Bacillus anthracis Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu

Schnicker, Nicholas J.; Razzaghi, Mortezaali; Guha Thakurta, Sanjukta; Chakravarthy, Srinivas; Dey, Mishtu

doi:10.1021/acs.biochem.7b00601

Title: Bacillus anthracis Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu

Journal Article · Thu Oct 05 00:00:00 EDT 2017 · Biochemistry

DOI:https://doi.org/10.1021/acs.biochem.7b00601· OSTI ID:1413302

Schnicker, Nicholas J. ^[1]; Razzaghi, Mortezaali ^[1]; Guha Thakurta, Sanjukta ^[2]; Chakravarthy, Srinivas ^[3];

^[1]

Univ. of Iowa, Iowa City, IA (United States)
Harvard Medical School, Boston, MA (United States)
Argonne National Lab. (ANL), Argonne, IL (United States)

Prolyl hydroxylation is a very common post-translational modification and plays many roles in eukaryotes such as collagen stabilization, hypoxia sensing, and controlling protein transcription and translation. There is a growing body of evidence that suggests that prokaryotes contain prolyl 4-hydroxylases (P4Hs) homologous to the hypoxia-inducible factor (HIF) prolyl hydroxylase domain (PHD) enzymes that act on elongation factor Tu (EFTu) and are likely involved in the regulation of bacterial translation. Recent biochemical and structural studies with a PHD from Pseudomonas putida (PPHD) determined that it forms a complex with EFTu and hydroxylates a prolyl residue of EFTu. Moreover, while animal, plant, and viral P4Hs act on peptidyl proline, most prokaryotic P4Hs have been known to target free l-proline; the exceptions include PPHD and a P4H from Bacillus anthracis (BaP4H) that modifies collagen-like proline-rich peptides. Here we use biophysical and mass spectrometric methods to demonstrate that BaP4H recognizes full-length BaEFTu and a BaEFTu 9-mer peptide for site-specific proline hydroxylation. Using size-exclusion chromatography coupled small-angle X-ray scattering (SEC–SAXS) and binding studies, we determined that BaP4H forms a 1:1 heterodimeric complex with BaEFTu. The SEC–SAXS studies reveal dissociation of BaP4H dimeric subunits upon interaction with BaEFTu. While BaP4H is unusual within bacteria in that it is structurally and functionally similar to the animal PHDs and collagen P4Hs, respectively, this work provides further evidence of its promiscuous substrate recognition. Lastly, it is possible that the enzyme might have evolved to hydroxylate a universally conserved protein in prokaryotes, similar to the PHDs, and implies a functional role in B. anthracis.

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

Sponsoring Organization:: USDOE; National Science Foundation (NSF); National Inst. of Health

Grant/Contract Number:: P41 GM103622

OSTI ID:: 1413302

Journal Information:: Biochemistry, Vol. 56, Issue 43; ISSN 0006-2960

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Cited by: 6 works

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References (59)

OH, the Places You’ll Go! Hydroxylation, Gene Expression, and Cancer Ploumakis, Athanasios; Coleman, Mathew L. Molecular Cell, Vol. 58, Issue 5 https://doi.org/10.1016/j.molcel.2015.05.026	journal	June 2015
Oxygen Sensing, Hypoxia-Inducible Factors, and Disease Pathophysiology Semenza, Gregg L. Annual Review of Pathology: Mechanisms of Disease, Vol. 9, Issue 1 https://doi.org/10.1146/annurev-pathol-012513-104720	journal	January 2014
Prolyl 4 Hydroxylase: A Critical Target in the Pathophysiology of Diseases Kant, Ravi; Bali, Anjana; Singh, Nirmal The Korean Journal of Physiology & Pharmacology, Vol. 17, Issue 2 https://doi.org/10.4196/kjpp.2013.17.2.111	journal	January 2013
Prolyl 4-hydroxylase Gorres, Kelly L.; Raines, Ronald T. Critical Reviews in Biochemistry and Molecular Biology, Vol. 45, Issue 2 https://doi.org/10.3109/10409231003627991	journal	February 2010
Prolyl 4-hydroxylases, key enzymes in the synthesis of collagens and regulation of the response to hypoxia, and their roles as treatment targets Myllyharju, Johanna Annals of Medicine, Vol. 40, Issue 6 https://doi.org/10.1080/07853890801986594	journal	January 2008
Fe(II)/α-Ketoglutarate-Dependent Hydroxylases and Related Enzymes Hausinger, Robert P. Critical Reviews in Biochemistry and Molecular Biology, Vol. 39, Issue 1 https://doi.org/10.1080/10409230490440541	journal	January 2004
Role of the jelly-roll fold in substrate binding by 2-oxoglutarate oxygenases Aik, WeiShen; McDonough, Michael A.; Thalhammer, Armin Current Opinion in Structural Biology, Vol. 22, Issue 6 https://doi.org/10.1016/j.sbi.2012.10.001	journal	December 2012
Expanding chemical biology of 2-oxoglutarate oxygenases Loenarz, Christoph; Schofield, Christopher J. Nature Chemical Biology, Vol. 4, Issue 3 https://doi.org/10.1038/nchembio0308-152	journal	March 2008
Structural studies on 2-oxoglutarate oxygenases and related double-stranded β-helix fold proteins Clifton, Ian J.; McDonough, Michael A.; Ehrismann, Dominic Journal of Inorganic Biochemistry, Vol. 100, Issue 4 https://doi.org/10.1016/j.jinorgbio.2006.01.024	journal	April 2006
Dioxygen Activation at Mononuclear Nonheme Iron Active Sites: Enzymes, Models, and Intermediates Costas, Miquel; Mehn, Mark P.; Jensen, Michael P. Chemical Reviews, Vol. 104, Issue 2 https://doi.org/10.1021/cr020628n	journal	February 2004
Structural studies on human 2-oxoglutarate dependent oxygenases McDonough, Michael A.; Loenarz, Christoph; Chowdhury, Rasheduzzaman Current Opinion in Structural Biology, Vol. 20, Issue 6 https://doi.org/10.1016/j.sbi.2010.08.006	journal	December 2010
Structural and mechanistic studies on 2-oxoglutarate-dependent oxygenases and related enzymes Schofield, Christopher J.; Zhang, Zhihong Current Opinion in Structural Biology, Vol. 9, Issue 6 https://doi.org/10.1016/S0959-440X(99)00036-6	journal	December 1999
Protein Hydroxylation Catalyzed by 2-Oxoglutarate-dependent Oxygenases Markolovic, Suzana; Wilkins, Sarah E.; Schofield, Christopher J. Journal of Biological Chemistry, Vol. 290, Issue 34 https://doi.org/10.1074/jbc.R115.662627	journal	August 2015
The Structural Motifs for Substrate Binding and Dimerization of the α Subunit of Collagen Prolyl 4-Hydroxylase Anantharajan, Jothi; Koski, M. Kristian; Kursula, Petri Structure, Vol. 21, Issue 12 https://doi.org/10.1016/j.str.2013.09.005	journal	December 2013
Genome-based Identification and Analysis of Collagen-related Structural Motifs in Bacterial and Viral Proteins Rasmussen, Magnus; Jacobsson, Micael; Björck, Lars Journal of Biological Chemistry, Vol. 278, Issue 34 https://doi.org/10.1074/jbc.M304709200	journal	June 2003
Polyproline-II Helix in Proteins: Structure and Function Adzhubei, Alexei A.; Sternberg, Michael J. E.; Makarov, Alexander A. Journal of Molecular Biology, Vol. 425, Issue 12 https://doi.org/10.1016/j.jmb.2013.03.018	journal	June 2013
Structural bases of collagen stabilization induced by proline hydroxylation Vitagliano, Luigi; Berisio, Rita; Mazzarella, Lelio Biopolymers, Vol. 58, Issue 5 https://doi.org/10.1002/1097-0282(20010415)58:5<459::AID-BIP1021>3.0.CO;2-V	journal	January 2001
HIF Prolyl 4-Hydroxylases and their Potential as Drug Targets Myllyharju, Johanna Current Pharmaceutical Design, Vol. 15, Issue 33 https://doi.org/10.2174/138161209789649457	journal	November 2009
Prolyl Hydroxylase-dependent Modulation of Eukaryotic Elongation Factor 2 Activity and Protein Translation under Acute Hypoxia Romero-Ruiz, Antonio; Bautista, Lucía; Navarro, Virginia Journal of Biological Chemistry, Vol. 287, Issue 12 https://doi.org/10.1074/jbc.M111.299180	journal	March 2012
Structure and Mechanism of a Viral Collagen Prolyl Hydroxylase Longbotham, James E.; Levy, Colin; Johannissen, Linus O. Biochemistry, Vol. 54, Issue 39 https://doi.org/10.1021/acs.biochem.5b00789	journal	September 2015
Emerging novel functions of the oxygen-sensing prolyl hydroxylase domain enzymes Wong, Brian W.; Kuchnio, Anna; Bruning, Ulrike Trends in Biochemical Sciences, Vol. 38, Issue 1 https://doi.org/10.1016/j.tibs.2012.10.004	journal	January 2013
The Crystal Structure of an Algal Prolyl 4-Hydroxylase Complexed with a Proline-rich Peptide Reveals a Novel Buried Tripeptide Binding Motif Koski, M. Kristian; Hieta, Reija; Hirsilä, Maija Journal of Biological Chemistry, Vol. 284, Issue 37 https://doi.org/10.1074/jbc.M109.014050	journal	June 2009
Crystal Structure of Prolyl 4-Hydroxylase from Bacillus anthracis Culpepper, Megen A.; Scott, Emily E.; Limburg, Julian Biochemistry, Vol. 49, Issue 1 https://doi.org/10.1021/bi901771z	journal	January 2010
Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases Chowdhury, Rasheduzzaman; Leung, Ivanhoe K. H.; Tian, Ya-Min Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms12673	journal	August 2016
Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation Gupta, N.; Tanner, S.; Jaitly, N. Genome Research, Vol. 17, Issue 9 https://doi.org/10.1101/gr.6427907	journal	July 2007
Human oxygen sensing may have origins in prokaryotic elongation factor Tu prolyl-hydroxylation Scotti, John S.; Leung, Ivanhoe K. H.; Ge, Wei Proceedings of the National Academy of Sciences, Vol. 111, Issue 37 https://doi.org/10.1073/pnas.1409916111	journal	September 2014
Structural analysis of cofactor binding for a prolyl 4-hydroxylase from the pathogenic bacterium Bacillus anthracis Schnicker, Nicholas J.; Dey, Mishtu Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 5 https://doi.org/10.1107/S2059798316004198	journal	April 2016
Expression, purification, crystallization and preliminary X-ray studies of a prolyl-4-hydroxylase protein from Bacillus anthracis Miller, Megen A.; Scott, Emily E.; Limburg, Julian Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 64, Issue 9 https://doi.org/10.1107/S1744309108023439	journal	August 2008
Biochemical, Kinetic, and Spectroscopic Characterization of Ruegeria pomeroyi DddW—A Mononuclear Iron-Dependent DMSP Lyase Brummett, Adam E.; Schnicker, Nicholas J.; Crider, Alexander PLOS ONE, Vol. 10, Issue 5 https://doi.org/10.1371/journal.pone.0127288	journal	May 2015
A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression Huttlin, Edward L.; Jedrychowski, Mark P.; Elias, Joshua E. Cell, Vol. 143, Issue 7 https://doi.org/10.1016/j.cell.2010.12.001	journal	December 2010
Liquid-chromatography-coupled SAXS for accurate sizing of aggregating proteins Mathew, Elizabeth; Mirza, Ahmed; Menhart, Nick Journal of Synchrotron Radiation, Vol. 11, Issue 4 https://doi.org/10.1107/S0909049504014086	journal	June 2004
PRIMUS: a Windows PC-based system for small-angle scattering data analysis Konarev, Petr V.; Volkov, Vladimir V.; Sokolova, Anna V. Journal of Applied Crystallography, Vol. 36, Issue 5, p. 1277-1282 https://doi.org/10.1107/S0021889803012779	journal	September 2003
New developments in the ATSAS program package for small-angle scattering data analysis Petoukhov, Maxim V.; Franke, Daniel; Shkumatov, Alexander V. Journal of Applied Crystallography, Vol. 45, Issue 2 https://doi.org/10.1107/S0021889812007662	journal	March 2012
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution Putnam, Christopher D.; Hammel, Michal; Hura, Greg L. Quarterly Reviews of Biophysics, Vol. 40, Issue 3 https://doi.org/10.1017/S0033583507004635	journal	August 2007
DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering Franke, Daniel; Svergun, Dmitri I. Journal of Applied Crystallography, Vol. 42, Issue 2, p. 342-346 https://doi.org/10.1107/S0021889809000338	journal	January 2009
VMD: Visual molecular dynamics Humphrey, William; Dalke, Andrew; Schulten, Klaus Journal of Molecular Graphics, Vol. 14, Issue 1 https://doi.org/10.1016/0263-7855(96)00018-5	journal	February 1996
Automated matching of high- and low-resolution structural models Kozin, M. B.; Svergun, D. I. Journal of Applied Crystallography, Vol. 34, Issue 1, p. 33-41 https://doi.org/10.1107/S0021889800014126	journal	February 2001
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
How good are my data and what is the resolution? Evans, Philip R.; Murshudov, Garib N. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7 https://doi.org/10.1107/S0907444913000061	journal	June 2013
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Collaboration gets the most out of software Morin, Andrew; Eisenbraun, Ben; Key, Jason eLife, Vol. 2 https://doi.org/10.7554/eLife.01456	journal	September 2013
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers Pierce, B. G.; Wiehe, K.; Hwang, H. Bioinformatics, Vol. 30, Issue 12 https://doi.org/10.1093/bioinformatics/btu097	journal	February 2014
Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions London, Nir; Raveh, Barak; Cohen, Eyal Nucleic Acids Research, Vol. 39, Issue suppl_2 https://doi.org/10.1093/nar/gkr431	journal	May 2011
Sub-angstrom modeling of complexes between flexible peptides and globular proteins Raveh, Barak; London, Nir; Schueler-Furman, Ora Proteins: Structure, Function, and Bioinformatics https://doi.org/10.1002/prot.22716	journal	January 2010
I-TASSER: a unified platform for automated protein structure and function prediction Roy, Ambrish; Kucukural, Alper; Zhang, Yang Nature Protocols, Vol. 5, Issue 4 https://doi.org/10.1038/nprot.2010.5	journal	March 2010
Accurate Flexible Fitting of High-Resolution Protein Structures to Small-Angle X-Ray Scattering Data Using a Coarse-Grained Model with Implicit Hydration Shell Zheng, Wenjun; Tekpinar, Mustafa Biophysical Journal, Vol. 101, Issue 12 https://doi.org/10.1016/j.bpj.2011.11.003	journal	December 2011
Structural insight into antibiotic fosfomycin biosynthesis by a mononuclear iron enzyme Higgins, Luke J.; Yan, Feng; Liu, Pinghua Nature, Vol. 437, Issue 7060 https://doi.org/10.1038/nature03924	journal	July 2005
Structural Basis of Regiospecificity of a Mononuclear Iron Enzyme in Antibiotic Fosfomycin Biosynthesis Yun, Danny; Dey, Mishtu; Higgins, Luke J. Journal of the American Chemical Society, Vol. 133, Issue 29 https://doi.org/10.1021/ja2025728	journal	July 2011
The Crystal Structure of the Bacillus anthracis Spore Surface Protein BclA Shows Remarkable Similarity to Mammalian Proteins Réty, Stéphane; Salamitou, Sylvie; Garcia-Verdugo, Ignacio Journal of Biological Chemistry, Vol. 280, Issue 52 https://doi.org/10.1074/jbc.M510087200	journal	December 2005
Novel Oligosaccharide Side Chains of the Collagen-like Region of BclA, the Major Glycoprotein of the Bacillus anthracis Exosporium Daubenspeck, James M.; Zeng, Huadong; Chen, Ping Journal of Biological Chemistry, Vol. 279, Issue 30 https://doi.org/10.1074/jbc.M401613200	journal	May 2004
Polymorphism in the Collagen-Like Region of the Bacillus anthracis BclA Protein Leads to Variation in Exosporium Filament Length Sylvestre, P.; Couture-Tosi, E.; Mock, M. Journal of Bacteriology, Vol. 185, Issue 5 https://doi.org/10.1128/JB.185.5.1555-1563.2003	journal	March 2003
Structure of the Ribosomal Oxygenase OGFOD1 Provides Insights into the Regio- and Stereoselectivity of Prolyl Hydroxylases Horita, Shoichiro; Scotti, John S.; Thinnes, Cyrille Structure, Vol. 23, Issue 4 https://doi.org/10.1016/j.str.2015.01.014	journal	April 2015
Structural Basis for Binding of Hypoxia-Inducible Factor to the Oxygen-Sensing Prolyl Hydroxylases Chowdhury, Rasheduzzaman; McDonough, Michael A.; Mecinović, Jasmin Structure, Vol. 17, Issue 7 https://doi.org/10.1016/j.str.2009.06.002	journal	July 2009
Polyproline and Triple Helix Motifs in Host-Pathogen Recognition Berisio, Rita; Vitagliano, Luigi Current Protein and Peptide Science, Vol. 13, Issue 8 https://doi.org/10.2174/138920312804871157	journal	December 2012
Post-translational hydroxylation by 2OG/Fe(II)-dependent oxygenases as a novel regulatory mechanism in bacteria van Staalduinen, Laura M.; Jia, Zongchao Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00798	journal	January 2015
The N Terminus of Bacterial Elongation Factor Tu Elicits Innate Immunity in Arabidopsis Plants Kunze, Gernot; Zipfel, Cyril; Robatzek, Silke The Plant Cell, Vol. 16, Issue 12 https://doi.org/10.1105/tpc.104.026765	journal	November 2004
CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates Svergun, D.; Barberato, C.; Koch, M. H. J. Journal of Applied Crystallography, Vol. 28, Issue 6 https://doi.org/10.1107/S0021889895007047	journal	December 1995

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