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Title: The N-terminal Domain of Escherichia coli Assimilatory NADPH-Sulfite Reductase Hemoprotein Is an Oligomerization Domain That Mediates Holoenzyme Assembly

Abstract

Assimilatory NADPH-sulfite reductase (SiR) from Escherichia coli is a structurally complex oxidoreductase that catalyzes the six-electron reduction of sulfite to sulfide. Two subunits, one a flavin-binding flavoprotein (SiRFP, the α subunit) and the other an iron-containing hemoprotein (SiRHP, the β subunit), assemble to make a holoenzyme of about 800 kDa. How the two subunits assemble is not known. The iron-rich cofactors in SiRHP are unique because they are a covalent arrangement of a Fe4S4 cluster attached through a cysteine ligand to an iron-containing porphyrinoid called siroheme. The link between cofactor biogenesis and SiR stability is also ill-defined. By use of hydrogen/deuterium exchange and biochemical analysis, we show that the α8β4 SiR holoenzyme assembles through the N terminus of SiRHP and the NADPH binding domain of SiRFP. By use of small angle x-ray scattering, we explore the structure of the SiRHP N-terminal oligomerization domain. We additionally report a novel form of the hemoprotein that occurs in the absence of its cofactors. Apo-SiRHP forms a homotetramer, also dependent on its N terminus, that is unable to assemble with SiRFP. Finally, from these results, we propose that homotetramerization of apo-SiRHP serves as a quality control mechanism to prevent formation of inactive holoenzyme inmore » the case of limiting cellular siroheme.« less

Authors:
 [1];  [1];  [1];  [2];  [3];  [4];  [1]
  1. Florida State Univ., Tallahassee, FL (United States)
  2. Florida State Univ., Tallahassee, FL (United States); National High Magnetic Field Lab. (MagLab), Tallahassee, FL (United States)
  3. National High Magnetic Field Lab. (MagLab), Tallahassee, FL (United States)
  4. Illinois Inst. of Technology, Chicago, IL (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
National Science Foundation (NSF); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Scientific User Facilities Division
OSTI Identifier:
1418603
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
Journal Volume: 290; Journal Issue: 31; Journal ID: ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Askenasy, Isabel, Pennington, Joseph M., Tao, Yeqing, Marshall, Alan G., Young, Nicolas L., Shang, Weifeng, and Stroupe, M. Elizabeth. The N-terminal Domain of Escherichia coli Assimilatory NADPH-Sulfite Reductase Hemoprotein Is an Oligomerization Domain That Mediates Holoenzyme Assembly. United States: N. p., 2015. Web. doi:10.1074/jbc.M115.662379.
Askenasy, Isabel, Pennington, Joseph M., Tao, Yeqing, Marshall, Alan G., Young, Nicolas L., Shang, Weifeng, & Stroupe, M. Elizabeth. The N-terminal Domain of Escherichia coli Assimilatory NADPH-Sulfite Reductase Hemoprotein Is an Oligomerization Domain That Mediates Holoenzyme Assembly. United States. doi:10.1074/jbc.M115.662379.
Askenasy, Isabel, Pennington, Joseph M., Tao, Yeqing, Marshall, Alan G., Young, Nicolas L., Shang, Weifeng, and Stroupe, M. Elizabeth. Fri . "The N-terminal Domain of Escherichia coli Assimilatory NADPH-Sulfite Reductase Hemoprotein Is an Oligomerization Domain That Mediates Holoenzyme Assembly". United States. doi:10.1074/jbc.M115.662379. https://www.osti.gov/servlets/purl/1418603.
@article{osti_1418603,
title = {The N-terminal Domain of Escherichia coli Assimilatory NADPH-Sulfite Reductase Hemoprotein Is an Oligomerization Domain That Mediates Holoenzyme Assembly},
author = {Askenasy, Isabel and Pennington, Joseph M. and Tao, Yeqing and Marshall, Alan G. and Young, Nicolas L. and Shang, Weifeng and Stroupe, M. Elizabeth},
abstractNote = {Assimilatory NADPH-sulfite reductase (SiR) from Escherichia coli is a structurally complex oxidoreductase that catalyzes the six-electron reduction of sulfite to sulfide. Two subunits, one a flavin-binding flavoprotein (SiRFP, the α subunit) and the other an iron-containing hemoprotein (SiRHP, the β subunit), assemble to make a holoenzyme of about 800 kDa. How the two subunits assemble is not known. The iron-rich cofactors in SiRHP are unique because they are a covalent arrangement of a Fe4S4 cluster attached through a cysteine ligand to an iron-containing porphyrinoid called siroheme. The link between cofactor biogenesis and SiR stability is also ill-defined. By use of hydrogen/deuterium exchange and biochemical analysis, we show that the α8β4 SiR holoenzyme assembles through the N terminus of SiRHP and the NADPH binding domain of SiRFP. By use of small angle x-ray scattering, we explore the structure of the SiRHP N-terminal oligomerization domain. We additionally report a novel form of the hemoprotein that occurs in the absence of its cofactors. Apo-SiRHP forms a homotetramer, also dependent on its N terminus, that is unable to assemble with SiRFP. Finally, from these results, we propose that homotetramerization of apo-SiRHP serves as a quality control mechanism to prevent formation of inactive holoenzyme in the case of limiting cellular siroheme.},
doi = {10.1074/jbc.M115.662379},
journal = {Journal of Biological Chemistry},
number = 31,
volume = 290,
place = {United States},
year = {2015},
month = {7}
}

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Works referenced in this record:

Cofactor-Induced Refolding:  Refolding of Molten Globule Carbonic Anhydrase Induced by Zn(II) and Co(II)
journal, March 2001

  • Andersson, Dick; Hammarström, Per; Carlsson, Uno
  • Biochemistry, Vol. 40, Issue 9
  • DOI: 10.1021/bi000957e

Global Rigid Body Modeling of Macromolecular Complexes against Small-Angle Scattering Data
journal, August 2005


A switch III motif relays signaling between a B12 enzyme and its G-protein chaperone
journal, July 2013

  • Lofgren, Michael; Padovani, Dominique; Koutmos, Markos
  • Nature Chemical Biology, Vol. 9, Issue 9
  • DOI: 10.1038/nchembio.1298

CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates
journal, December 1995

  • Svergun, D.; Barberato, C.; Koch, M. H. J.
  • Journal of Applied Crystallography, Vol. 28, Issue 6
  • DOI: 10.1107/S0021889895007047

A Simplifed Functional Version of the Escherichia coli Sulfite Reductase
journal, September 2000

  • Zeghouf, Mahel; Fontecave, Marc; Covès, Jacques
  • Journal of Biological Chemistry, Vol. 275, Issue 48
  • DOI: 10.1074/jbc.M005619200

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants the Keio collection
journal, February 2006

  • Baba, Tomoya; Ara, Takeshi; Hasegawa, Miki
  • Molecular Systems Biology, Vol. 2, Article No. 2006.0008
  • DOI: 10.1038/msb4100050

High-Performance Mass Spectrometry: Fourier Transform Ion Cyclotron Resonance at 14.5 Tesla
journal, June 2008

  • Schaub, Tanner M.; Hendrickson, Christopher L.; Horning, Stevan
  • Analytical Chemistry, Vol. 80, Issue 11
  • DOI: 10.1021/ac800386h

Iron-Sulfur Cluster Biogenesis in Chloroplasts. Involvement of the Scaffold Protein CpIscA
journal, May 2005

  • Abdel-Ghany, Salah E.; Ye, Hong; Garifullina, Gulnara F.
  • Plant Physiology, Vol. 138, Issue 1
  • DOI: 10.1104/pp.104.058602

Electrically Compensated Fourier Transform Ion Cyclotron Resonance Cell for Complex Mixture Mass Analysis
journal, September 2011

  • Kaiser, Nathan K.; Savory, Joshua J.; McKenna, Amy M.
  • Analytical Chemistry, Vol. 83, Issue 17
  • DOI: 10.1021/ac201546d

Advantages of High Magnetic Field for Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
journal, November 1996


Blue silver: A very sensitive colloidal Coomassie G-250 staining for proteome analysis
journal, May 2004

  • Candiano, Giovanni; Bruschi, Maurizio; Musante, Luca
  • ELECTROPHORESIS, Vol. 25, Issue 9
  • DOI: 10.1002/elps.200305844

The Copper Chaperone CCS Directly Interacts with Copper/Zinc Superoxide Dismutase
journal, September 1998

  • Casareno, Ruby Leah B.; Waggoner, Darrel; Gitlin, Jonathan D.
  • Journal of Biological Chemistry, Vol. 273, Issue 37
  • DOI: 10.1074/jbc.273.37.23625

Improved ion extraction from a linear octopole ion trap: SIMION analysis and experimental demonstration
journal, November 2002

  • Wilcox, Bruce E.; Hendrickson, Christopher L.; Marshall, Alan G.
  • Journal of the American Society for Mass Spectrometry, Vol. 13, Issue 11
  • DOI: 10.1016/S1044-0305(02)00622-0

The octahaem MccA is a haem c–copper sulfite reductase
journal, February 2015

  • Hermann, Bianca; Kern, Melanie; La Pietra, Luigi
  • Nature, Vol. 520, Issue 7549
  • DOI: 10.1038/nature14109

Flavin Mononucleotide-Binding Domain of the Flavoprotein Component of the Sulfite Reductase from Escherichia coli
journal, May 1997

  • Covès, Jacques; Zeghouf, Mahel; Macherel, David
  • Biochemistry, Vol. 36, Issue 19
  • DOI: 10.1021/bi9623744

Structure of Spinach Nitrite Reductase:  Implications for Multi-electron Reactions by the Iron−Sulfur:Siroheme Cofactor ,
journal, December 2005

  • Swamy, Uma; Wang, Meitian; Tripathy, Jatinda N.
  • Biochemistry, Vol. 44, Issue 49
  • DOI: 10.1021/bi050981y

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Sulfite Reductase Structure at 1.6  : Evolution and Catalysis for Reduction of Inorganic Anions
journal, October 1995


Mutational Analysis of Sulfite Reductase Hemoprotein Reveals the Mechanism for Coordinated Electron and Proton Transfer
journal, November 2012

  • Smith, Kyle W.; Stroupe, M. Elizabeth
  • Biochemistry, Vol. 51, Issue 49
  • DOI: 10.1021/bi300947a

Iron–sulfur cluster biosynthesis
journal, November 2008

  • Bandyopadhyay, Sibali; Chandramouli, Kala; Johnson, Michael K.
  • Biochemical Society Transactions, Vol. 36, Issue 6
  • DOI: 10.1042/BST0361112

The Structure of Holo and Metal-deficient Wild-type Human Cu, Zn Superoxide Dismutase and its Relevance to Familial Amyotrophic Lateral Sclerosis
journal, May 2003


Transcriptional control of the cysG gene of Escherichia coli K-12 during aerobic and anaerobic growth
journal, July 1990


A two-dimensional quadrupole ion trap mass spectrometer
journal, June 2002

  • Schwartz, Jae C.; Senko, Michael W.; Syka, John E. P.
  • Journal of the American Society for Mass Spectrometry, Vol. 13, Issue 6
  • DOI: 10.1016/S1044-0305(02)00384-7

The FNR-like domain of the Escherichia coli sulfite reductase flavoprotein component: crystallization and preliminary X-ray analysis
journal, January 1998

  • Gruez, Arnaud; Zeghouf, Mahel; Bertrand, Jay
  • Acta Crystallographica Section D Biological Crystallography, Vol. 54, Issue 1
  • DOI: 10.1107/S090744499701069X

Solution Structure of the Sulfite Reductase Flavodoxin-like Domain from Escherichia coli ,
journal, June 2005

  • Sibille, Nathalie; Blackledge, Martin; Brutscher, Bernhard
  • Biochemistry, Vol. 44, Issue 25
  • DOI: 10.1021/bi050437p

Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering
journal, February 2015


Studies of the molten globule state of ferredoxin: Structural characterization and implications on protein folding and iron-sulfur center assembly
journal, May 2007

  • Leal, Sónia S.; Gomes, Cláudio M.
  • Proteins: Structure, Function, and Bioinformatics, Vol. 68, Issue 3
  • DOI: 10.1002/prot.21448

New developments in the ATSAS program package for small-angle scattering data analysis
journal, March 2012

  • Petoukhov, Maxim V.; Franke, Daniel; Shkumatov, Alexander V.
  • Journal of Applied Crystallography, Vol. 45, Issue 2
  • DOI: 10.1107/S0021889812007662

The Escherichia coli cysG promoter belongs to the ‘extended −10’ class of bacterial promoters
journal, December 1993

  • Belyaeva, T.; Griffiths, L.; Minchin, S.
  • Biochemical Journal, Vol. 296, Issue 3
  • DOI: 10.1042/bj2960851

The relationship between structure and function for the sulfite reductases
journal, December 1996


External accumulation of ions for enhanced electrospray ionization fourier transform ion cyclotron resonance mass spectrometry
journal, September 1997

  • Senko, Michael W.; Hendrickson, Christopher L.; Emmett, Mark R.
  • Journal of the American Society for Mass Spectrometry, Vol. 8, Issue 9
  • DOI: 10.1016/S1044-0305(97)00126-8

Four crystal structures of the 60 kDa flavoprotein monomer of the sulfite reductase indicate a disordered flavodoxin-like module 1 1Edited by R. Huber
journal, May 2000

  • Gruez, Arnaud; Pignol, David; Zeghouf, Mahel
  • Journal of Molecular Biology, Vol. 299, Issue 1
  • DOI: 10.1006/jmbi.2000.3748

Human recombinant [C22A] FK506-binding protein amide hydrogen exchange rates from mass spectrometry match and extend those from NMR
journal, October 1997


NarJ is a specific chaperone required for molybdenum cofactor assembly in nitrate reductase A of Escherichia coli
journal, April 1998


Comparison and interconversion of the two most common frequency-to-mass calibration functions for Fourier transform ion cyclotron resonance mass spectrometry
journal, January 2000

  • Shi, Stone D. -H.; Drader, Jared J.; Freitas, Michael A.
  • International Journal of Mass Spectrometry, Vol. 195-196
  • DOI: 10.1016/S1387-3806(99)00226-2

Three-dimensional structure of NADPH-cytochrome P450 reductase: Prototype for FMN- and FAD-containing enzymes
journal, August 1997

  • Wang, M.; Roberts, D. L.; Paschke, R.
  • Proceedings of the National Academy of Sciences, Vol. 94, Issue 16
  • DOI: 10.1073/pnas.94.16.8411

Space charge effects in Fourier transform mass spectrometry. II. Mass calibration
journal, December 1984

  • Ledford, Edward B.; Rempel, Don L.; Gross, M. L.
  • Analytical Chemistry, Vol. 56, Issue 14
  • DOI: 10.1021/ac00278a027

Conformational Changes of NADPH-Cytochrome P450 Oxidoreductase Are Essential for Catalysis and Cofactor Binding
journal, February 2011

  • Xia, Chuanwu; Hamdane, Djemel; Shen, Anna L.
  • Journal of Biological Chemistry, Vol. 286, Issue 18
  • DOI: 10.1074/jbc.M111.230532

Biogenesis of iron-sulfur clusters in mammalian cells: new insights and relevance to human disease
journal, March 2012


The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the Advanced Photon Source
journal, August 2004

  • Fischetti, R.; Stepanov, S.; Rosenbaum, G.
  • Journal of Synchrotron Radiation, Vol. 11, Issue 5
  • DOI: 10.1107/S0909049504016760

Regulation of the HscA ATPase Reaction Cycle by the Co-chaperone HscB and the Iron-Sulfur Cluster Assembly Protein IscU
journal, October 2004

  • Silberg, Jonathan J.; Tapley, Tim L.; Hoff, Kevin G.
  • Journal of Biological Chemistry, Vol. 279, Issue 52
  • DOI: 10.1074/jbc.M410117200

Crystal Structure of the FAD/NADPH-binding Domain of Rat Neuronal Nitric-oxide Synthase: COMPARISONS WITH NADPH-CYTOCHROME P450 OXIDOREDUCTASE
journal, July 2001

  • Zhang, Jian; Martàsek, Pavel; Paschke, Rosemary
  • Journal of Biological Chemistry, Vol. 276, Issue 40
  • DOI: 10.1074/jbc.M105503200