Hirofumi Komori

Hirofumi Komori

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Hirofumi Komori

Hirofumi Komori

Publications by authors named "Hirofumi Komori"

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Biochemical, spectroscopic and X-ray structural analysis of deuterated multicopper oxidase CueO prepared from a new expression construct for neutron crystallography.

Acta Crystallogr F Struct Biol Commun 2016 10 22;72(Pt 10):788-794. Epub 2016 Sep 22.

Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako-gun, Hyogo 678-1297, Japan.

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http://dx.doi.org/10.1107/S2053230X1601400XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5053165PMC
October 2016

Exogenous acetate ion reaches the type II copper centre in CueO through the water-excretion channel and potentially affects the enzymatic activity.

Acta Crystallogr F Struct Biol Commun 2016 07 22;72(Pt 7):558-63. Epub 2016 Jun 22.

Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan.

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http://dx.doi.org/10.1107/S2053230X16009237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4933006PMC
July 2016

Domain swapping oligomerization of thermostable c-type cytochrome in E. coli cells.

Sci Rep 2016 Feb 3;6:19334. Epub 2016 Feb 3.

Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.

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http://dx.doi.org/10.1038/srep19334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4738263PMC
February 2016

Oligomerization enhancement and two domain swapping mode detection for thermostable cytochrome c552 via the elongation of the major hinge loop.

Mol Biosyst 2015 Dec;11(12):3218-21

Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.

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http://dx.doi.org/10.1039/c5mb00545kDOI Listing
December 2015

Structural insights into the O2 reduction mechanism of multicopper oxidase.

J Biochem 2015 Oct 12;158(4):293-8. Epub 2015 Aug 12.

RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan and Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan

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http://jb.oxfordjournals.org/content/early/2015/08/05/jb.mvv
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http://jb.oxfordjournals.org/content/158/4/293.full.pdf
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http://jb.oxfordjournals.org/lookup/doi/10.1093/jb/mvv079
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http://dx.doi.org/10.1093/jb/mvv079DOI Listing
October 2015

Crystallographic analysis of FAD-dependent glucose dehydrogenase.

Acta Crystallogr F Struct Biol Commun 2015 Aug 28;71(Pt 8):1017-9. Epub 2015 Jul 28.

RIKEN SPring-8 Center, 1-1-1 Koto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198, Japan.

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http://dx.doi.org/10.1107/S2053230X15010742DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528934PMC
August 2015

[Relationship between histamine and dopamine synthesizing enzymes].

Seikagaku 2015 Jun;87(3):321-5

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June 2015

Change in structure and ligand binding properties of hyperstable cytochrome c555 from Aquifex aeolicus by domain swapping.

Protein Sci 2015 Mar 14;24(3):366-75. Epub 2015 Jan 14.

Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.

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http://dx.doi.org/10.1002/pro.2627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4353362PMC
March 2015

Role of the C-terminal extension stacked on the re-face of the isoalloxazine ring moiety of the flavin adenine dinucleotide prosthetic group in ferredoxin-NADP(+) oxidoreductase from Bacillus subtilis.

Plant Physiol Biochem 2014 Aug 30;81:143-8. Epub 2014 Jan 30.

Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan.

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http://dx.doi.org/10.1016/j.plaphy.2014.01.011DOI Listing
August 2014

Formation of domain-swapped oligomer of cytochrome C from its molten globule state oligomer.

Biochemistry 2014 Jul 9;53(28):4696-703. Epub 2014 Jul 9.

Graduate School of Materials Science, Nara Institute of Science and Technology , 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.

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http://dx.doi.org/10.1021/bi500497sDOI Listing
July 2014

New insights into the catalytic active-site structure of multicopper oxidases.

Acta Crystallogr D Biol Crystallogr 2014 Mar 22;70(Pt 3):772-9. Epub 2014 Feb 22.

Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan.

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http://dx.doi.org/10.1107/S1399004713033051DOI Listing
March 2014

Formation of oligomeric cytochrome c during folding by intermolecular hydrophobic interaction between N- and C-terminal α-helices.

Biochemistry 2013 Dec 20;52(48):8732-44. Epub 2013 Nov 20.

Graduate School of Materials Science, Nara Institute of Science and Technology , 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.

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http://dx.doi.org/10.1021/bi400986gDOI Listing
December 2013

Crystal structure of the CueO mutants at Glu506, the key amino acid located in the proton transfer pathway for dioxygen reduction.

Biochem Biophys Res Commun 2013 Sep 8;438(4):686-90. Epub 2013 Aug 8.

Faculty of Education, Kagawa University, 1-1 Saiwai, Takamatsu 760-8522, Japan.

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http://dx.doi.org/10.1016/j.bbrc.2013.07.121DOI Listing
September 2013

Photosensitivity of the Ni-A state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F with visible light.

Biochem Biophys Res Commun 2013 Jan 15;430(1):284-8. Epub 2012 Nov 15.

Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.

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http://dx.doi.org/10.1016/j.bbrc.2012.10.136DOI Listing
January 2013

Domain swapping of the heme and N-terminal α-helix in Hydrogenobacter thermophilus cytochrome c(552) dimer.

Biochemistry 2012 Oct 18;51(43):8608-16. Epub 2012 Oct 18.

Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.

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http://dx.doi.org/10.1021/bi3011303DOI Listing
October 2012

Structural study reveals that Ser-354 determines substrate specificity on human histidine decarboxylase.

J Biol Chem 2012 Aug 5;287(34):29175-83. Epub 2012 Jul 5.

Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.

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http://dx.doi.org/10.1074/jbc.M112.381897DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436558PMC
August 2012

Purification, crystallization and preliminary X-ray analysis of human histidine decarboxylase.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2012 Jun 23;68(Pt 6):675-7. Epub 2012 May 23.

Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.

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http://dx.doi.org/10.1107/S1744309112015692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370908PMC
June 2012

Structural and enzymatic characterization of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis.

Protein Sci 2012 May 30;21(5):707-16. Epub 2012 Mar 30.

Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Ako-gun, Hyogo 678-1297, Japan.

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http://doi.wiley.com/10.1002/pro.2058
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http://dx.doi.org/10.1002/pro.2058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3403468PMC
May 2012

An O-centered structure of the trinuclear copper center in the Cys500Ser/Glu506Gln mutant of CueO and structural changes in low to high X-ray dose conditions.

Angew Chem Int Ed Engl 2012 Feb 16;51(8):1861-4. Epub 2012 Jan 16.

Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamigori-cho, Ako-gun 678-1297, Japan.

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http://dx.doi.org/10.1002/anie.201107739DOI Listing
February 2012

Crystallographic characterization of the DIX domain of the Wnt signalling positive regulator Ccd1.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2011 Jul 30;67(Pt 7):758-61. Epub 2011 Jun 30.

Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.

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http://dx.doi.org/10.1107/S1744309111016526DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144790PMC
July 2011

Crystal structure analysis of Bacillus subtilis ferredoxin-NADP(+) oxidoreductase and the structural basis for its substrate selectivity.

Protein Sci 2010 Dec 3;19(12):2279-90. Epub 2010 Nov 3.

Department of Life Science, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan.

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http://doi.wiley.com/10.1002/pro.508
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http://dx.doi.org/10.1002/pro.508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009396PMC
December 2010

Crystallization and preliminary X-ray analysis of dimeric and trimeric cytochromes c from horse heart.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2010 Nov 28;66(Pt 11):1477-9. Epub 2010 Oct 28.

Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.

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http://dx.doi.org/10.1107/S1744309110034913DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001652PMC
November 2010

Crystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3.

Kobe J Med Sci 2010 Oct 21;56(3):E125-39. Epub 2010 Oct 21.

Division of Molecular Pharmacology and Pharmacogenomics, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe, Japan.

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October 2010

Cytochrome c polymerization by successive domain swapping at the C-terminal helix.

Proc Natl Acad Sci U S A 2010 Jul 6;107(29):12854-9. Epub 2010 Jul 6.

Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.

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http://dx.doi.org/10.1073/pnas.1001839107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919943PMC
July 2010

Expression, crystallization and preliminary X-ray crystallographic study of ethanolamine ammonia-lyase from Escherichia coli.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2010 Jun 29;66(Pt 6):709-11. Epub 2010 May 29.

Department of Life Science, Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.

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http://dx.doi.org/10.1107/S1744309110014478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882776PMC
June 2010

Structure and molecular evolution of multicopper blue proteins.

Biomol Concepts 2010 May;1(1):31-40

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http://dx.doi.org/10.1515/bmc.2010.004DOI Listing
May 2010

Crystallization and preliminary X-ray studies of ferredoxin-NADP+ oxidoreductase encoded by Bacillus subtilis yumC.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2010 Mar 24;66(Pt 3):301-3. Epub 2010 Feb 24.

Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.

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http://scripts.iucr.org/cgi-bin/paper?S1744309110000151
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http://dx.doi.org/10.1107/S1744309110000151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2833042PMC
March 2010

X-ray structure of a two-domain type laccase: a missing link in the evolution of multi-copper proteins.

FEBS Lett 2009 Apr 11;583(7):1189-95. Epub 2009 Mar 11.

Department of Life Science, Graduate School of Life Science, University of Hyogo and Himeji Institute of Technology, Ako-gun, Hyogo 678-1297, Japan.

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http://doi.wiley.com/10.1016/j.febslet.2009.03.008
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http://dx.doi.org/10.1016/j.febslet.2009.03.008DOI Listing
April 2009

Crystallization and preliminary X-ray diffraction analysis of a putative two-domain-type laccase from a metagenome.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2009 Mar 26;65(Pt 3):264-6. Epub 2009 Feb 26.

Department of Life Science, University of Hyogo, Koto, Kamigori-cho, Ako-gun, Japan.

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http://dx.doi.org/10.1107/S1744309109002462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2650455PMC
March 2009

Strategic roles of axial histidines in structure formation and redox regulation of tetraheme cytochrome c3.

Biochemistry 2008 Sep 15;47(36):9405-15. Epub 2008 Aug 15.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://pubs.acs.org/doi/abs/10.1021/bi8005708
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http://dx.doi.org/10.1021/bi8005708DOI Listing
September 2008

Crystallization and preliminary X-ray analysis of a class II release factor RF3 from a sulfate-reducing bacterium.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2008 Jul 11;64(Pt 7):622-4. Epub 2008 Jun 11.

Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.

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http://dx.doi.org/10.1107/S1744309108015583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2443967PMC
July 2008

Crystal structures of hydrogenase maturation protein HypE in the Apo and ATP-bound forms.

J Mol Biol 2007 Sep 26;372(4):1045-1054. Epub 2007 Jul 26.

Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-gun, Sayo-cho, Hyogo 679-5148, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2007.07.023DOI Listing
September 2007

Crystallization and preliminary X-ray crystallographic studies of the axin DIX domain.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2007 Jun 18;63(Pt 6):529-31. Epub 2007 May 18.

Department of Life Science, Graduate School of Science, University of Hyogo, Koto, Kamigori-cho, Ako-gun, Hyogo, Japan.

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http://dx.doi.org/10.1107/S1744309107022579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2335085PMC
June 2007

Human DNA replication-related element binding factor (hDREF) self-association via hATC domain is necessary for its nuclear accumulation and DNA binding.

J Biol Chem 2007 Mar 5;282(10):7563-75. Epub 2007 Jan 5.

Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Hyogo 678-1297, Japan.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M607180200
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http://dx.doi.org/10.1074/jbc.M607180200DOI Listing
March 2007

Crystal structure of CO-sensing transcription activator CooA bound to exogenous ligand imidazole.

J Mol Biol 2007 Mar 23;367(3):864-71. Epub 2007 Jan 23.

Department of Life Science, Graduate School of Life Science, University of Hyogo and Himeji Institute of Technology, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.

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http://dx.doi.org/10.1016/j.jmb.2007.01.043DOI Listing
March 2007

Crystal structure of TTHA1657 (AT-rich DNA-binding protein; p25) from Thermus thermophilus HB8 at 2.16 A resolution.

Proteins 2007 Feb;66(3):755-9

Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.

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http://dx.doi.org/10.1002/prot.21222DOI Listing
February 2007

Head module control of mediator interactions.

Mol Cell 2006 Aug;23(3):355-64

Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA.

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http://dx.doi.org/10.1016/j.molcel.2006.06.007DOI Listing
August 2006

Roles of charged residues in pH-dependent redox properties of cytochrome from Miyazaki F.

Biophysics (Nagoya-shi) 2006 21;2:45-56. Epub 2006 Jul 21.

Institute for Protein Research, Osaka University, Yamadaoka, Suita 565-0871, Japan.

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http://dx.doi.org/10.2142/biophysics.2.45DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5036644PMC
July 2006

Crystallization and preliminary X-ray analysis of CooA from Carboxydothermus hydrogenoformans.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2006 May 21;62(Pt 5):471-3. Epub 2006 Apr 21.

Department of Life Science, Graduate School of Life Science, University of Hyogo, Japan.

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http://dx.doi.org/10.1107/S1744309106012826DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2219970PMC
May 2006

Structure of a conserved hypothetical protein, TTHA0849 from Thermus thermophilus HB8, at 2.4 A resolution: a putative member of the StAR-related lipid-transfer (START) domain superfamily.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2005 Dec 5;61(Pt 12):1027-31. Epub 2005 Nov 5.

Department of Life Science, Graduate School of Life Science, University of Hyogo, Himeji Institute of Technology, 3-2-1 Koto, Ako-gun, Hyogo 678-1297, Japan.

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http://scripts.iucr.org/cgi-bin/paper?S1744309105035372
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http://dx.doi.org/10.1107/S1744309105035372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1978151PMC
December 2005

Activation process of [NiFe] hydrogenase elucidated by high-resolution X-ray analyses: conversion of the ready to the unready state.

Structure 2005 Nov;13(11):1635-42

Department of Life Science, Graduate School of Life Science, University of Hyogo and Himeji Institute of Technology, 3-2-1 Koto, Ako-gun, Hyogo 678-1297, Japan.

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http://dx.doi.org/10.1016/j.str.2005.07.018DOI Listing
November 2005

Ubiquitin ligase activity of TFIIH and the transcriptional response to DNA damage.

Mol Cell 2005 Apr;18(2):237-43

Department of Structural Biology, School of Medicine, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1016/j.molcel.2005.03.007DOI Listing
April 2005

DNA apophotolyase from Anacystis nidulans: 1.8 A structure, 8-HDF reconstitution and X-ray-induced FAD reduction.

Acta Crystallogr D Biol Crystallogr 2004 Jul 22;60(Pt 7):1205-13. Epub 2004 Jun 22.

Laboratory for Microbiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.

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http://scripts.iucr.org/cgi-bin/paper?S0907444904009321
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http://dx.doi.org/10.1107/S0907444904009321DOI Listing
July 2004

The N-terminal domain of the replication initiator protein RepE is a dimerization domain forming a stable dimer.

Biochem Biophys Res Commun 2004 Feb;315(1):10-5

Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.

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http://dx.doi.org/10.1016/j.bbrc.2004.01.018DOI Listing
February 2004

Revised subunit structure of yeast transcription factor IIH (TFIIH) and reconciliation with human TFIIH.

J Biol Chem 2003 Nov 18;278(45):43897-900. Epub 2003 Sep 18.

Department of Structural Biology, Stanford University School of Medicine, California 94305-5400, USA.

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http://dx.doi.org/10.1074/jbc.C300417200DOI Listing
November 2003