functionally diverse set of enzymes that catalyzes predominantly hydrolysis reactions involving sugars, nucleic acids, amino acids, and organophosphate esters. One of the most divergent members of this superfamily, uronate isomerase from Escherichia coli, catalyzes the isomerization of D-glucuronate to D-fructuronate and D-galacturonate to D-tagaturonate and is the only uronate isomerase in this organism. A gene encoding a putative uronate isomerase in Bacillus halodurans (Bh0705) was identified based on sequence similarity to uronate isomerases from other organisms. Kinetic evidence indicates that Bh0705 is relatively specific for the isomerization of D-glucuronate to D-fructuronate, confirming this functional assignment. Despite a low sequence identity to all other characterized uronate isomerases, phylogenetic and network-based analysis suggests that a second gene in this organism, Bh0493, is also a uronate isomerase, although it is an outlier in the group, with <20% sequence identity to any other characterized uronate isomerase from another species. The elucidation of the X-ray structure at a resolution of 2.0 Å confirms that Bh0493 is a member of the amidohydrolase superfamily with conserved residues common to other members of the uronate isomerase family. Functional characterization of this protein shows that unlike Bh0705, Bh0493 can utilize both D-glucuronate and D-galacturonate as substrates. In B. halodurans, Bh0705 is found in an operon for the metabolism of D-glucuronate, whereas Bh0493 is in an operon for the metabolism of D-galacturonate. These results provide the first identification of a uronate isomerase that operates in a pathway distinct from that for D-glucuronate. While most organisms that contain this pathway have only one gene for a uronate isomerase, sequence analysis and operon context show that five other organisms also appear to have two genes and one organism appears to have three genes for this activity.

UR - http://www.scopus.com/inward/record.url?scp=38549133831&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=38549133831&partnerID=8YFLogxK

U2 - 10.1021/bi7017738

DO - 10.1021/bi7017738

M3 - Article

VL - 47

SP - 1194

EP - 1206

JO - Biochemistry

JF - Biochemistry

SN - 0006-2960

IS - 4

ER -