skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE

Abstract

Detailed crystallographic characterization of a tri-aspartate metal-binding site previously identified on the three-fold symmetry axis of a hexameric enzyme, LarE from Lactobacillus plantarum, was conducted. By screening an array of monovalent, divalent, and trivalent metal ions, we demonstrated that this metal binding site stoichiometrically binds Ca2+, Mn2+, Fe2+/Fe3+, Co2+, Ni2+, Cu2+, Zn2+, and Cd2+, but not monovalent metal ions, Cr3+, Mg2+, Y3+, Sr2+ or Ba2+. Extensive database searches resulted in only 13 similar metal binding sites in other proteins, indicative of the rareness of tri-aspartate architectures, which allows for engineering such a selective multivalent metal ion binding site into target macromolecules for structural and biophysical characterization.

Authors:
 [1];  [2];  [2];  [2]
  1. Univ. of Otago, Dunedin, Otago (New Zealand); Michigan State Univ., East Lansing, MI (United States)
  2. Michigan State Univ., East Lansing, MI (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE; National Science Foundation (NSF); National Institutes of Health (NIH)
OSTI Identifier:
1608895
Grant/Contract Number:  
CHE1516126; CHE1807073; GM128959
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; biochemistry; structural biology

Citation Formats

Fellner, Matthias, Huizenga, Kamren G., Hausinger, Robert P., and Hu, Jian. Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE. United States: N. p., 2020. Web. doi:10.1038/s41598-020-62847-6.
Fellner, Matthias, Huizenga, Kamren G., Hausinger, Robert P., & Hu, Jian. Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE. United States. doi:https://doi.org/10.1038/s41598-020-62847-6
Fellner, Matthias, Huizenga, Kamren G., Hausinger, Robert P., and Hu, Jian. Thu . "Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE". United States. doi:https://doi.org/10.1038/s41598-020-62847-6. https://www.osti.gov/servlets/purl/1608895.
@article{osti_1608895,
title = {Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE},
author = {Fellner, Matthias and Huizenga, Kamren G. and Hausinger, Robert P. and Hu, Jian},
abstractNote = {Detailed crystallographic characterization of a tri-aspartate metal-binding site previously identified on the three-fold symmetry axis of a hexameric enzyme, LarE from Lactobacillus plantarum, was conducted. By screening an array of monovalent, divalent, and trivalent metal ions, we demonstrated that this metal binding site stoichiometrically binds Ca2+, Mn2+, Fe2+/Fe3+, Co2+, Ni2+, Cu2+, Zn2+, and Cd2+, but not monovalent metal ions, Cr3+, Mg2+, Y3+, Sr2+ or Ba2+. Extensive database searches resulted in only 13 similar metal binding sites in other proteins, indicative of the rareness of tri-aspartate architectures, which allows for engineering such a selective multivalent metal ion binding site into target macromolecules for structural and biophysical characterization.},
doi = {10.1038/s41598-020-62847-6},
journal = {Scientific Reports},
number = 1,
volume = 10,
place = {United States},
year = {2020},
month = {4}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Metal Preferences and Metallation
journal, August 2014

  • Foster, Andrew W.; Osman, Deenah; Robinson, Nigel J.
  • Journal of Biological Chemistry, Vol. 289, Issue 41
  • DOI: 10.1074/jbc.R114.588145

Short-distance probes for protein backbone structure based on energy transfer between bimane and transition metal ions
journal, September 2009

  • Taraska, J. W.; Puljung, M. C.; Zagotta, W. N.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 38
  • DOI: 10.1073/pnas.0905207106

Nickel-pincer cofactor biosynthesis involves LarB-catalyzed pyridinium carboxylation and LarE-dependent sacrificial sulfur insertion
journal, April 2016

  • Desguin, Benoît; Soumillion, Patrice; Hols, Pascal
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 20
  • DOI: 10.1073/pnas.1600486113

A structural perspective on the PP-loop ATP pyrophosphatase family
journal, October 2018

  • Fellner, Matthias; Hausinger, Robert P.; Hu, Jian
  • Critical Reviews in Biochemistry and Molecular Biology, Vol. 53, Issue 6
  • DOI: 10.1080/10409238.2018.1516728

Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
journal, January 2007

  • Berman, H.; Henrick, K.; Nakamura, H.
  • Nucleic Acids Research, Vol. 35, Issue Database
  • DOI: 10.1093/nar/gkl971

Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE
journal, August 2017

  • Fellner, Matthias; Desguin, Benoît; Hausinger, Robert P.
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 34
  • DOI: 10.1073/pnas.1704967114

A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase
journal, July 2015


Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides
journal, September 1976


The crystallographic structure of Panicum Mosaic Virus (PMV)
journal, January 2013

  • Makino, Debora L.; Larson, Steven B.; McPherson, Alexander
  • Journal of Structural Biology, Vol. 181, Issue 1
  • DOI: 10.1016/j.jsb.2012.10.012

Structures of C1q-like Proteins Reveal Unique Features among the C1q/TNF Superfamily
journal, April 2015


MetalPDB in 2018: a database of metal sites in biological macromolecular structures
journal, October 2017

  • Putignano, Valeria; Rosato, Antonio; Banci, Lucia
  • Nucleic Acids Research, Vol. 46, Issue D1
  • DOI: 10.1093/nar/gkx989

Transition metal ion FRET uncovers K+ regulation of a neurotransmitter/sodium symporter
journal, September 2016

  • Billesbølle, Christian B.; Mortensen, Jonas S.; Sohail, Azmat
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12755

Functional and Structural Characterization of an Unusual Cofactor-Independent Oxygenase
journal, January 2015

  • Baas, Bert-Jan; Poddar, Harshwardhan; Geertsema, Edzard M.
  • Biochemistry, Vol. 54, Issue 5
  • DOI: 10.1021/bi501200j

Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Three-dimensional structure and ligand-binding site of carp fishelectin (FEL)
journal, April 2015

  • Capaldi, Stefano; Faggion, Beniamino; Carrizo, Maria E.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 5
  • DOI: 10.1107/S1399004715004174

ZincBind—the database of zinc binding sites
journal, January 2019


MIPS: metal interactions in protein structures
journal, December 2009

  • Hemavathi, K.; Kalaivani, M.; Udayakumar, A.
  • Journal of Applied Crystallography, Vol. 43, Issue 1
  • DOI: 10.1107/S002188980903982x

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Discovery of a Novel Class of Potent Human Deoxyuridine Triphosphatase Inhibitors Remarkably Enhancing the Antitumor Activity of Thymidylate Synthase Inhibitors
journal, March 2012

  • Miyahara, Seiji; Miyakoshi, Hitoshi; Yokogawa, Tatsushi
  • Journal of Medicinal Chemistry, Vol. 55, Issue 7
  • DOI: 10.1021/jm201628y

Recognition- and Reactivity-Based Fluorescent Probes for Studying Transition Metal Signaling in Living Systems
journal, July 2015

  • Aron, Allegra T.; Ramos-Torres, Karla M.; Cotruvo, Joseph A.
  • Accounts of Chemical Research, Vol. 48, Issue 8
  • DOI: 10.1021/acs.accounts.5b00221

Factors Governing the Metal Coordination Number in Metal Complexes from Cambridge Structural Database Analyses
journal, February 2006

  • Dudev, Minko; Wang, Jonathan; Dudev, Todor
  • The Journal of Physical Chemistry B, Vol. 110, Issue 4
  • DOI: 10.1021/jp054975n

Analysis of the Active Site Cysteine Residue of the Sacrificial Sulfur Insertase LarE from Lactobacillus plantarum
journal, August 2018


Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase
journal, June 2018

  • Desguin, Benoît; Fellner, Matthias; Riant, Olivier
  • Journal of Biological Chemistry, Vol. 293, Issue 32
  • DOI: 10.1074/jbc.RA118.003741

Channel specificity: structural basis for sugar discrimination and differential flux rates in maltoporin 1 1Edited by R. Huber
journal, September 1997

  • Wang, Yan-Fei; Dutzler, Raimund; Rizkallah, Pierre J.
  • Journal of Molecular Biology, Vol. 272, Issue 1
  • DOI: 10.1006/jmbi.1997.1224

Structure of maltoporin from Salmonella typhimurium ligated with a nitrophenyl-maltotrioside
journal, March 1997

  • Meyer, Joachim E. W.; Hofnung, Maurice; Schulz, Georg E.
  • Journal of Molecular Biology, Vol. 266, Issue 4
  • DOI: 10.1006/jmbi.1996.0823

MetalS3, a database-mining tool for the identification of structurally similar metal sites
journal, April 2014

  • Valasatava, Yana; Rosato, Antonio; Cavallaro, Gabriele
  • JBIC Journal of Biological Inorganic Chemistry, Vol. 19, Issue 6
  • DOI: 10.1007/s00775-014-1128-3

Structure of the infectious salmon anemia virus receptor complex illustrates a unique binding strategy for attachment
journal, March 2017

  • Cook, Jonathan D.; Sultana, Azmiri; Lee, Jeffrey E.
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 14
  • DOI: 10.1073/pnas.1617993114

Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy
journal, April 2011


Monodentate versus Bidentate Carboxylate Binding in Magnesium and Calcium Proteins:  What Are the Basic Principles?
journal, April 2004

  • Dudev, Todor; Lim, Carmay
  • The Journal of Physical Chemistry B, Vol. 108, Issue 14
  • DOI: 10.1021/jp0310347

Lactate Racemase Nickel-Pincer Cofactor Operates by a Proton-Coupled Hydride Transfer Mechanism
journal, February 2018


MetalMine: a database of functional metal-binding sites in proteins
journal, January 2009


Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system
journal, April 2014

  • Desguin, Benoît; Goffin, Philippe; Viaene, Eric
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms4615

Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server
journal, December 2013

  • Zheng, Heping; Chordia, Mahendra D.; Cooper, David R.
  • Nature Protocols, Vol. 9, Issue 1
  • DOI: 10.1038/nprot.2013.172

Nickel–pincer nucleotide cofactor
journal, December 2018

  • Hausinger, Robert P.; Desguin, Benoît; Fellner, Matthias
  • Current Opinion in Chemical Biology, Vol. 47
  • DOI: 10.1016/j.cbpa.2018.06.019

A stability ruler for metal ion complexes
journal, May 1987

  • Martin, R. Bruce
  • Journal of Chemical Education, Vol. 64, Issue 5
  • DOI: 10.1021/ed064p402

XDS
journal, January 2010

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
  • DOI: 10.1107/S0907444909047337

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

Many-body effect determines the selectivity for Ca 2+ and Mg 2+ in proteins
journal, July 2018

  • Jing, Zhifeng; Liu, Chengwen; Qi, Rui
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 32
  • DOI: 10.1073/pnas.1805049115

Structural Basis of Biological NO Generation by Octaheme Oxidoreductases
journal, December 2013

  • Maalcke, Wouter J.; Dietl, Andreas; Marritt, Sophie J.
  • Journal of Biological Chemistry, Vol. 289, Issue 3
  • DOI: 10.1074/jbc.M113.525147

Engineering Novel Metalloproteins:  Design of Metal-Binding Sites into Native Protein Scaffolds
journal, October 2001

  • Lu, Yi; Berry, Steven M.; Pfister, Thomas D.
  • Chemical Reviews, Vol. 101, Issue 10
  • DOI: 10.1021/cr0000574

Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination
journal, February 2008

  • Dokmanić, Ivan; Šikić, Mile; Tomić, Sanja
  • Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 3
  • DOI: 10.1107/S090744490706595X

An Artificial Metalloenzyme: Creation of a Designed Copper Binding Site in a Thermostable Protein
journal, June 2010

  • Podtetenieff, John; Taglieber, Andreas; Bill, Eckhard
  • Angewandte Chemie International Edition, Vol. 49, Issue 30
  • DOI: 10.1002/anie.201002106