N-terminal domain swapping: A new paradigm for spermidine/spermine N-acetyltransferase (SSAT) protein structures?

Mayer-Harnisch, Claudia E.; Paniagua, Daniel Figueroa; Maltseva, Natalia; Kim, Youngchang; Le, Van Thi Bich; Joachimiak, Andrzej; Kuhn, Misty L.

doi:10.1016/j.bbrc.2025.151302

Title: N-terminal domain swapping: A new paradigm for spermidine/spermine N-acetyltransferase (SSAT) protein structures?

Journal Article · 09 January 2025 · Biochemical and Biophysical Research Communications

DOI: https://doi.org/10.1016/j.bbrc.2025.151302 · OSTI ID:2501001

^[1]; Paniagua, Daniel Figueroa ^[1];

^[2];

^[1]; Joachimiak, Andrzej ^[2]; Kuhn, Misty L. ^[1]

San Francisco State Univ., CA (United States)
Univ. of Chicago, IL (United States); Argonne National Laboratory (ANL), Argonne, IL (United States)

Enterococcus faecalis is a multi-drug-resistant human pathogen that is found in a variety of environments and is challenging to treat. Under stress conditions, some bacteria regulate intracellular polyamine concentrations via polyamine acetyltransferases to reduce their toxicity. The E. faecalis genome encodes two polyamine acetyltransferases: PmvE and BltD. Both of these proteins belong to the Gcn5-related N-acetyltransferase (GNAT) superfamily. It is unclear why there are two enzymes with similar substrate specificities in this organism. To better understand the structure/function relationship of the E. faecalis BltD enzyme, we determined its crystal structure and performed additional assays to explore its oligomeric state and enzymatic activity. The goal was to determine whether there were structural or catalytic differences between this enzyme and other polyamine acetyltransferases that could explain this redundancy and be exploited for future development of targeted inhibitors for this important human pathogen. We found the BltD enzyme was structurally unique due to its N-terminal domain swapped dimer. However, this enzyme adopts a catalytically active monomer rather than dimer in solution. This indicates the crystal structure we obtained may represent a state that forms at high protein and salt concentrations and at low pH used during crystallization. The BltD dimer found in the crystal may represent a unique view of how an inhibitory peptide or molecule could be designed to occupy its active site. Additionally, this structure shows the extensive flexibility of the N-terminal portion of the E. faecalis BltD enzyme.

View Journal Article

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: Camille and Henry Dreyfus Foundation; National Institutes of Health (NIH); USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 2501001

Journal Information:: Biochemical and Biophysical Research Communications, Journal Name: Biochemical and Biophysical Research Communications Vol. 748; ISSN 0006-291X

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (57)

Broad-substrate screen as a tool to identify substrates for bacterial Gcn5-related N -acetyltransferases with unknown substrate specificity : Broad-Substrate Screen for GNATs Kuhn, Misty L.; Majorek, Karolina A.; Minor, Wladek Protein Science, Vol. 22, Issue 2 https://doi.org/10.1002/pro.2199	journal	December 2012
3D domain swapping: A mechanism for oligomer assembly Bennett, Melanie J.; Schlunegger, Michael P.; Eisenberg, David Protein Science, Vol. 4, Issue 12 https://doi.org/10.1002/pro.5560041202	journal	December 1995
Controlled Intracellular Processing of Fusion Proteins by TEV Protease Kapust, Rachel B.; Waugh, David S. Protein Expression and Purification, Vol. 19, Issue 2 https://doi.org/10.1006/prep.2000.1251	journal	July 2000
Protein Production for Structural Genomics Using E. coli Expression Makowska-Grzyska, Magdalena; Kim, Youngchang; Maltseva, Natalia Structural Genomics and Drug Discovery https://doi.org/10.1007/978-1-4939-0354-2_7	book	January 2014
Polyamine transport inEscherichia coli Igarashi, K.; Kashiwagi, K. Amino Acids, Vol. 10, Issue 1 https://doi.org/10.1007/BF00806095	journal	January 1996
A wider role for polyamines in biofilm formation Karatan, Ece; Michael, Anthony J. Biotechnology Letters, Vol. 35, Issue 11 https://doi.org/10.1007/s10529-013-1286-3	journal	July 2013
New LIC vectors for production of proteins from genes containing rare codons Eschenfeldt, William H.; Makowska-Grzyska, Magdalena; Stols, Lucy Journal of Structural and Functional Genomics, Vol. 14, Issue 4 https://doi.org/10.1007/s10969-013-9163-9	journal	September 2013
The gram reaction and cell composition: Diamines and polyamines Herbst, Edward J.; Weaver, Robert H.; Keister, Donald L. Archives of Biochemistry and Biophysics, Vol. 75, Issue 1 https://doi.org/10.1016/0003-9861(58)90407-7	journal	May 1958
Effects of pH, temperature and NaCl concentration on the growth kinetics, proteolytic activity and biogenic amine production of Enterococcus faecalis Gardini, Fausto; Martuscelli, Maria; Caruso, Marisa Carmela International Journal of Food Microbiology, Vol. 64, Issue 1-2 https://doi.org/10.1016/S0168-1605(00)00445-1	journal	February 2001
Taxonomic Studies on Streptococcus bovis and Streptococcus equinus: Description of Streptococcus alactolyticus sp. nov. and Streptococcus saccharolyticus sp. nov. Farrow, J. A. E.; Kruze, J.; Phillips, B. A. Systematic and Applied Microbiology, Vol. 5, Issue 4 https://doi.org/10.1016/S0723-2020(84)80004-1	journal	December 1984
The Unfolding Story of Three-Dimensional Domain Swapping Rousseau, Frederic; Schymkowitz, Joost W. H.; Itzhaki, Laura S. Structure, Vol. 11, Issue 3 https://doi.org/10.1016/S0969-2126(03)00029-7	journal	March 2003
Insight into the 3D structure and substrate specificity of previously uncharacterized GNAT superfamily acetyltransferases from pathogenic bacteria Majorek, Karolina A.; Osinski, Tomasz; Tran, David T. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1865, Issue 1 https://doi.org/10.1016/j.bbapap.2016.10.011	journal	January 2017
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
A Novel Polyamine Allosteric Site of SpeG from Vibrio cholerae Is Revealed by Its Dodecameric Structure Filippova, Ekaterina V.; Kuhn, Misty L.; Osipiuk, Jerzy Journal of Molecular Biology, Vol. 427, Issue 6 https://doi.org/10.1016/j.jmb.2015.01.009	journal	March 2015
SpeG polyamine acetyltransferase enzyme from Bacillus thuringiensis forms a dodecameric structure and exhibits high catalytic efficiency Tsimbalyuk, Sofiya; Shornikov, Aleksander; Thi Bich Le, Van Journal of Structural Biology, Vol. 210, Issue 3 https://doi.org/10.1016/j.jsb.2020.107506	journal	June 2020
Enterococcus thailandicus, an unusual pathogen in humans encountered in an intra-abdominal infection Mbouche, Patricia; Blairon, Laurent; Cupaiolo, Roberto New Microbes and New Infections, Vol. 53 https://doi.org/10.1016/j.nmni.2023.101137	journal	June 2023
Protein Domain-Swapping Can Be a Consequence of Functional Residues Mascarenhas, Nahren Manuel; Gosavi, Shachi The Journal of Physical Chemistry B, Vol. 120, Issue 28 https://doi.org/10.1021/acs.jpcb.6b03968	journal	July 2016
Mechanistic and Structural Analysis of Human Spermidine/Spermine N ¹ -Acetyltransferase ^† ^, ^‡ Hegde, Subray S.; Chandler, Jonathan; Vetting, Matthew W. Biochemistry, Vol. 46, Issue 24 https://doi.org/10.1021/bi700256z	journal	June 2007
Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander Nature https://doi.org/10.1038/s41586-021-03819-2	journal	July 2021
Biosynthesis of polyamines and polyamine-containing molecules Michael, Anthony J. Biochemical Journal, Vol. 473, Issue 15 https://doi.org/10.1042/BCJ20160185	journal	July 2016
Characterization of a novel spermidine/spermine acetyltransferase, BltD, from Bacillus subtilis Woolridge, Dale P.; Martinez, Jesse D.; Stringer, David E. Biochemical Journal, Vol. 340, Issue 3 https://doi.org/10.1042/bj3400753	journal	June 1999
Specificity of cell-cell adhesion by classical cadherins: Critical role for low-affinity dimerization through -strand swapping Chen, C. P.; Posy, S.; Ben-Shaul, A. Proceedings of the National Academy of Sciences, Vol. 102, Issue 24 https://doi.org/10.1073/pnas.0503319102	journal	June 2005
Different 3D domain-swapped oligomeric cyanovirin-N structures suggest trapped folding intermediates Koharudin, Leonardus M. I.; Liu, Lin; Gronenborn, Angela M. Proceedings of the National Academy of Sciences, Vol. 110, Issue 19 https://doi.org/10.1073/pnas.1300327110	journal	April 2013
Short-chain diamines are the physiological substrates of PACE family efflux pumps Hassan, Karl A.; Naidu, Varsha; Edgerton, Jacob R. Proceedings of the National Academy of Sciences, Vol. 116, Issue 36 https://doi.org/10.1073/pnas.1901591116	journal	August 2019
Efflux of the Natural Polyamine Spermidine Facilitated by the Bacillus subtilis Multidrug Transporter Blt Woolridge, Dale P.; Vazquez-Laslop, Nora; Markham, Penelope N. Journal of Biological Chemistry, Vol. 272, Issue 14 https://doi.org/10.1074/jbc.272.14.8864	journal	April 1997
Evolution and Multiplicity of Arginine Decarboxylases in Polyamine Biosynthesis and Essential Role in Bacillus subtilis Biofilm Formation Burrell, Matthew; Hanfrey, Colin C.; Murray, Ewan J. Journal of Biological Chemistry, Vol. 285, Issue 50 https://doi.org/10.1074/jbc.M110.163154	journal	December 2010
The Protein Acetyltransferase PatZ from Escherichia coli Is Regulated by Autoacetylation-induced Oligomerization de Diego Puente, Teresa; Gallego-Jara, Julia; Castaño-Cerezo, Sara Journal of Biological Chemistry, Vol. 290, Issue 38 https://doi.org/10.1074/jbc.M115.649806	journal	August 2015
Spermidine promotes Bacillus subtilis biofilm formation by activating expression of the matrix regulator slrR Hobley, Laura; Li, Bin; Wood, Jennifer L. Journal of Biological Chemistry, Vol. 292, Issue 29 https://doi.org/10.1074/jbc.M117.789644	journal	May 2017
Structural and Functional Evidence for Bacillus subtilis PaiA as a Novel N ¹ -Spermidine/Spermine Acetyltransferase Forouhar, Farhad; Lee, In-Sun; Vujcic, Jelena Journal of Biological Chemistry, Vol. 280, Issue 48 https://doi.org/10.1074/jbc.M505332200	journal	October 2005
Polyamines in Eukaryotes, Bacteria, and Archaea Michael, Anthony J. Journal of Biological Chemistry, Vol. 291, Issue 29 https://doi.org/10.1074/jbc.R116.734780	journal	June 2016
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes Davis, I. W.; Murray, L. W.; Richardson, J. S. Nucleic Acids Research, Vol. 32, Issue Web Server https://doi.org/10.1093/nar/gkh398	journal	July 2004
Enterococcus alcedinis sp. nov., isolated from common kingfisher (Alcedo atthis) Frolková, Petra; Švec, Pavel; Sedláček, Ivo International Journal of Systematic and Evolutionary Microbiology, Vol. 63, Issue Pt_8 https://doi.org/10.1099/ijs.0.049833-0	journal	August 2013
Enterococcus thailandicus sp. nov., isolated from fermented sausage ('mum') in Thailand Tanasupawat, S.; Sukontasing, S.; Lee, J. -S. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 7 https://doi.org/10.1099/ijs.0.65535-0	journal	July 2008
Enterococcus florum sp. nov., isolated from a cotton flower (Gossypium hirsutum L.) Techo, Sujitra; Shiwa, Yuh; Tanaka, Naoto International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 8 https://doi.org/10.1099/ijsem.0.003524	journal	August 2019
The ecology, epidemiology and virulence of Enterococcus Fisher, Katie; Phillips, Carol Microbiology, Vol. 155, Issue 6 https://doi.org/10.1099/mic.0.026385-0	journal	June 2009
PROCHECK: a program to check the stereochemical quality of protein structures Laskowski, R. A.; MacArthur, M. W.; Moss, D. S. Journal of Applied Crystallography, Vol. 26, Issue 2 https://doi.org/10.1107/S0021889892009944	journal	April 1993
HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes Minor, Wladek; Cymborowski, Marcin; Otwinowski, Zbyszek Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8 https://doi.org/10.1107/S0907444906019949	journal	July 2006
Molecular replacement with MOLREP Vagin, Alexei; Teplyakov, Alexei Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042589	journal	December 2009
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
REFMAC 5 for the refinement of macromolecular crystal structures Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911001314	journal	March 2011
Enterococcus sulfureus, a new yellow-pigmentedEnterococcusspecies Martinez-Murcia, A. J.; Collins, M. D. FEMS Microbiology Letters, Vol. 80, Issue 1 https://doi.org/10.1111/j.1574-6968.1991.tb04638.x	journal	May 1991
SlyA regulator is involved in bile salts stress response of Enterococcus faecalis Michaux, Charlotte; Martini, Cecilia; Hanin, Aurélie FEMS Microbiology Letters, Vol. 324, Issue 2 https://doi.org/10.1111/j.1574-6968.2011.02390.x	journal	October 2011
Enterococcal biofilm—A nidus for antibiotic resistance transfer? Conwell, Michael; Dooley, James S. G.; Naughton, Patrick J. Journal of Applied Microbiology, Vol. 132, Issue 5 https://doi.org/10.1111/jam.15441	journal	May 2022
Polyamine-independent growth and biofilm formation, and functional spermidine/spermine N -acetyltransferases in Staphylococcus aureus and Enterococcus faecalis: Polyamine independent growth and biofilm formation Li, Bin; Maezato, Yukari; Kim, Sok Ho Molecular Microbiology, Vol. 111, Issue 1 https://doi.org/10.1111/mmi.14145	journal	November 2018
Role of Mobile DNA in the Evolution of Vancomycin-Resistant Enterococcus faecalis Paulsen, I. T. Science, Vol. 299, Issue 5615 https://doi.org/10.1126/science.1080613	journal	March 2003
Linking Crystallographic Model and Data Quality Karplus, P. A.; Diederichs, K. Science, Vol. 336, Issue 6084 https://doi.org/10.1126/science.1218231	journal	May 2012
Diurnal Variation in Enterococcus Species Composition in Polluted Ocean Water and a Potential Role for the Enterococcal Carotenoid in Protection against Photoinactivation Maraccini, Peter A.; Ferguson, Donna M.; Boehm, Alexandria B. Applied and Environmental Microbiology, Vol. 78, Issue 2 https://doi.org/10.1128/AEM.06821-11	journal	January 2012
SlyA Is a Transcriptional Regulator Involved in the Virulence of Enterococcus faecalis Michaux, Charlotte; Sanguinetti, Maurizio; Reffuveille, Fany Infection and Immunity, Vol. 79, Issue 7 https://doi.org/10.1128/IAI.01132-10	journal	May 2011
The Polyamine N -Acetyltransferase-Like Enzyme PmvE Plays a Role in the Virulence of Enterococcus faecalis Martini, Cecilia; Michaux, Charlotte; Bugli, Francesca Infection and Immunity, Vol. 83, Issue 1 https://doi.org/10.1128/IAI.02585-14	journal	January 2015
Enterococcus gilvus sp. nov. and Enterococcus pallens sp. nov. Isolated from Human Clinical Specimens Tyrrell, Gregory J.; Turnbull, LeeAnn; Teixeira, Lúcia M. Journal of Clinical Microbiology, Vol. 40, Issue 4 https://doi.org/10.1128/JCM.40.4.1140-1145.2002	journal	April 2002
Enterococci in the Environment Byappanahalli, Muruleedhara N.; Nevers, Meredith B.; Korajkic, Asja Microbiology and Molecular Biology Reviews, Vol. 76, Issue 4 https://doi.org/10.1128/MMBR.00023-12	journal	December 2012
Two highly similar multidrug transporters of Bacillus subtilis whose expression is differentially regulated. Ahmed, M.; Lyass, L.; Markham, P. N. Journal of Bacteriology, Vol. 177, Issue 14 https://doi.org/10.1128/jb.177.14.3904-3910.1995	journal	July 1995
Effect of Polyamine Structure on Growth Stimulation and Spermine and Spermidine Content of Lactic acid Bacteria Guirard, Beverly M.; Snell, Esmond E. Journal of Bacteriology, Vol. 88, Issue 1 https://doi.org/10.1128/jb.88.1.72-80.1964	journal	July 1964
Pathogenicity of Enterococci Fiore, Elizabeth; Van Tyne, Daria; Gilmore, Michael S. Microbiology Spectrum, Vol. 7, Issue 4 https://doi.org/10.1128/microbiolspec.GPP3-0053-2018	journal	July 2019
Automated evaluation of quaternary structures from protein crystals Bliven, Spencer; Lafita, Aleix; Parker, Althea PLOS Computational Biology, Vol. 14, Issue 4 https://doi.org/10.1371/journal.pcbi.1006104	journal	April 2018
The Vibrio cholerae SpeG Spermidine/Spermine N-Acetyltransferase Allosteric Loop and β6-β7 Structural Elements Are Critical for Kinetic Activity Le, Van Thi Bich; Tsimbalyuk, Sofiya; Lim, Ee Qi Frontiers in Molecular Biosciences, Vol. 8 https://doi.org/10.3389/fmolb.2021.645768	journal	April 2021
Structural and Kinetic Characterization of the SpeG Spermidine/Spermine N-acetyltransferase from Methicillin-Resistant Staphylococcus aureus USA300 Tsimbalyuk, Sofiya; Shornikov, Aleksander; Srivastava, Parul Cells, Vol. 12, Issue 14 https://doi.org/10.3390/cells12141829	journal	July 2023

Similar Records

Structural and Functional Evidence for Bacillus subtilis PaiA as a Novel N1-spermidine/spermine acetyltransferase (SSAT)

Journal Article · 2004 · J. Biol. Chem. · OSTI ID:913699

Forouhar, F; Lee, I; Vujcic, J; +6 more

Structural characterization of a GNAT family acetyltransferase from Elizabethkingia anophelis bound to acetyl-CoA reveals a new dimeric interface

Journal Article · 2021 · Scientific Reports · OSTI ID:1763086

Shirmast, P.; Ghafoori, S. M.; Irwin, R. M.; +5 more

Structural, functional, and regulatory evaluation of a cysteine post-translationally modified Gcn5-related N-acetyltransferase

Journal Article · 2025 · Biochemical and Biophysical Research Communications · OSTI ID:2506839

Uychoco, Patricia; Majorek, Karolina A.; Ives, Ashley N.; +7 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Domain-swapped dimer
Gcn5-related N-Acetyltransferase (GNAT)
N-terminal Domain Swapping
Polyamine Acetylation
Polyamine Acetyltransferase
Spermidine/Spermine N-Acetyltransferase (SSAT)

Title: N-terminal domain swapping: A new paradigm for spermidine/spermine N-acetyltransferase (SSAT) protein structures?

Citation Formats

References (57)

Similar Records

Related Subjects