Skip to main content
OSTI.GOVU.S. Department of Energy Office of Scientific and Technical Information
U.S. Department of Energy
Office of Scientific and Technical Information
 

Mechanistic insight into protein modification and sulfur mobilization activities of noncanonical E1 and associated ubiquitin-like proteins of Archaea

Journal Article · · Federation of European Biochemical Societies (FEBS) Journal
DOI:https://doi.org/10.1111/febs.13819· OSTI ID:1463111
 [1];  [2];  [3];  [3];  [3];  [3];  [3];  [4];  [4];  [4];  [2];  [3]
  1. Univ. of Florida, Gainesville, FL (United States); OSTI
  2. Scripps Research Inst., Jupiter, FL (United States)
  3. Univ. of Florida, Gainesville, FL (United States)
  4. Yale Univ., New Haven, CT (United States)
+ Show Author Affiliations
Here we provide the first detailed biochemical study of a noncanonical E1-like enzyme with broad specificity for cognate ubiquitin-like (Ubl) proteins that mediates Ubl protein modification and sulfur mobilization to form molybdopterin and thiolated tRNA. Isothermal titration calorimetry and in vivo analyses proved useful in discovering that environmental conditions, ATP binding and Ubl type controlled the mechanism of association of the Ubl protein with its cognate E1-like enzyme (SAMP and UbaA of the archaeon Haloferax volcanii, respectively). Further analysis revealed ATP hydrolysis triggered the formation of thioester and peptide bonds within the Ubl:E1-like complex. Importantly, the thioester was an apparent precursor to Ubl protein modification but not sulfur mobilization. Comparative modeling to MoeB/ThiF guided the discovery of key residues within the adenylation domain of UbaA that were needed to bind ATP as well as residues that were specifically needed to catalyze the downstream reactions of sulfur mobilization and/or Ubl protein modification. UbaA was also found to be Ubl-automodified at lysine residues required for early (ATP binding) and late (sulfur mobilization) stages of enzyme activity revealing multiple layers of auto-regulation. Cysteine residues, distinct from the canonical E1 ‘active site’ cysteine, were found important in UbaA function supporting a model that this non-canonical E1 is structurally flexible in its active site to allow Ubl~adenylate, Ubl~E1-like thioester and cysteine persulfide(s) intermediates to form.
Research Organization:
Univ. of Florida, Gainesville, FL (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
FG02-05ER15650
OSTI ID:
1463111
Alternate ID(s):
OSTI ID: 1401001
Journal Information:
Federation of European Biochemical Societies (FEBS) Journal, Journal Name: Federation of European Biochemical Societies (FEBS) Journal Journal Issue: 19 Vol. 283; ISSN 1742-464X
Publisher:
Federation of European Biochemical SocietiesCopyright Statement
Country of Publication:
United States
Language:
English

References (65)

The Lysine48-Based Polyubiquitin Chain Proteasomal Signal: Not a Single Child Anymore journal November 2012
Proteome targets of ubiquitin-like samp1ylation are associated with sulfur metabolism and oxidative stress in Haloferax volcanii journal April 2016
Crystal structure of the ubiquitin-like small archaeal modifier protein 2 from Haloferax volcanii : Structures of journal July 2013
The dual role of ubiquitin-like protein Urm1 as a protein modifier and sulfur carrier journal August 2011
Substrate properties of site-specific mutant ubiquitin protein (G76A) reveal unexpected mechanistic features of ubiquitin-activating enzyme (E1). journal March 1994
The mechanism of ubiquitin activating enzyme. A kinetic and equilibrium analysis. journal September 1982
Ubiquitin-activating enzyme. Mechanism and role in protein-ubiquitin conjugation. journal March 1982
Crystal structure of ubiquitin-like small archaeal modifier protein 1 (SAMP1) from Haloferax volcanii journal February 2011
Solution Structure and Activation Mechanism of Ubiquitin-Like Small Archaeal Modifier Proteins journal January 2011
Mechanistic Insight into Site-Restricted Monoubiquitination of FANCD2 by Ube2t, FANCL, and FANCI journal December 2008
N-terminal ubiquitination: more protein substrates join in journal March 2004
Ubiquitin-like proteins and their roles in archaea journal January 2013
Empirical Statistical Model To Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search journal October 2002
A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry journal September 2003
Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for the Analysis of Small Ubiquitin-like Modifier (SUMO) Modification:  Identification of Lysines in RanBP2 and SUMO Targeted for Modification during the E3 AutoSUMOylation Reaction journal October 2005
Ubiquitin adenylate: structure and role in ubiquitin activation journal September 1983
Biosynthesis of the Thiazole Moiety of Thiamin Pyrophosphate (Vitamin B1) † journal October 2003
Molybdenum Cofactor Biosynthesis in Humans:  Identification of a Persulfide Group in the Rhodanese-like Domain of MOCS3 by Mass Spectrometry † journal May 2005
Structure of the Escherichia coli ThiS−ThiF Complex, a Key Component of the Sulfur Transfer System in Thiamin Biosynthesis † , ‡ journal January 2006
Role of the C-Terminal Gly-Gly Motif of Escherichia Coli MoaD, a Molybdenum Cofactor Biosynthesis Protein with a Ubiquitin Fold † journal January 2007
The Sulfurtransferase Activity of Uba4 Presents a Link between Ubiquitin-like Protein Conjugation and Activation of Sulfur Carrier Proteins † journal June 2008
Identification of Sumoylation Activating Enzyme 1 Inhibitors by Structure-Based Virtual Screening journal April 2013
Mechanism of ubiquitin activation revealed by the structure of a bacterial MoeB–MoaD complex journal November 2001
Common thiolation mechanism in the biosynthesis of tRNA thiouridine and sulphur-containing cofactors journal November 2008
Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA journal January 2009
Origin and function of ubiquitin-like proteins journal March 2009
Ubiquitin-like small archaeal modifier proteins (SAMPs) in Haloferax volcanii journal January 2010
Active site remodelling accompanies thioester bond formation in the SUMO E1 journal February 2010
Co-opting sulphur-carrier proteins from primary metabolic pathways for 2-thiosugar biosynthesis journal May 2014
Involvement of a eukaryotic-like ubiquitin-related modifier in the proteasome pathway of the archaeon Sulfolobus acidocaldarius journal September 2015
The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability journal September 2007
The Phyre2 web portal for protein modeling, prediction and analysis journal May 2015
Extracellular vesicles from symbiotic vaginal lactobacilli inhibit HIV-1 infection of human tissues journal December 2019
Ubiquitin-like protein activation journal March 2004
Ionic strength-dependent conformations of a ubiquitin-like small archaeal modifier protein (SAMP2) from Haloferax volcanii journal July 2013
Evidence for the physiological role of a rhodanese-like protein for the biosynthesis of the molybdenum cofactor in humans journal April 2004
E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea journal February 2011
Differentiation of Hdm2-mediated p53 ubiquitination and Hdm2 autoubiquitination activity by small molecular weight inhibitors journal October 2002
Thiamin Biosynthesis in Escherichia coli : IDENTIFICATION OF ThiS THIOCARBOXYLATE AS THE IMMEDIATE SULFUR DONOR IN THE THIAZOLE FORMATION journal June 1998
A Protein Conjugation System in Yeast with Homology to Biosynthetic Enzyme Reaction of Prokaryotes journal March 2000
Characterization of Escherichia coli MoeB and Its Involvement in the Activation of Molybdopterin Synthase for the Biosynthesis of the Molybdenum Cofactor journal July 2001
Thiocarboxylation of Molybdopterin Synthase Provides Evidence for the Mechanism of Dithiolene Formation in Metal-binding Pterins journal July 2001
Role of the Zn 2+ Motif of E1 in SUMO Adenylation journal May 2010
UBC9 Autosumoylation Negatively Regulates Sumoylation of Septins in Saccharomyces cerevisiae journal April 2011
The Identification of a Novel Protein Involved in Molybdenum Cofactor Biosynthesis in Escherichia coli journal August 2011
Small Ubiquitin-like Modifier (SUMO) Modification of E1 Cys Domain Inhibits E1 Cys Domain Enzymatic Activity journal March 2012
Posttranslational Modification of Cellular Proteins by a Ubiquitin-like Protein in Bacteria journal March 2012
Autoubiquitination of the BRCA1·BARD1 RING Ubiquitin Ligase journal April 2002
Archaeal Ubiquitin-like SAMP3 is Isopeptide-linked to Proteins via a UbaA-dependent Mechanism journal October 2013
Mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at tRNA wobble positions journal January 2009
3DLigandSite: predicting ligand-binding sites using similar structures journal May 2010
Structure of the ubiquitin-activating enzyme loaded with two ubiquitin molecules journal April 2014
Site-directed mutagenesis of the active site loop of the rhodanese-like domain of the human molybdopterin synthase sulfurase MOCS3: Major differences in substrate specificity between eukaryotic and bacterial homologs journal April 2007
Archaeal JAB1/MPN/MOV34 metalloenzyme (HvJAMM1) cleaves ubiquitin-like small archaeal modifier proteins (SAMPs) from protein-conjugates: Archaeal JAMM isopeptidase journal October 2012
Archaeal Inorganic Pyrophosphatase Displays Robust Activity under High-Salt Conditions and in Organic Solvents journal November 2015
The N-Terminal Penultimate Residue of 20S Proteasome  1 Influences its N  Acetylation and Protein Levels as Well as Growth Rate and Stress Responses of Haloferax volcanii journal April 2009
The Rhodanese Domain of ThiI Is Both Necessary and Sufficient for Synthesis of the Thiazole Moiety of Thiamine in Salmonella enterica journal July 2011
Halophilic 20S Proteasomes of the ArchaeonHaloferax volcanii: Purification, Characterization, and Gene Sequence Analysis journal September 1999
Structural and Functional Insights to Ubiquitin-Like Protein Conjugation journal May 2014
Prokaryotic Ubiquitin-Like Protein Modification journal September 2014
Archaeal Ubiquitin-Like Proteins: Functional Versatility and Putative Ancestral Involvement in tRNA Modification Revealed by Comparative Genomic Analysis journal January 2010
Autoubiquitination of BCA2 RING E3 Ligase Regulates Its Own Stability and Affects Cell Migration journal September 2008
The L-Cysteine Desulfurase NFS1 Is Localized in the Cytosol where it Provides the Sulfur for Molybdenum Cofactor Biosynthesis in Humans journal April 2013
Archaeal Tuc1/Ncs6 Homolog Required for Wobble Uridine tRNA Thiolation Is Associated with Ubiquitin-Proteasome, Translation, and RNA Processing System Homologs journal June 2014
Ubiquitin-Like Protein SAMP1 and JAMM/MPN+ Metalloprotease HvJAMM1 Constitute a System for Reversible Regulation of Metabolic Enzyme Activity in Archaea journal May 2015

Cited By (6)

Methionine Sulfoxide Reductase A (MsrA) and Its Function in Ubiquitin-Like Protein Modification in Archaea journal September 2017
Methionine Sulfoxide Reductases of Archaea journal September 2018
Biosynthesis of Sulfur-Containing tRNA Modifications: A Comparison of Bacterial, Archaeal, and Eukaryotic Pathways journal March 2017
Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system journal July 2018
The Uba4 domain interplay is mediated via a thioester that is critical for tRNA thiolation through Urm1 thiocarboxylation journal April 2018
Several One-Domain Zinc Finger µ-Proteins of Haloferax Volcanii Are Important for Stress Adaptation, Biofilm Formation, and Swarming journal May 2019

Similar Records

Rhodanese-Like Domain Protein UbaC and Its Role in Ubiquitin-Like Protein Modification and Sulfur Mobilization in Archaea
Journal Article · Wed Jul 10 00:00:00 EDT 2019 · Journal of Bacteriology · OSTI ID:1609593
Crystal Structure of the Human Ubiquitin-activating Enzyme 5 (UBA5) Bound to ATP Mechanistic Insights into a Minimalistic E1 Enzyme
Journal Article · Mon Aug 30 00:00:00 EDT 2010 · J. Biol. Chem. · OSTI ID:1002485

Related Subjects

59 BASIC BIOLOGICAL SCIENCES