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Title: Chloroplastic Serine Hydroxymethyltransferase From Medicago truncatula: A Structural Characterization

Authors:
; ; ;
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
NCINIH
OSTI Identifier:
1498386
Resource Type:
Journal Article
Journal Name:
Frontiers in Plant Science
Additional Journal Information:
Journal Volume: 9; Journal Issue: 05, 2018; Journal ID: ISSN 1664-462X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
ENGLISH

Citation Formats

Ruszkowski, Milosz, Sekula, Bartosz, Ruszkowska, Agnieszka, and Dauter, Zbigniew. Chloroplastic Serine Hydroxymethyltransferase From Medicago truncatula: A Structural Characterization. United States: N. p., 2018. Web. doi:10.3389/fpls.2018.00584.
Ruszkowski, Milosz, Sekula, Bartosz, Ruszkowska, Agnieszka, & Dauter, Zbigniew. Chloroplastic Serine Hydroxymethyltransferase From Medicago truncatula: A Structural Characterization. United States. doi:10.3389/fpls.2018.00584.
Ruszkowski, Milosz, Sekula, Bartosz, Ruszkowska, Agnieszka, and Dauter, Zbigniew. Fri . "Chloroplastic Serine Hydroxymethyltransferase From Medicago truncatula: A Structural Characterization". United States. doi:10.3389/fpls.2018.00584.
@article{osti_1498386,
title = {Chloroplastic Serine Hydroxymethyltransferase From Medicago truncatula: A Structural Characterization},
author = {Ruszkowski, Milosz and Sekula, Bartosz and Ruszkowska, Agnieszka and Dauter, Zbigniew},
abstractNote = {},
doi = {10.3389/fpls.2018.00584},
journal = {Frontiers in Plant Science},
issn = {1664-462X},
number = 05, 2018,
volume = 9,
place = {United States},
year = {2018},
month = {5}
}

Works referenced in this record:

Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
journal, January 1997

  • Nielsen, H.; Engelbrecht, J.; Brunak, S.
  • Protein Engineering Design and Selection, Vol. 10, Issue 1, p. 1-6
  • DOI: 10.1093/protein/10.1.1

HKL2MAP : a graphical user interface for macromolecular phasing with SHELX programs
journal, September 2004


Electrostatics of nanosystems: Application to microtubules and the ribosome
journal, August 2001

  • Baker, N. A.; Sept, D.; Joseph, S.
  • Proceedings of the National Academy of Sciences, Vol. 98, Issue 18, p. 10037-10041
  • DOI: 10.1073/pnas.181342398

Antimalarial Inhibitors Targeting Serine Hydroxymethyltransferase (SHMT) with in Vivo Efficacy and Analysis of their Binding Mode Based on X-ray Cocrystal Structures
journal, June 2017

  • Schwertz, Geoffrey; Witschel, Matthias C.; Rottmann, Matthias
  • Journal of Medicinal Chemistry, Vol. 60, Issue 12
  • DOI: 10.1021/acs.jmedchem.7b00008

p73 regulates serine biosynthesis in cancer
journal, November 2013


Serine, but Not Glycine, Supports One-Carbon Metabolism and Proliferation of Cancer Cells
journal, May 2014

  • Labuschagne, Christiaan F.; van den Broek, Niels J. F.; Mackay, Gillian M.
  • Cell Reports, Vol. 7, Issue 4
  • DOI: 10.1016/j.celrep.2014.04.045

Dali server: conservation mapping in 3D
journal, May 2010

  • Holm, Liisa; Rosenstr�m, P�ivi
  • Nucleic Acids Research, Vol. 38, Issue suppl_2
  • DOI: 10.1093/nar/gkq366

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
journal, December 2007

  • Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1
  • DOI: 10.1107/S090744490705024X

How pyridoxal 5′-phosphate differentially regulates human cytosolic and mitochondrial serine hydroxymethyltransferase oligomeric state
journal, February 2015

  • Giardina, Giorgio; Brunotti, Paolo; Fiascarelli, Alessio
  • FEBS Journal, Vol. 282, Issue 7
  • DOI: 10.1111/febs.13211

Plant γ-Glutamyl Hydrolases and Folate Polyglutamates: CHARACTERIZATION, COMPARTMENTATION, AND CO-OCCURRENCE IN VACUOLES
journal, June 2005

  • Orsomando, Giuseppe; de la Garza, Rocío Díaz; Green, Brian J.
  • Journal of Biological Chemistry, Vol. 280, Issue 32
  • DOI: 10.1074/jbc.M504306200

INTERMEDIATE CLEAVAGE PEPTIDASE55 Modifies Enzyme Amino Termini and Alters Protein Stability in Arabidopsis Mitochondria
journal, April 2015

  • Huang, Shaobai; Nelson, Clark J.; Li, Lei
  • Plant Physiology, Vol. 168, Issue 2
  • DOI: 10.1104/pp.15.00300

Photorespiration: players, partners and origin
journal, June 2010


High-throughput protein purification and quality assessment for crystallization
journal, September 2011


Structure of a Murine Cytoplasmic Serine Hydroxymethyltransferase Quinonoid Ternary Complex:  Evidence for Asymmetric Obligate Dimers
journal, November 2000

  • Szebenyi, Doletha M. E.; Liu, Xiaowen; Kriksunov, Irina A.
  • Biochemistry, Vol. 39, Issue 44
  • DOI: 10.1021/bi000635a

The glycine decarboxylase system: a fascinating complex
journal, April 2001


Mitochondria Are a Major Site for Folate and Thymidylate Synthesis in Plants
journal, April 1996

  • Neuburger, Michel; Rébeillé, Fabrice; Jourdain, Agnès
  • Journal of Biological Chemistry, Vol. 271, Issue 16
  • DOI: 10.1074/jbc.271.16.9466

Structures of Plasmodium vivax serine hydroxymethyltransferase: implications for ligand-binding specificity and functional control
journal, November 2014

  • Chitnumsub, Penchit; Jaruwat, Aritsara; Riangrungroj, Pinpunya
  • Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 12
  • DOI: 10.1107/S1399004714023128

Serine and glycine metabolism in cancer
journal, April 2014

  • Amelio, Ivano; Cutruzzolá, Francesca; Antonov, Alexey
  • Trends in Biochemical Sciences, Vol. 39, Issue 4
  • DOI: 10.1016/j.tibs.2014.02.004

Bioinformatics analysis of the serine and glycine pathway in cancer cells
journal, November 2014


Glycine cleavage system: reaction mechanism, physiological significance, and hyperglycinemia
journal, January 2008

  • Kikuchi, Goro; Motokawa, Yutaro; Yoshida, Tadashi
  • Proceedings of the Japan Academy, Series B, Vol. 84, Issue 7
  • DOI: 10.2183/pjab.84.246

WoLF PSORT: protein localization predictor
journal, May 2007

  • Horton, P.; Park, K. -J.; Obayashi, T.
  • Nucleic Acids Research, Vol. 35, Issue Web Server
  • DOI: 10.1093/nar/gkm259

5-Formyltetrahydrofolate Regulates Homocysteine Remethylation in Human Neuroblastoma
journal, February 1997

  • Girgis, Sameh; Suh, Jae Rin; Jolivet, Jacques
  • Journal of Biological Chemistry, Vol. 272, Issue 8
  • DOI: 10.1074/jbc.272.8.4729

ACHESYM : an algorithm and server for standardized placement of macromolecular models in the unit cell
journal, November 2014

  • Kowiel, Marcin; Jaskolski, Mariusz; Dauter, Zbigniew
  • Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 12
  • DOI: 10.1107/S1399004714024572

Evolutionary relationships among pyridoxal-5'-phosphate-dependent enzymes. Regio-specific alpha, beta and gamma families
journal, February 1994


Resurgence of Serine: An Often Neglected but Indispensable Amino Acid
journal, May 2012

  • Kalhan, Satish C.; Hanson, Richard W.
  • Journal of Biological Chemistry, Vol. 287, Issue 24
  • DOI: 10.1074/jbc.R112.357194

The role of Glu74 and Tyr82 in the reaction catalyzed by sheep liver cytosolic serine hydroxymethyltransferase: Role of E74 and Y82 in the catalysis of SHMT
journal, October 2000


Folate deprivation reduces homocysteine remethylation in a human intestinal epithelial cell culture model: role of serine in one-carbon donation
journal, April 2004

  • Townsend, Justin H.; Davis, Steven R.; Mackey, Amy D.
  • American Journal of Physiology-Gastrointestinal and Liver Physiology, Vol. 286, Issue 4
  • DOI: 10.1152/ajpgi.00454.2003

XDS
journal, January 2010

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

Integrated Temporal Regulation of the Photorespiratory Pathway. Circadian Regulation of Two Arabidopsis Genes Encoding Serine Hydroxymethyltransferase
journal, May 2000

  • McClung, C. Robertson; Hsu, Meier; Painter, Janet E.
  • Plant Physiology, Vol. 123, Issue 1
  • DOI: 10.1104/pp.123.1.381

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

Interaction between glycine decarboxylase, serine hydroxymethyltransferase and tetrahydrofolate polyglutamates in pea leaf mitochondria
journal, August 1994

  • Rebeille, F.; Neuburger, M.; Douce, R.
  • Biochemical Journal, Vol. 302, Issue 1
  • DOI: 10.1042/bj3020223

The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy
journal, September 1998


InterPro in 2017—beyond protein family and domain annotations
journal, November 2016

  • Finn, Robert D.; Attwood, Teresa K.; Babbitt, Patricia C.
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw1107

Importance of the Amino Terminus in Maintenance of Oligomeric Structure of Sheep Liver Cytosolic Serine Hydroxymethyltransferase
journal, July 1997

  • Jagath, Junutula Reddy; Sharma, Balasubramanya; Bhaskar, Brahatheeswaran
  • European Journal of Biochemistry, Vol. 247, Issue 1
  • DOI: 10.1111/j.1432-1033.1997.00372.x

Photorespiration: current status and approaches for metabolic engineering
journal, June 2010

  • Maurino, Veronica G.; Peterhansel, Christoph
  • Current Opinion in Plant Biology, Vol. 13, Issue 3
  • DOI: 10.1016/j.pbi.2010.01.006

Serine hydroxymethyltransferase revisited
journal, October 2005


Overexpression and characterization of dimeric and tetrameric forms of recombinant serine hydroxymethyltransferase fromBacillus stearothermophilus
journal, June 2002

  • Jala, Venkatakrishna R.; Prakash, V.; Rao, N. Appaji
  • Journal of Biosciences, Vol. 27, Issue 3
  • DOI: 10.1007/BF02704912

Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures
journal, November 2016


Conformational Aspects in the Design of Inhibitors for Serine Hydroxymethyltransferase (SHMT): Biphenyl, Aryl Sulfonamide, and Aryl Sulfone Motifs
journal, October 2017

  • Schwertz, Geoffrey; Frei, Michelle S.; Witschel, Matthias C.
  • Chemistry - A European Journal, Vol. 23, Issue 57
  • DOI: 10.1002/chem.201703244

A short history of SHELX
journal, December 2007

  • Sheldrick, George M.
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 1, p. 112-122
  • DOI: 10.1107/S0108767307043930

In silico and in vitro validation of serine hydroxymethyltransferase as a chemotherapeutic target of the antifolate drug pemetrexed
journal, May 2011

  • Daidone, Frederick; Florio, Rita; Rinaldo, Serena
  • European Journal of Medicinal Chemistry, Vol. 46, Issue 5
  • DOI: 10.1016/j.ejmech.2011.02.009

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

The rapid generation of mutation data matrices from protein sequences
journal, January 1992


One-carbon metabolism in plants: characterization of a plastid serine hydroxymethyltransferase
journal, July 2010

  • Zhang, Yi; Sun, Kehan; Sandoval, Francisco J.
  • Biochemical Journal, Vol. 430, Issue 1
  • DOI: 10.1042/BJ20100566

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

The structure of Plasmodium falciparum serine hydroxymethyltransferase reveals a novel redox switch that regulates its activities
journal, May 2014

  • Chitnumsub, Penchit; Ittarat, Wanwipa; Jaruwat, Aritsara
  • Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 6
  • DOI: 10.1107/S1399004714005598

REFMAC 5 for the refinement of macromolecular crystal structures
journal, March 2011

  • Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444911001314

Role of Tyrosine 65 in the Mechanism of Serine Hydroxymethyltransferase
journal, June 2000

  • Contestabile, Roberto; Angelaccio, Sebastiana; Bossa, Francesco
  • Biochemistry, Vol. 39, Issue 25
  • DOI: 10.1021/bi000032z

Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
  • DOI: 10.1016/S0022-2836(05)80360-2

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
journal, March 2016

  • Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro
  • Molecular Biology and Evolution, Vol. 33, Issue 7
  • DOI: 10.1093/molbev/msw054

Crystal Structure of Rabbit Cytosolic Serine Hydroxymethyltransferase at 2.8 Å Resolution:  Mechanistic Implications ,
journal, June 1999

  • Scarsdale, J. N.; Kazanina, G.; Radaev, S.
  • Biochemistry, Vol. 38, Issue 26
  • DOI: 10.1021/bi9904151

Predicting Subcellular Localization of Proteins Based on their N-terminal Amino Acid Sequence
journal, July 2000

  • Emanuelsson, Olof; Nielsen, Henrik; Brunak, Søren
  • Journal of Molecular Biology, Vol. 300, Issue 4
  • DOI: 10.1006/jmbi.2000.3903

Location of the Pteroylpolyglutamate-binding Site on Rabbit Cytosolic Serine Hydroxymethyltransferase
journal, November 2002

  • Fu, Tzu-Fun; Scarsdale, J. Neel; Kazanina, Galina
  • Journal of Biological Chemistry, Vol. 278, Issue 4
  • DOI: 10.1074/jbc.M210649200

The folic acid biosynthesis pathway in bacteria: evaluation of potential for antibacterial drug discovery
journal, June 2002

  • Bermingham, Alun; Derrick, Jeremy P.
  • BioEssays, Vol. 24, Issue 7
  • DOI: 10.1002/bies.10114

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
journal, July 2004

  • Dolinsky, T. J.; Nielsen, J. E.; McCammon, J. A.
  • Nucleic Acids Research, Vol. 32, Issue Web Server, p. W665-W667
  • DOI: 10.1093/nar/gkh381

O NE -C ARBON M ETABOLISM IN H IGHER P LANTS
journal, June 2001


Stock-based detection of protein oligomeric states in jsPISA
journal, April 2015


The Protein Data Bank
journal, January 2000


MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
journal, May 2016

  • Ashkenazy, Haim; Abadi, Shiran; Martz, Eric
  • Nucleic Acids Research, Vol. 44, Issue W1
  • DOI: 10.1093/nar/gkw408

Serine in plants: biosynthesis, metabolism, and functions
journal, September 2014


Conformational transitions driven by pyridoxal-5′-phosphate uptake in the psychrophilic serine hydroxymethyltransferase from P sychromonas ingrahamii : Psychrophilic SHMT Conformational Transitions
journal, August 2014

  • Angelaccio, Sebastiana; Dworkowski, Florian; Di Bello, Angela
  • Proteins: Structure, Function, and Bioinformatics, Vol. 82, Issue 10
  • DOI: 10.1002/prot.24646

Serine Hydroxymethyltransferase:  Role of Glu75 and Evidence that Serine Is Cleaved by a Retroaldol Mechanism
journal, June 2004

  • Szebenyi, Doletha M. E.; Musayev, Faik N.; di Salvo, Martino L.
  • Biochemistry, Vol. 43, Issue 22
  • DOI: 10.1021/bi049791y

Nuclear Localised MORE SULPHUR ACCUMULATION1 Epigenetically Regulates Sulphur Homeostasis in Arabidopsis thaliana
journal, September 2016


Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206