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Title: Structural Analysis of a Ternary Complex of Allantoate Amidohydrolase from Escherichia Coli Reveals its Mechanics

Abstract

Purine metabolism plays a major role in regulating the availability of purine nucleotides destined for nucleic acid synthesis. Allantoate amidohydrolase catalyzes the conversion of allantoate to (S)-ureidoglycolate, one of the crucial alternate steps in purine metabolism. The crystal structure of a ternary complex of allantoate amidohydrolase with its substrate allantoate and an allosteric effector, a sulfate ion, from Escherichia coli was determined to understand better the catalytic mechanism and substrate specificity. The 2.25 {angstrom} resolution X-ray structure reveals an {alpha}/{beta} scaffold akin to zinc exopeptidases of the peptidase M20 family and lacks the ({beta}/{alpha}){sub 8}-barrel fold characteristic of the amidohydrolases. Arrangement of the substrate and the two co-catalytic zinc ions at the active site governs catalytic specificity for hydrolysis of N-carbamyl versus the peptide bond in exopeptidases. In its crystalline form, allantoate amidohydrolase adopts a relatively open conformation. However, structural analysis reveals the possibility of a significant movement of domains via rotation about two hinge regions upon allosteric effector and substrate binding resulting in a closed catalytically competent conformation by bringing the substrate allantoate closer to co-catalytic zinc ions. Two cis-prolyl peptide bonds found on either side of the dimerization domain in close proximity to the substrate and ligand-binding sitesmore » may be involved in protein folding and in preserving the integrity of the catalytic site.« less

Authors:
; ;
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL) National Synchrotron Light Source
Sponsoring Org.:
Doe - Office Of Science
OSTI Identifier:
930384
Report Number(s):
BNL-81106-2008-JA
Journal ID: ISSN 0022-2836; JMOBAK; TRN: US200904%%667
DOE Contract Number:
DE-AC02-98CH10886
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Molecular Biology; Journal Volume: 368; Journal Issue: 2
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; AVAILABILITY; CRYSTAL STRUCTURE; DIMERIZATION; ESCHERICHIA COLI; HYDROLYSIS; METABOLISM; NUCLEIC ACIDS; NUCLEOTIDES; PEPTIDES; PROTEINS; PURINES; RESOLUTION; ROTATION; SPECIFICITY; SUBSTRATES; SULFATES; SYNTHESIS; ZINC; ZINC IONS; national synchrotron light source

Citation Formats

Agarwal,R., Burley, S., and Swaminathan, S. Structural Analysis of a Ternary Complex of Allantoate Amidohydrolase from Escherichia Coli Reveals its Mechanics. United States: N. p., 2007. Web. doi:10.1016/j.jmb.2007.02.028.
Agarwal,R., Burley, S., & Swaminathan, S. Structural Analysis of a Ternary Complex of Allantoate Amidohydrolase from Escherichia Coli Reveals its Mechanics. United States. doi:10.1016/j.jmb.2007.02.028.
Agarwal,R., Burley, S., and Swaminathan, S. Mon . "Structural Analysis of a Ternary Complex of Allantoate Amidohydrolase from Escherichia Coli Reveals its Mechanics". United States. doi:10.1016/j.jmb.2007.02.028.
@article{osti_930384,
title = {Structural Analysis of a Ternary Complex of Allantoate Amidohydrolase from Escherichia Coli Reveals its Mechanics},
author = {Agarwal,R. and Burley, S. and Swaminathan, S.},
abstractNote = {Purine metabolism plays a major role in regulating the availability of purine nucleotides destined for nucleic acid synthesis. Allantoate amidohydrolase catalyzes the conversion of allantoate to (S)-ureidoglycolate, one of the crucial alternate steps in purine metabolism. The crystal structure of a ternary complex of allantoate amidohydrolase with its substrate allantoate and an allosteric effector, a sulfate ion, from Escherichia coli was determined to understand better the catalytic mechanism and substrate specificity. The 2.25 {angstrom} resolution X-ray structure reveals an {alpha}/{beta} scaffold akin to zinc exopeptidases of the peptidase M20 family and lacks the ({beta}/{alpha}){sub 8}-barrel fold characteristic of the amidohydrolases. Arrangement of the substrate and the two co-catalytic zinc ions at the active site governs catalytic specificity for hydrolysis of N-carbamyl versus the peptide bond in exopeptidases. In its crystalline form, allantoate amidohydrolase adopts a relatively open conformation. However, structural analysis reveals the possibility of a significant movement of domains via rotation about two hinge regions upon allosteric effector and substrate binding resulting in a closed catalytically competent conformation by bringing the substrate allantoate closer to co-catalytic zinc ions. Two cis-prolyl peptide bonds found on either side of the dimerization domain in close proximity to the substrate and ligand-binding sites may be involved in protein folding and in preserving the integrity of the catalytic site.},
doi = {10.1016/j.jmb.2007.02.028},
journal = {Journal of Molecular Biology},
number = 2,
volume = 368,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2007},
month = {Mon Jan 01 00:00:00 EST 2007}
}