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Title: Structural Analysis of Papain-Like NlpC/P60 Superfamily Enzymes with a Circularly Permuted Topology Reveals Potential Lipid Binding Sites

Abstract

NlpC/P60 superfamily papain-like enzymes play important roles in all kingdoms of life. Two members of this superfamily, LRAT-like and YaeF/YiiX-like families, were predicted to contain a catalytic domain that is circularly permuted such that the catalytic cysteine is located near the C-terminus, instead of at the N-terminus. These permuted enzymes are widespread in virus, pathogenic bacteria, and eukaryotes. We determined the crystal structure of a member of the YaeF/YiiX-like family from Bacillus cereus in complex with lysine. The structure, which adopts a ligand-induced, 'closed' conformation, confirms the circular permutation of catalytic residues. A comparative analysis of other related protein structures within the NlpC/P60 superfamily is presented. Permutated NlpC/P60 enzymes contain a similar conserved core and arrangement of catalytic residues, including a Cys/His-containing triad and an additional conserved tyrosine. More surprisingly, permuted enzymes have a hydrophobic S1 binding pocket that is distinct from previously characterized enzymes in the family, indicative of novel substrate specificity. Further analysis of a structural homolog, YiiX (PDB 2if6) identified a fatty acid in the conserved hydrophobic pocket, thus providing additional insights into possible function of these novel enzymes.

Authors:
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  1. SG
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
NIHNIGMS
OSTI Identifier:
1045033
Resource Type:
Journal Article
Journal Name:
PLoS One
Additional Journal Information:
Journal Volume: 6; Journal Issue: 7
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; BACILLUS CEREUS; BACTERIA; CARBOXYLIC ACIDS; CRYSTAL STRUCTURE; CYSTEINE; ENZYMES; LIPIDS; LYSINE; PROTEIN STRUCTURE; RESIDUES; SPECIFICITY; SUBSTRATES; TOPOLOGY; TYROSINE

Citation Formats

Xu, Qingping, Rawlings, Neil D, Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Elsliger, Marc-Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, and Wellcome). Structural Analysis of Papain-Like NlpC/P60 Superfamily Enzymes with a Circularly Permuted Topology Reveals Potential Lipid Binding Sites. United States: N. p., 2012. Web. doi:10.1371/journal.pone.0022013.
Xu, Qingping, Rawlings, Neil D, Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Elsliger, Marc-Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, & Wellcome). Structural Analysis of Papain-Like NlpC/P60 Superfamily Enzymes with a Circularly Permuted Topology Reveals Potential Lipid Binding Sites. United States. doi:10.1371/journal.pone.0022013.
Xu, Qingping, Rawlings, Neil D, Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Elsliger, Marc-Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, and Wellcome). Wed . "Structural Analysis of Papain-Like NlpC/P60 Superfamily Enzymes with a Circularly Permuted Topology Reveals Potential Lipid Binding Sites". United States. doi:10.1371/journal.pone.0022013.
@article{osti_1045033,
title = {Structural Analysis of Papain-Like NlpC/P60 Superfamily Enzymes with a Circularly Permuted Topology Reveals Potential Lipid Binding Sites},
author = {Xu, Qingping and Rawlings, Neil D and Chiu, Hsiu-Ju and Jaroszewski, Lukasz and Klock, Heath E and Knuth, Mark W and Miller, Mitchell D and Elsliger, Marc-Andre and Deacon, Ashley M and Godzik, Adam and Lesley, Scott A and Wilson, Ian A and Wellcome)},
abstractNote = {NlpC/P60 superfamily papain-like enzymes play important roles in all kingdoms of life. Two members of this superfamily, LRAT-like and YaeF/YiiX-like families, were predicted to contain a catalytic domain that is circularly permuted such that the catalytic cysteine is located near the C-terminus, instead of at the N-terminus. These permuted enzymes are widespread in virus, pathogenic bacteria, and eukaryotes. We determined the crystal structure of a member of the YaeF/YiiX-like family from Bacillus cereus in complex with lysine. The structure, which adopts a ligand-induced, 'closed' conformation, confirms the circular permutation of catalytic residues. A comparative analysis of other related protein structures within the NlpC/P60 superfamily is presented. Permutated NlpC/P60 enzymes contain a similar conserved core and arrangement of catalytic residues, including a Cys/His-containing triad and an additional conserved tyrosine. More surprisingly, permuted enzymes have a hydrophobic S1 binding pocket that is distinct from previously characterized enzymes in the family, indicative of novel substrate specificity. Further analysis of a structural homolog, YiiX (PDB 2if6) identified a fatty acid in the conserved hydrophobic pocket, thus providing additional insights into possible function of these novel enzymes.},
doi = {10.1371/journal.pone.0022013},
journal = {PLoS One},
number = 7,
volume = 6,
place = {United States},
year = {2012},
month = {7}
}