Literature DB >> 24915100

Preliminary joint X-ray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP+.

Qun Wan1, Andrey Y Kovalevsky2, Mark A Wilson3, Brad C Bennett4, Paul Langan2, Chris Dealwis5.   

Abstract

A crystal of Escherichia coli dihydrofolate reductase (ecDHFR) complexed with folate and NADP+ of 4×1.3×0.7 mm (3.6 mm3) in size was obtained by sequential application of microseeding and macroseeding. A neutron diffraction data set was collected to 2.0 Å resolution using the IMAGINE diffractometer at the High Flux Isotope Reactor within Oak Ridge National Laboratory. A 1.6 Å resolution X-ray data set was also collected from a smaller crystal at room temperature. The neutron and X-ray data were used together for joint refinement of the ecDHFR-folate-NADP+ ternary-complex structure in order to examine the protonation state, protein dynamics and solvent structure of the complex, furthering understanding of the catalytic mechanism.

Entities:  

Keywords:  Escherichia coli; dihydrofolate reductase; protonation state

Mesh:

Substances:

Year:  2014        PMID: 24915100      PMCID: PMC4051544          DOI: 10.1107/S2053230X1400942X

Source DB:  PubMed          Journal:  Acta Crystallogr F Struct Biol Commun        ISSN: 2053-230X            Impact factor:   1.056


  29 in total

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Authors:  N Sukumar; F S Mathews; P Langan; V L Davidson
Journal:  Proc Natl Acad Sci U S A       Date:  2010-03-29       Impact factor: 11.205

2.  Joint X-ray and neutron refinement with phenix.refine.

Authors:  Pavel V Afonine; Marat Mustyakimov; Ralf W Grosse-Kunstleve; Nigel W Moriarty; Paul Langan; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-10-20

3.  Neutron protein crystallography: beyond the folding structure of biological macromolecules.

Authors:  Nobuo Niimura; Robert Bau
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

4.  On the determinants of amide backbone exchange in proteins: a neutron crystallographic comparative study.

Authors:  Brad C Bennett; Anna S Gardberg; Matthew D Blair; Chris G Dealwis
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2008-06-18

5.  Energetically most likely substrate and active-site protonation sites and pathways in the catalytic mechanism of dihydrofolate reductase.

Authors:  P L Cummins; J E Gready
Journal:  J Am Chem Soc       Date:  2001-04-18       Impact factor: 15.419

6.  Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate.

Authors:  Brad Bennett; Paul Langan; Leighton Coates; Marat Mustyakimov; Benno Schoenborn; Elizabeth E Howell; Chris Dealwis
Journal:  Proc Natl Acad Sci U S A       Date:  2006-11-27       Impact factor: 11.205

7.  PHENIX: a comprehensive Python-based system for macromolecular structure solution.

Authors:  Paul D Adams; Pavel V Afonine; Gábor Bunkóczi; Vincent B Chen; Ian W Davis; Nathaniel Echols; Jeffrey J Headd; Li-Wei Hung; Gary J Kapral; Ralf W Grosse-Kunstleve; Airlie J McCoy; Nigel W Moriarty; Robert Oeffner; Randy J Read; David C Richardson; Jane S Richardson; Thomas C Terwilliger; Peter H Zwart
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-01-22

8.  Crystal structure of the anthrax drug target, Bacillus anthracis dihydrofolate reductase.

Authors:  Brad C Bennett; Hai Xu; Richard F Simmerman; Richard E Lee; Chris G Dealwis
Journal:  J Med Chem       Date:  2007-08-14       Impact factor: 7.446

Review 9.  Neutron crystallography: opportunities, challenges, and limitations.

Authors:  Matthew P Blakeley; Paul Langan; Nobuo Niimura; Alberto Podjarny
Journal:  Curr Opin Struct Biol       Date:  2008-08-07       Impact factor: 6.809

10.  Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.

Authors:  Paul D Adams; Marat Mustyakimov; Pavel V Afonine; Paul Langan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-05-15
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  2 in total

1.  Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography.

Authors:  Qun Wan; Brad C Bennett; Mark A Wilson; Andrey Kovalevsky; Paul Langan; Elizabeth E Howell; Chris Dealwis
Journal:  Proc Natl Acad Sci U S A       Date:  2014-12-01       Impact factor: 11.205

2.  Capturing the Catalytic Proton of Dihydrofolate Reductase: Implications for General Acid-Base Catalysis.

Authors:  Qun Wan; Brad C Bennett; Troy Wymore; Zhihong Li; Mark A Wilson; Charles L Brooks; Paul Langan; Andrey Kovalevsky; Chris G Dealwis
Journal:  ACS Catal       Date:  2021-04-28       Impact factor: 13.084

  2 in total

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