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

Title: Pterocarpan synthase (PTS) structures suggest a common quinone methide–stabilizing function in dirigent proteins and proteins with dirigent-like domains

Abstract

The biochemical activities of dirigent proteins (DPs) give rise to distinct complex classes of plant phenolics. DPs apparently began to emerge during the aquatic-to-land transition, with phylogenetic analyses revealing the presence of numerous DP subfamilies in the plant kingdom. The vast majority (>95%) of DPs in these large multigene families still await discovery of their biochemical functions. Here, we elucidated the 3D structures of two pterocarpan-forming proteins with dirigent-like domains. Both proteins stereospecifically convert distinct diastereomeric chiral isoflavonoid precursors to the chiral pterocarpans, (–)- and (+)-medicarpin, respectively. Their 3D structures enabled comparisons with stereoselective lignan– and aromatic terpenoid–forming DP orthologs. Furthermore, each protein provides entry into diverse plant natural products classes, and our experiments suggest a common biochemical mechanism in binding and stabilizing distinct plant phenol–derived mono- and bis-quinone methide intermediates during different C–C and C–O bond–forming processes. These observations provide key insights into both their appearance and functional diversification of DPs during land plant evolution/adaptation. The proposed biochemical mechanisms based on our findings provide important clues to how additional physiological roles for DPs and proteins harboring dirigent-like domains can now be rationally and systematically identified.

Authors:
 [1]; ORCiD logo [1];  [1];  [1];  [1]; ORCiD logo [2]; ORCiD logo [2];  [3]; ORCiD logo [4]; ORCiD logo [1]; ORCiD logo [1]
  1. Washington State Univ., Pullman, WA (United States). Inst. of Biological Chemistry
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  3. SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
  4. Washington State Univ., Pullman, WA (United States). Inst. of Biological Chemistry; Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
OSTI Identifier:
1668325
Report Number(s):
PNNL-SA-150677
Journal ID: ISSN 0021-9258
Grant/Contract Number:  
AC05-76RL01830; AC02-76SF00515; P41GM103393
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
Journal Volume: 295; Journal Issue: 33; Journal ID: ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
English
Subject:
Dirigent, Lignin, Pterocarpan, X-ray crystallography, Structure, Protein; Crystallography; Dimerization; Docking; Plant biochemistry; Plant defense; Dirigent protein; Quinone methides

Citation Formats

Meng, Qingyan, Moinuddin, Syed A., Kim, Sung-Jin, Bedgar, Diana L., Costa, Michael A., Thomas, Dennis G., Young, Robert P., Smith, Clyde A., Cort, John R., Davin, Laurence B., and Lewis, Norman G. Pterocarpan synthase (PTS) structures suggest a common quinone methide–stabilizing function in dirigent proteins and proteins with dirigent-like domains. United States: N. p., 2020. Web. doi:10.1074/jbc.ra120.012444.
Meng, Qingyan, Moinuddin, Syed A., Kim, Sung-Jin, Bedgar, Diana L., Costa, Michael A., Thomas, Dennis G., Young, Robert P., Smith, Clyde A., Cort, John R., Davin, Laurence B., & Lewis, Norman G. Pterocarpan synthase (PTS) structures suggest a common quinone methide–stabilizing function in dirigent proteins and proteins with dirigent-like domains. United States. doi:10.1074/jbc.ra120.012444.
Meng, Qingyan, Moinuddin, Syed A., Kim, Sung-Jin, Bedgar, Diana L., Costa, Michael A., Thomas, Dennis G., Young, Robert P., Smith, Clyde A., Cort, John R., Davin, Laurence B., and Lewis, Norman G. Sun . "Pterocarpan synthase (PTS) structures suggest a common quinone methide–stabilizing function in dirigent proteins and proteins with dirigent-like domains". United States. doi:10.1074/jbc.ra120.012444. https://www.osti.gov/servlets/purl/1668325.
@article{osti_1668325,
title = {Pterocarpan synthase (PTS) structures suggest a common quinone methide–stabilizing function in dirigent proteins and proteins with dirigent-like domains},
author = {Meng, Qingyan and Moinuddin, Syed A. and Kim, Sung-Jin and Bedgar, Diana L. and Costa, Michael A. and Thomas, Dennis G. and Young, Robert P. and Smith, Clyde A. and Cort, John R. and Davin, Laurence B. and Lewis, Norman G.},
abstractNote = {The biochemical activities of dirigent proteins (DPs) give rise to distinct complex classes of plant phenolics. DPs apparently began to emerge during the aquatic-to-land transition, with phylogenetic analyses revealing the presence of numerous DP subfamilies in the plant kingdom. The vast majority (>95%) of DPs in these large multigene families still await discovery of their biochemical functions. Here, we elucidated the 3D structures of two pterocarpan-forming proteins with dirigent-like domains. Both proteins stereospecifically convert distinct diastereomeric chiral isoflavonoid precursors to the chiral pterocarpans, (–)- and (+)-medicarpin, respectively. Their 3D structures enabled comparisons with stereoselective lignan– and aromatic terpenoid–forming DP orthologs. Furthermore, each protein provides entry into diverse plant natural products classes, and our experiments suggest a common biochemical mechanism in binding and stabilizing distinct plant phenol–derived mono- and bis-quinone methide intermediates during different C–C and C–O bond–forming processes. These observations provide key insights into both their appearance and functional diversification of DPs during land plant evolution/adaptation. The proposed biochemical mechanisms based on our findings provide important clues to how additional physiological roles for DPs and proteins harboring dirigent-like domains can now be rationally and systematically identified.},
doi = {10.1074/jbc.ra120.012444},
journal = {Journal of Biological Chemistry},
number = 33,
volume = 295,
place = {United States},
year = {2020},
month = {6}
}

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

Save / Share:

Works referenced in this record:

CHAINSAW : a program for mutating pdb files used as templates in molecular replacement
journal, April 2008


Dirigent domain-containing protein is part of the machinery required for formation of the lignin-based Casparian strip in the root
journal, August 2013

  • Hosmani, P. S.; Kamiya, T.; Danku, J.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 35
  • DOI: 10.1073/pnas.1308412110

Linking Crystallographic Model and Data Quality
journal, May 2012


The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants
journal, May 2011


The Pfam protein families database in 2019
journal, October 2018

  • El-Gebali, Sara; Mistry, Jaina; Bateman, Alex
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky995

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

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
journal, December 2009

  • Morris, Garrett M.; Huey, Ruth; Lindstrom, William
  • Journal of Computational Chemistry, Vol. 30, Issue 16
  • DOI: 10.1002/jcc.21256

Opposite Stereoselectivities of Dirigent Proteins in Arabidopsis and Schizandra Species
journal, August 2012

  • Kim, Kye-Won; Moinuddin, Syed G. A.; Atwell, Kathleen M.
  • Journal of Biological Chemistry, Vol. 287, Issue 41
  • DOI: 10.1074/jbc.M112.387423

Improved R-factors for diffraction data analysis in macromolecular crystallography
journal, April 1997

  • Diederichs, Kay; Karplus, P. Andrew
  • Nature Structural Biology, Vol. 4, Issue 4
  • DOI: 10.1038/nsb0497-269

Non-host disease resistance response in pea (Pisum sativum) pods: Biochemical function of DRR206 and phytoalexin pathway localization
journal, May 2015


Substituent Effects on Carbocation Stability:  The p K R for p -Quinone Methide
journal, July 2003

  • Toteva, Maria M.; Moran, Michael; Amyes, Tina L.
  • Journal of the American Chemical Society, Vol. 125, Issue 29
  • DOI: 10.1021/ja029588v

MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

Stereoselective coupling of hemigossypol to form (+)-gossypol in moco cotton is mediated by a dirigent protein
journal, December 2008


A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation
journal, April 2018

  • Corbin, Cyrielle; Drouet, Samantha; Markulin, Lucija
  • Plant Molecular Biology, Vol. 97, Issue 1-2
  • DOI: 10.1007/s11103-018-0725-x

ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
journal, May 1994

  • Abagyan, Ruben; Totrov, Maxim; Kuznetsov, Dmitry
  • Journal of Computational Chemistry, Vol. 15, Issue 5
  • DOI: 10.1002/jcc.540150503

The Missing Link in Leguminous Pterocarpan Biosynthesis is a Dirigent Domain-Containing Protein with Isoflavanol Dehydratase Activity
journal, February 2017

  • Uchida, Kai; Akashi, Tomoyoshi; Aoki, Toshio
  • Plant and Cell Physiology, Vol. 58, Issue 2
  • DOI: 10.1093/pcp/pcw213

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution
journal, January 2018

  • Lang, Daniel; Ullrich, Kristian K.; Murat, Florent
  • The Plant Journal, Vol. 93, Issue 3
  • DOI: 10.1111/tpj.13801

Solvent content of protein crystals
journal, April 1968


Monolignol radical–radical coupling networks in western red cedar and Arabidopsis and their evolutionary implications
journal, October 2002


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

The Phyre2 web portal for protein modeling, prediction and analysis
journal, May 2015

  • Kelley, Lawrence A.; Mezulis, Stefans; Yates, Christopher M.
  • Nature Protocols, Vol. 10, Issue 6
  • DOI: 10.1038/nprot.2015.053

Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
journal, November 2004

  • Krissinel, E.; Henrick, K.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12
  • DOI: 10.1107/S0907444904026460

Trimeric Structure of (+)-Pinoresinol-forming Dirigent Protein at 1.95 Å Resolution with Three Isolated Active Sites
journal, November 2014

  • Kim, Kye-Won; Smith, Clyde A.; Daily, Michael D.
  • Journal of Biological Chemistry, Vol. 290, Issue 3
  • DOI: 10.1074/jbc.M114.611780

Regiochemical control of monolignol radical coupling: A new paradigm for lignin and lignan biosynthesis
journal, March 1999


How good are my data and what is the resolution?
journal, June 2013

  • Evans, Philip R.; Murshudov, Garib N.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
  • DOI: 10.1107/S0907444913000061

Dirigent-mediated podophyllotoxin biosynthesis in Linum flavum and Podophyllum peltatum
journal, November 2000


Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
journal, October 2006


An Enantiocomplementary Dirigent Protein for the Enantioselective Laccase-Catalyzed Oxidative Coupling of Phenols
journal, November 2009

  • Pickel, Benjamin; Constantin, Mihaela-Anca; Pfannstiel, Jens
  • Angewandte Chemie International Edition, Vol. 49, Issue 1
  • DOI: 10.1002/anie.200904622

Dirigent Protein-Mediated Lignan and Cyanogenic Glucoside Formation in Flax Seed: Integrated Omics and MALDI Mass Spectrometry Imaging
journal, May 2015


Stereoselective Bimolecular Phenoxy Radical Coupling by an Auxiliary (Dirigent) Protein Without an Active Center
journal, January 1997


Dirigent Protein Mode of Action Revealed by the Crystal Structure of AtDIR6
journal, October 2016

  • Gasper, Raphael; Effenberger, Isabelle; Kolesinski, Piotr
  • Plant Physiology, Vol. 172, Issue 4
  • DOI: 10.1104/pp.16.01281

Scaling and assessment of data quality
journal, December 2005

  • Evans, Philip
  • Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 1, p. 72-82
  • DOI: 10.1107/S0907444905036693

XDS
journal, January 2010

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

The MYB36 transcription factor orchestrates Casparian strip formation
journal, June 2015

  • Kamiya, Takehiro; Borghi, Monica; Wang, Peng
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 33
  • DOI: 10.1073/pnas.1507691112

A deliberate approach to screening for initial crystallization conditions of biological macromolecules
journal, April 2003


Full-length de novo assembly of RNA-seq data in pea ( Pisum sativum L.) provides a gene expression atlas and gives insights into root nodulation in this species
journal, October 2015

  • Alves-Carvalho, Susete; Aubert, Grégoire; Carrère, Sébastien
  • The Plant Journal, Vol. 84, Issue 1
  • DOI: 10.1111/tpj.12967

Global indicators of X-ray data quality
journal, April 2001


Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome
journal, October 2017


Dirigent Proteins from Cotton ( Gossypium sp.) for the Atropselective Synthesis of Gossypol
journal, October 2015

  • Effenberger, Isabelle; Zhang, Bin; Li, Ling
  • Angewandte Chemie International Edition, Vol. 54, Issue 49
  • DOI: 10.1002/anie.201507543