skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Structure of a Novel N-acetyl-L-citrulline Deacetylase from Xanthomonas campestris

Abstract

The structure of a novel acetylcitrulline deacetylase from the plant pathogen Xanthomonas campestris has been solved by multiple-wavelength anomalous dispersion (MAD) using crystals grown from selenomethionine-substituted protein and refined at 1.75 {angstrom} resolution. The asymmetric unit of the crystal contains one monomer consisting of two domains, a catalytic domain and a dimerization domain. The catalytic domain is able to bind a single Co(II) ion at the active site with no change in confirmation. the dimerization domain forms an interface between two monomers related by a crystallographic two-fold symmetry axis. The interface is maintained by hydrophobic interactions between helices and hydrogen bonding between two {beta} strands that form a continuous {beta} sheet across the dimer interface. Because the dimers are also related by two-fold crystallographic axes, they pack together across the crystal via the dimerization domain, suggesting that higher order oligomers may form in solution. The polypeptide fold of the monomer is similar to the fold of Pseudomonas sp. carboxypeptidase G2 and Neisseria meningitidis succinyl diaminopimelate desuccinylase. Structural comparison among these enzymes allowed modeling of substrate binding and suggests a possible catalytic mechanism, in which Glu130 functions as a bifunctional general acid-base catalyst and the metal ion polarizes the carbonyl ofmore » the acetyl group.« less

Authors:
; ; ; ;
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL) National Synchrotron Light Source
Sponsoring Org.:
Doe - Office Of Science
OSTI Identifier:
930367
Report Number(s):
BNL-81087-2008-JA
Journal ID: ISSN 0301-4622; BICIAZ; TRN: US200904%%655
DOE Contract Number:
DE-AC02-98CH10886
Resource Type:
Journal Article
Resource Relation:
Journal Name: Biophysical Chemistry; Journal Volume: 126
Country of Publication:
United States
Language:
English
Subject:
08 HYDROGEN; 36 MATERIALS SCIENCE; CARBONYLS; CARBOXYPEPTIDASES; CATALYSTS; CRYSTAL STRUCTURE; DIMERIZATION; DIMERS; ENZYMES; HYDROGEN; MONOMERS; PATHOGENS; POLYPEPTIDES; PROTEINS; PSEUDOMONAS; RESOLUTION; SIMULATION; SUBSTRATES; SYMMETRY; national synchrotron light source

Citation Formats

Shi,D., Yu, X., Roth, L., Tuchman, M., and Allewell, N. Structure of a Novel N-acetyl-L-citrulline Deacetylase from Xanthomonas campestris. United States: N. p., 2007. Web. doi:10.1016/j.bpc.2006.05.013.
Shi,D., Yu, X., Roth, L., Tuchman, M., & Allewell, N. Structure of a Novel N-acetyl-L-citrulline Deacetylase from Xanthomonas campestris. United States. doi:10.1016/j.bpc.2006.05.013.
Shi,D., Yu, X., Roth, L., Tuchman, M., and Allewell, N. Mon . "Structure of a Novel N-acetyl-L-citrulline Deacetylase from Xanthomonas campestris". United States. doi:10.1016/j.bpc.2006.05.013.
@article{osti_930367,
title = {Structure of a Novel N-acetyl-L-citrulline Deacetylase from Xanthomonas campestris},
author = {Shi,D. and Yu, X. and Roth, L. and Tuchman, M. and Allewell, N.},
abstractNote = {The structure of a novel acetylcitrulline deacetylase from the plant pathogen Xanthomonas campestris has been solved by multiple-wavelength anomalous dispersion (MAD) using crystals grown from selenomethionine-substituted protein and refined at 1.75 {angstrom} resolution. The asymmetric unit of the crystal contains one monomer consisting of two domains, a catalytic domain and a dimerization domain. The catalytic domain is able to bind a single Co(II) ion at the active site with no change in confirmation. the dimerization domain forms an interface between two monomers related by a crystallographic two-fold symmetry axis. The interface is maintained by hydrophobic interactions between helices and hydrogen bonding between two {beta} strands that form a continuous {beta} sheet across the dimer interface. Because the dimers are also related by two-fold crystallographic axes, they pack together across the crystal via the dimerization domain, suggesting that higher order oligomers may form in solution. The polypeptide fold of the monomer is similar to the fold of Pseudomonas sp. carboxypeptidase G2 and Neisseria meningitidis succinyl diaminopimelate desuccinylase. Structural comparison among these enzymes allowed modeling of substrate binding and suggests a possible catalytic mechanism, in which Glu130 functions as a bifunctional general acid-base catalyst and the metal ion polarizes the carbonyl of the acetyl group.},
doi = {10.1016/j.bpc.2006.05.013},
journal = {Biophysical Chemistry},
number = ,
volume = 126,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2007},
month = {Mon Jan 01 00:00:00 EST 2007}
}
  • A novel N-acetyl-{sub L}-citrulline deacetylase that is able to catalyze the hydrolysis of N-acetyl-l-citrulline to acetate and citrulline was identified from Xanthomonas campestris. The protein was overexpressed, purified and crystallized. The crystals belong to the monoclinic space group C2 and diffract to 1.75 Angstrom resolution, with unit-cell parameters a = 94.13, b = 95.23, c = 43.61 Angstroms, {beta} = 93.76. Since attempts to use homologous structural models to solve the structure via molecular replacement were unsuccessful, the selenomethionine-substituted protein was prepared using an overnight auto-induction overexpression system. Selenomethionine incorporation into the protein was verified by MALDI-TOF/TOF mass-spectroscopic analysis aftermore » trypsin digestion. The crystals of the selenomethionine-substituted protein were prepared using crystallization conditions similar to those for the native protein. Multiple anomalous dispersion (MAD) data were collected at Brookhaven National Laboratory. Structure determination is under way using the MAD phasing method.« less
  • The expression, purification and preliminary X-ray diffraction studies of a novel N-acetyl-l-citrulline deacetylase from X. campestris are reported. A novel N-acetyl-l-citrulline deacetylase that is able to catalyze the hydrolysis of N-acetyl-l-citrulline to acetate and citrulline was identified from Xanthomonas campestris. The protein was overexpressed, purified and crystallized. The crystals belong to the monoclinic space group C2 and diffract to 1.75 Å resolution, with unit-cell parameters a = 94.13, b = 95.23, c = 43.61 Å, β = 93.76°. Since attempts to use homologous structural models to solve the structure via molecular replacement were unsuccessful, the selenomethionine-substituted protein was prepared usingmore » an overnight auto-induction overexpression system. Selenomethionine incorporation into the protein was verified by MALDI–TOF/TOF mass-spectroscopic analysis after trypsin digestion. The crystals of the selenomethionine-substituted protein were prepared using crystallization conditions similar to those for the native protein. Multiple anomalous dispersion (MAD) data were collected at Brookhaven National Laboratory. Structure determination is under way using the MAD phasing method.« less
  • Expression, crystallization and preliminary X-ray diffraction studies of a novel bifunctional N-acetylglutamate synthase/kinase from X. campestris homologous to vertebrate N-acetylglutamate synthase are reported. A novel N-acetylglutamate synthase/kinase bifunctional enzyme of arginine biosynthesis that was homologous to vertebrate N-acetylglutamate synthases was identified in Xanthomonas campestris. The protein was overexpressed, purified and crystallized. The crystals belong to the hexagonal space group P6{sub 2}22, with unit-cell parameters a = b = 134.60, c = 192.11 Å, and diffract to about 3.0 Å resolution. Selenomethionine-substituted recombinant protein was produced and selenomethionine substitution was verified by mass spectroscopy. Multiple anomalous dispersion (MAD) data were collectedmore » at three wavelengths at SER-CAT, Advanced Photon Source, Argonne National Laboratory. Structure determination is under way using the MAD phasing method.« less
  • Many members of the mechanistically diverse enolase superfamily have unknown functions. In this report the authors use both genome (operon) context and screening of a library of acid sugars to assign the L-fuconate dehydratase (FucD) function to a member of the mandelate racemase (MR) subgroup of the superfamily encoded by the Xanthomonas campestris pv. campestris str. ATCC 33913 genome (GI: 21233491). Orthologues of FucD are found in both bacteria and eukaryotes, the latter including the rTS beta protein in Homo sapiens that has been implicated in regulating thymidylate synthase activity. As suggested by sequence alignments and confirmed by high-resolution structuresmore » in the presence of active site ligands, FucD and MR share the same active site motif of functional groups: three carboxylate ligands for the essential Mg2+ located at the ends of th third, fourth, and fifth-strands in the (/)7-barrel domain (Asp 248, Glu 274, and Glu 301, respectively), a Lys-x-Lys motif at the end of the second-strand (Lys 218 and Lys 220), a His-Asp dyad at the end of the seventh and sixth-strands (His 351 and Asp 324, respectively), and a Glue at the end of the eighth-strand (Glu 382). The mechanism of the FucD reaction involves initial abstraction of the 2-proton by Lys 220, acid catalysis of the vinylogous-elimination of the 3-OH group by His 351, and stereospecific ketonization of the resulting 2-keto-3-deoxy-L-fuconate product. Screening of the library of acid sugars revealed substrate and functional promiscuity: In addition to L-fuconate, FucD also catalyzes the dehydration of L-galactonate, D-arabinonate, D-altronate, L-talonate, and D-ribonate. The dehydrations of L-fuconate, L-galactonate, and D-arabinonate are initiated by abstraction of the 2-protons by Lys 220. The dehydrations of L-talonate and D-ribonate are initiated by abstraction of the 2-protons by His 351; however, protonation of the enediolate intermediates by the conjugate acid of Lys 220 yields L-galactonate and D-arabinonate in competition with dehydration. The functional promiscuity discovered for FucD highlights possible structural mechanisms for evolution of function in the enolase superfamily.« less