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Bae LJ, Kang GB, Kim M, Lee GS, Sohn JH, Nam CH, Cho BI. Diagnosis of ultrafast surface dynamics of thin foil targets irradiated by intense laser pulses. Opt Express 2023; 31:5767-5776. [PMID: 36823849 DOI: 10.1364/oe.474759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
The temporal modulation of an electron bunch train accelerated from a foil target irradiated by an intense laser pulse is studied by measuring the coherent transition radiation (CTR) from the rear surface of a target. We experimentally obtained CTR spectra from a 1 µm thick foil target irradiated at a maximum intensity of 6.5 × 1019 W/cm2. Spectral redshifts of the emitted radiation corresponding to increases in laser intensity were observed. These measurements were compared with the theoretical calculation of CTR spectra considering ultrafast surface dynamics, such as plasma surface oscillation and relativistically induced transparency. Plasma surface oscillations induce a spectral redshift, while relativistic transparency causes a spectral blueshift. Both effects are required to find reasonable agreement with the experiment over the entire range of laser intensities.
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An JY, Sharif H, Kang GB, Park KJ, Lee JG, Lee S, Jin MS, Song JJ, Wang J, Eom SH. Structural insights into the oligomerization of FtsH periplasmic domain from Thermotoga maritima. Biochem Biophys Res Commun 2018; 495:1201-1207. [PMID: 29180014 DOI: 10.1016/j.bbrc.2017.11.158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 11/23/2017] [Indexed: 11/25/2022]
Abstract
Prompt removal of misfolded membrane proteins and misassembled membrane protein complexes is essential for membrane homeostasis. However, the elimination of these toxic proteins from the hydrophobic membrane environment has high energetic barriers. The transmembrane protein, FtsH, is the only known ATP-dependent protease responsible for this task. The mechanisms by which FtsH recognizes, unfolds, translocates, and proteolyzes its substrates remain unclear. The structure and function of the ATPase and protease domains of FtsH have been previously characterized while the role of the FtsH periplasmic domain has not clearly identified. Here, we report the 1.5-1.95 Å resolution crystal structures of the Thermotoga maritima FtsH periplasmic domain (tmPD) and describe the dynamic features of tmPD oligomerization.
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Affiliation(s)
- Jun Yop An
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Humayun Sharif
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Gil Bu Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Kyung Jin Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Jung-Gyu Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mi Sun Jin
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Ji-Joon Song
- Department of Biological Sciences, KI for the BioCentury, Cancer Metastasis Control Center, KAIST, Daejeon 34141, Republic of Korea
| | - Jimin Wang
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Soo Hyun Eom
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.
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3
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Park DH, Kang GB, Kang DE, Hong JW, Lee MG, Kim KY, Han JW. A new manufacturing process to remove thrombogenic factors (II, VII, IX, X, and XI) from intravenous immunoglobulin gamma preparations. Biologicals 2016; 45:1-8. [PMID: 27876270 DOI: 10.1016/j.biologicals.2016.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 10/24/2016] [Accepted: 11/07/2016] [Indexed: 11/28/2022] Open
Abstract
Coagulation factors (II, VII, IX, X, and particularly XIa) remaining in high concentrations in intravenous immunoglobulin (IVIG) preparations can form thrombi, causing thromboembolic events, and in serious cases, result in death. Therefore, manufacturers of biological products must investigate the ability of their production processes to remove procoagulant activities. Previously, we were able to remove coagulation factors II, VII, IX, and X from our IVIG preparation through ethanol precipitation, but factor XIa, which plays an important role in thrombosis, remained in the intermediate products. Here, we used a chromatographic process using a new resin that binds with high capacity to IgG and removes procoagulant activities. The procoagulant activities were reduced to low levels as determined by the thrombin generation assay: <1.56 mIU/mL, chromogenic FXIa assay: <0.16 mIU/mL, non-activated partial thromboplastin time (NaPTT): >250 s, FXI/FXIa ELISA: <0.31 ng/mL. Even after spiking with FXIa at a concentration 32.5 times higher than the concentration in normal specimens, the procoagulant activities were below the detection limit (<0.31 ng/mL). These results demonstrate the ability of our manufacturing process to remove procoagulant activities to below the detection limit (except by NaPTT), suggesting a reduced risk of thromboembolic events that maybe potentially caused by our IVIG preparation.
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Affiliation(s)
- Dong Hwarn Park
- Green Cross Corp., Ihyeon-ro 30 beon-gil, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Gil Bu Kang
- Green Cross Corp., Ihyeon-ro 30 beon-gil, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Dae Eun Kang
- Green Cross Corp., Ihyeon-ro 30 beon-gil, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Jeung Woon Hong
- Green Cross Corp., Ihyeon-ro 30 beon-gil, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Min Gyu Lee
- Research Center for Epigenome Regulation, School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ki Yong Kim
- Green Cross Corp., Ihyeon-ro 30 beon-gil, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea.
| | - Jeung Whan Han
- Research Center for Epigenome Regulation, School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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4
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Youn HS, Kim TG, Kim MK, Kang GB, Kang JY, Lee JG, An JY, Park KR, Lee Y, Im YJ, Lee JH, Eom SH. Structural Insights into the Quaternary Catalytic Mechanism of Hexameric Human Quinolinate Phosphoribosyltransferase, a Key Enzyme in de novo NAD Biosynthesis. Sci Rep 2016; 6:19681. [PMID: 26805589 PMCID: PMC4726147 DOI: 10.1038/srep19681] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 12/14/2015] [Indexed: 11/09/2022] Open
Abstract
Quinolinate phosphoribosyltransferase (QPRT) catalyses the production of nicotinic
acid mononucleotide, a precursor of de novo biosynthesis of the ubiquitous
coenzyme nicotinamide adenine dinucleotide. QPRT is also essential for maintaining
the homeostasis of quinolinic acid in the brain, a possible neurotoxin causing
various neurodegenerative diseases. Although QPRT has been extensively analysed, the
molecular basis of the reaction catalysed by human QPRT remains unclear. Here, we
present the crystal structures of hexameric human QPRT in the apo form and its
complexes with reactant or product. We found that the interaction between dimeric
subunits was dramatically altered during the reaction process by conformational
changes of two flexible loops in the active site at the dimer-dimer interface. In
addition, the N-terminal short helix α1 was identified as a critical
hexamer stabilizer. The structural features, size distribution, heat aggregation and
ITC studies of the full-length enzyme and the enzyme lacking helix α1
strongly suggest that human QPRT acts as a hexamer for cooperative reactant binding
via three dimeric subunits and maintaining stability. Based on our comparison of
human QPRT structures in the apo and complex forms, we propose a drug design
strategy targeting malignant glioma.
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Affiliation(s)
- Hyung-Seop Youn
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Tae Gyun Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Mun-Kyoung Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Gil Bu Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Jung Youn Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Jung-Gyu Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Jun Yop An
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Kyoung Ryoung Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Youngjin Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Young Jun Im
- College of Pharmacy, Chonnam National University, Gwangju 500-757, South Korea
| | - Jun Hyuck Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, South Korea.,Department of Polar Sciences, Korea University of Science and Technology, Incheon 406-840, South Korea
| | - Soo Hyun Eom
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
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5
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An JY, Kim TG, Park KR, Lee JG, Youn HS, Lee Y, Kang JY, Kang GB, Eom SH. Crystal structure of the N-terminal domain of MinC dimerized via domain swapping. J Synchrotron Radiat 2013; 20:984-8. [PMID: 24121353 PMCID: PMC3795569 DOI: 10.1107/s0909049513022760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 08/13/2013] [Indexed: 06/02/2023]
Abstract
Proper cell division at the mid-site of gram-negative bacteria reflects critical regulation by the min system (MinC, MinD and MinE) of the cytokinetic Z ring, which is a polymer composed of FtsZ subunits. MinC and MinD act together to inhibit aberrantly positioned Z-ring formation. MinC consists of two domains: an N-terminal domain (MinCNTD), which interacts with FtsZ and inhibits FtsZ polymerization, and a C-terminal domain (MinCCTD), which interacts with MinD and inhibits the bundling of FtsZ filaments. These two domains reportedly function together, and both are essential for normal cell division. The full-length dimeric structure of MinC from Thermotoga maritima has been reported, and shows that MinC dimerization occurs via MinCCTD; MinCNTD is not involved in dimerization. Here the crystal structure of Escherichia coli MinCNTD (EcoMinCNTD) is reported. EcoMinCNTD forms a dimer via domain swapping between the first β strands in each subunit. It is therefore suggested that the dimerization of full-length EcoMinC occurs via both MinCCTD and MinCNTD, and that the dimerized EcoMinCNTD likely plays an important role in inhibiting aberrant Z-ring localization.
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Affiliation(s)
- Jun Yop An
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Tae Gyun Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Kyoung Ryoung Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Jung-Gyu Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Hyung-Seop Youn
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Youngjin Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Jung Youn Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Gil Bu Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Soo Hyun Eom
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
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6
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Youn HS, Kim MK, Kang GB, Kim TG, Lee JG, An JY, Park KR, Lee Y, Kang JY, Song HE, Park I, Cho C, Fukuoka SI, Eom SH. Crystal structure of Sus scrofa quinolinate phosphoribosyltransferase in complex with nicotinate mononucleotide. PLoS One 2013; 8:e62027. [PMID: 23626766 PMCID: PMC3633916 DOI: 10.1371/journal.pone.0062027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 03/17/2013] [Indexed: 11/25/2022] Open
Abstract
We have determined the crystal structure of porcine quinolinate phosphoribosyltransferase (QAPRTase) in complex with nicotinate mononucleotide (NAMN), which is the first crystal structure of a mammalian QAPRTase with its reaction product. The structure was determined from protein obtained from the porcine kidney. Because the full protein sequence of porcine QAPRTase was not available in either protein or nucleotide databases, cDNA was synthesized using reverse transcriptase-polymerase chain reaction to determine the porcine QAPRTase amino acid sequence. The crystal structure revealed that porcine QAPRTases have a hexameric structure that is similar to other eukaryotic QAPRTases, such as the human and yeast enzymes. However, the interaction between NAMN and porcine QAPRTase was different from the interaction found in prokaryotic enzymes, such as those of Helicobacter pylori and Mycobacterium tuberculosis. The crystal structure of porcine QAPRTase in complex with NAMN provides a structural framework for understanding the unique properties of the mammalian QAPRTase active site and designing new antibiotics that are selective for the QAPRTases of pathogenic bacteria, such as H. pylori and M. tuberculosis.
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Affiliation(s)
- Hyung-Seop Youn
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Mun-Kyoung Kim
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Gil Bu Kang
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Tae Gyun Kim
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Jung-Gyu Lee
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Jun Yop An
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Kyoung Ryoung Park
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Youngjin Lee
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Jung Youn Kang
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Hye-Eun Song
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Inju Park
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Chunghee Cho
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Shin-Ichi Fukuoka
- School of Culture and Creative Studies, Aoyama Gakuin University, Tokyo, Japan
| | - Soo Hyun Eom
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- * E-mail:
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7
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Youn HS, Kim MK, Kang GB, Kim TG, An JY, Lee JG, Park KR, Lee Y, Fukuoka SI, Eom SH. Crystallization and preliminary X-ray crystallographic analysis of quinolinate phosphoribosyltransferase from porcine kidney in complex with nicotinate mononucleotide. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012. [PMID: 23192029 DOI: 10.1107/s1744309112040638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Quinolinate phosphoribosyltransferase (QAPRTase) is a key enzyme in NAD biosynthesis; it catalyzes the formation of nicotinate mononucleotide (NAMN) from quinolinate and 5-phosphoribosyl-1-pyrophosphate. In order to elucidate the mechanism of NAMN biosynthesis, crystals of Sus scrofa QAPRTase (Ss-QAPRTase) purified from porcine kidney in complex with NAMN were obtained and diffraction data were collected and processed to 2.1 Å resolution. The Ss-QAPRTase-NAMN cocrystals belonged to space group P321, with unit-cell parameters a=119.1, b=119.1, c=93.7 Å, γ=120.0°. The Matthews coefficient and the solvent content were estimated as 3.10 Å3 Da(-1) and 60.3%, respectively, assuming the presence of two molecules in the asymmetric unit.
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Affiliation(s)
- Hyung-Seop Youn
- School of Life Sciences, Cell Dynamics Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
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8
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Kang GB, Kim MK, Youn HS, An JY, Lee JG, Park KR, Lee SH, Kim Y, Fukuoka SI, Eom SH. Crystallization and preliminary X-ray crystallographic analysis of human quinolinate phosphoribosyltransferase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 67:38-40. [PMID: 21206019 DOI: 10.1107/s1744309110041011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 10/12/2010] [Indexed: 11/10/2022]
Abstract
Quinolinate phosphoribosyltransferase (QPRTase) is a key NAD-biosynthetic enzyme which catalyzes the transfer of quinolinic acid to 5-phosphoribosyl-1-pyrophosphate, yielding nicotinic acid mononucleotide. Homo sapiens QPRTase (Hs-QPRTase) appeared as a hexamer during purification and the protein was crystallized. Diffraction data were collected and processed at 2.8 Å resolution. Native Hs-QPRTase crystals belonged to space group P2(1), with unit-cell parameters a=76.2, b=137.1, c=92.7 Å, β=103.8°. Assuming the presence of six molecules in the asymmetric unit, the calculated Matthews coefficient is 2.46 Å3 Da(-1), which corresponds to a solvent content of 49.9%.
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Affiliation(s)
- Gil Bu Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
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Ko S, Kang GB, Song SM, Lee JG, Shin DY, Yun JH, Sheng Y, Cheong C, Jeon YH, Jung YK, Arrowsmith CH, Avvakumov GV, Dhe-Paganon S, Yoo YJ, Eom SH, Lee W. Structural basis of E2-25K/UBB+1 interaction leading to proteasome inhibition and neurotoxicity. J Biol Chem 2010; 285:36070-80. [PMID: 20826778 DOI: 10.1074/jbc.m110.145219] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
E2-25K/Hip2 is an unusual ubiquitin-conjugating enzyme that interacts with the frameshift mutant of ubiquitin B (UBB(+1)) and has been identified as a crucial factor regulating amyloid-β neurotoxicity. To study the structural basis of the neurotoxicity mediated by the E2-25K-UBB(+1) interaction, we determined the three-dimensional structures of UBB(+1), E2-25K and the E2-25K/ubiquitin, and E2-25K/UBB(+1) complex. The structures revealed that ubiquitin or UBB(+1) is bound to E2-25K via the enzyme MGF motif and residues in α9 of the enzyme. Polyubiquitylation assays together with analyses of various E2-25K mutants showed that disrupting UBB(+1) binding markedly diminishes synthesis of neurotoxic UBB(+1)-anchored polyubiquitin. These results suggest that the interaction between E2-25K and UBB(+1) is critical for the synthesis and accumulation of UBB(+1)-anchored polyubiquitin, which results in proteasomal inhibition and neuronal cell death.
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Affiliation(s)
- Sunggeon Ko
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
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10
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Kang GB, Song HE, Kim MK, Youn HS, An JY, Lee JG, Park KR, Eom SH. Crystallization and preliminary X-ray crystallographic analysis of MinE, the cell-division topological specificity factor from Helicobacter pylori. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:527-9. [PMID: 20445251 DOI: 10.1107/s1744309110009784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 03/16/2010] [Indexed: 11/10/2022]
Abstract
Cell division in Gram-negative bacteria is driven by the formation of an FtsZ ring at the division site. MinE regulates the proper placement of the FtsZ ring at mid-cell by blocking the inhibitory action of the MinCD complex. Diffraction data were collected at 2.8 A resolution from a native crystal of full-length Helicobacter pylori MinE. The crystal belonged to space group P6(4). Assuming the presence of two molecules in the asymmetric unit, the calculated Matthews coefficient was 2.58 A(3) Da(-1), which corresponds to a solvent content of 52.3%. For MAD phasing, a four-wavelength data set was collected at 3.0 A resolution.
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Affiliation(s)
- Gil Bu Kang
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
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11
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Kang GB, Song HE, Kim MK, Youn HS, Lee JG, An JY, Chun JS, Jeon H, Eom SH. Crystal structure of Helicobacter pylori MinE, a cell division topological specificity factor. Mol Microbiol 2010; 76:1222-31. [PMID: 20398219 PMCID: PMC2883074 DOI: 10.1111/j.1365-2958.2010.07160.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In Gram-negative bacteria, proper placement of the FtsZ ring, mediated by nucleoid occlusion and the activities of the dynamic oscillating Min proteins MinC, MinD and MinE, is required for correct positioning of the cell division septum. MinE is a topological specificity factor that counters the activity of MinCD division inhibitor at the mid-cell division site. Its structure consists of an anti-MinCD domain and a topology specificity domain (TSD). Previous NMR analysis of truncated Escherichia coli MinE showed that the TSD domain contains a long alpha-helix and two anti-parallel beta-strands, which mediate formation of a homodimeric alpha/beta structure. Here we report the crystal structure of full-length Helicobacter pylori MinE and redefine its TSD based on that structure. The N-terminal region of the TSD (residues 19-26), previously defined as part of the anti-MinCD domain, forms a beta-strand (betaA) and participates in TSD folding. In addition, H. pylori MinE forms a dimer through the interaction of anti-parallel betaA-strands. Moreover, we observed serial dimer-dimer interactions within the crystal packing, resulting in the formation of a multimeric structure. We therefore redefine the functional domain of MinE and propose that a multimeric filamentous structure is formed through anti-parallel beta-strand interactions.
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Affiliation(s)
- Gil Bu Kang
- School of Life Science, Gwangju Institute of Science & Technology (GIST), Gwangju 500-712, Korea
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12
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Sahoo SK, Kim T, Kang GB, Lee JG, Eom SH, Kim DH. Characterization of calumenin-SERCA2 interaction in mouse cardiac sarcoplasmic reticulum. J Biol Chem 2009; 284:31109-21. [PMID: 19740751 DOI: 10.1074/jbc.m109.031989] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Calumenin is a multiple EF-hand Ca(2+)-binding protein localized in the sarcoplasmic reticulum (SR) with C-terminal SR retention signal HDEF. Recently, we showed evidence that calumenin interacts with SERCA2 in rat cardiac SR (Sahoo, S. K., and Kim, D. H. (2008) Mol. Cells 26, 265-269). The present study was undertaken to further characterize the association of calumenin with SERCA2 in mouse heart by various gene manipulation approaches. Immunocytochemical analysis showed that calumenin and SERCA2 were partially co-localized in HL-1 cells. Knockdown (KD) of calumenin was conducted in HL-1 cells and 80% reduction of calumenin did not induce any expressional changes of other Ca(2+)-cycling proteins. But it enhanced Ca(2+) transient amplitude and showed shortened time to reach peak and decreased time to reach 50% of baseline. Oxalate-supported Ca(2+) uptake showed increased Ca(2+) sensitivity of SERCA2 in calumenin KD HL-1 cells. Calumenin and SERCA2 interaction was significantly lower in the presence of thapsigargin, vanadate, or ATP, as compared with 1.3 mum Ca(2+), suggesting that the interaction is favored in the E1 state of SERCA2. A glutathione S-transferase-pulldown assay of calumenin deletion fragments and SERCA2 luminal domains suggested that regions of 132-222 amino acids of calumenin and 853-892 amino acids of SERCA2-L4 are the major binding partners. On the basis of our in vitro binding data and available information on three-dimensional structure of Ca(2+)-ATPases, a molecular model was proposed for the interaction between calumenin and SERCA2. Taken together, the present results suggest that calumenin is a novel regulator of SERCA2, and its expressional changes are tightly coupled with Ca(2+)-cycling of cardiomyocytes.
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Affiliation(s)
- Sanjaya Kumar Sahoo
- Department of Life Science and Systems Biology Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
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13
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Kang GB, Bae MH, Kim MK, Im I, Kim YC, Eom SH. Crystal structure of Rattus norvegicus Visfatin/PBEF/Nampt in complex with an FK866-based inhibitor. Mol Cells 2009; 27:667-71. [PMID: 19533035 DOI: 10.1007/s10059-009-0088-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 04/16/2009] [Accepted: 04/17/2009] [Indexed: 11/29/2022] Open
Abstract
Visfatin (Nampt/PBEF) plays a pivotal role in the salvage pathway for NAD(+) biosynthesis. Its potent inhibitor, FK866, causes cellular NAD(+) levels to decline, thereby inducing apoptosis in tumor cells. In an effort to improve the solubility and binding interactions of FK866, we designed and synthesized IS001, in which a ribose group is attached to the FK866 pyridyl ring. Here, we report the crystal structure of rat visfatin in complex with IS001. Like FK866, IS001 is positioned at the dimer interface, and all of the residues that interact with IS001 are involved in hydrophobic or pi-pi-stacking interactions. However, we were unable to detect any strong interactions between the added ribose ring of IS001 and visfatin, which implies that a bulkier modifying group is necessary for a tight interaction. This study provides additional structure-based information needed to optimize the design of visfatin inhibitors.
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Affiliation(s)
- Gil Bu Kang
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
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14
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Kim SH, Kang GB, Song HE, Park SJ, Bea MH, Eom SH. Structural studies on Helicobacter pyloriATP-dependent protease, FtsH. J Synchrotron Radiat 2008; 15:208-210. [PMID: 18421140 PMCID: PMC2394826 DOI: 10.1107/s090904950706846x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 01/11/2008] [Indexed: 05/26/2023]
Abstract
The ATP-dependent protease, FtsH, degrades misassembled membrane proteins for quality control like SecY, subunit a of FoF1-ATPase, and YccA, and digests short-lived soluble proteins in order to control their cellular regulation, including sigma32, LpxC and lambdacII. The FtsH protein has an N-terminal transmembrane segment and a large cytosolic region that consists of two domains, an ATPase and a protease domain. To provide a structural basis for the nucleotide-dependent domain motions and a better understanding of substrate translocation, the crystal structures of the Helicobacter pylori (Hp) FtsH ATPase domain in the nucleotide-free state and complexed with ADP, were determined. Two different structures of HpFtsH ATPase were observed, with the nucleotide-free state in an asymmetric unit, and these structures reveal the new forms and show other conformational differences between the nucleotide-free and ADP-bound state compared with previous structures. In particular, one HpFtsH Apo structure has a considerable rotation difference compared with the HpFtsH ADP complex, and this large conformational change reveals that FtsH may have the mechanical force needed for substrate translocation.
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Affiliation(s)
- Sung Hyun Kim
- Department of Life Science, Cell Dynamics Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Gil Bu Kang
- Department of Life Science, Cell Dynamics Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Hye-Eun Song
- Department of Life Science, Cell Dynamics Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Sang Jin Park
- Department of Life Science, Cell Dynamics Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Man-Ho Bea
- Department of Life Science, Cell Dynamics Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Soo Hyun Eom
- Department of Life Science, Cell Dynamics Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
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15
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Abstract
Quinolinic acid phosphoribosyltransferase (QAPRTase; NadC) catalyzes an indispensable step in NAD biosynthesis, one that is essential for cell survival in prokaryotes, which makes it an attractive target for antibacterial drug therapy. We recently reported the crystal structures of Helicobacter pylori QAPRTase with bound quinolinic acid, nicotinamide mononucleotide, and phthalic acid. The enzyme exists as a hexamer organized as a trimer of dimers, which is essential for full enzymatic activity. The loop between helix alpha7 and strand beta8 contributes significantly to the hydrophobic dimer-dimer interactions. Phe181Pro mutation within the alpha7-beta8 loop disrupts the hexamerization of QAPRTase, and the resultant dimer shows dramatically reduced protein stability and no activity. Our findings thus suggest that compounds able to disrupt its proper oligomerization could potentially function as selective inhibitors of Helicobacter pylori QAPRTase and represent a novel set of antibacterial agents.
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Affiliation(s)
- M-K Kim
- Department of Life Science, Gwangju Institute of Science & Technology, Gwangju, 500-712, Republic of Korea
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16
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Kim JY, Kim MK, Kang GB, Park CS, Eom SH. Crystal structure of the leucine zipper domain of small-conductance Ca2+-activated K+ (SK(Ca)) channel from Rattus norvegicus. Proteins 2008; 70:568-71. [PMID: 17910055 DOI: 10.1002/prot.21634] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ji-Yoen Kim
- Department of Life Science, Gwangju Institute of Science & Technology, Gwangju 500-712, Korea
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17
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Abstract
Ryanodine receptor 1 (RyR1) is a large homotetrameric calcium channel that plays a pivotal role in skeletal muscle contraction. Sequence comparison and mutagenesis studies indicate that the pore architecture of RyR1, including the last two transmembrane helices and the luminal loop linking them, is similar to that of the bacterial KcsA K(+) channel. Here, we describe the overexpression and purification of the C-terminal polyhistidine-tagged RyR1 pore-forming region. The nonionic detergent lauryldimethylamine oxide (LDAO) was selected for solubilization of the protein based on its ability to extract the protein from the membrane and to maintain it in a monodisperse state. The protein was then purified using nickel-affinity chromatography and gel filtration. Gel filtration analysis confirmed that the RyR1 fragment containing the pore-forming region (amino acids 4829-5037) is sufficient to form a tetramer.
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Affiliation(s)
- Gil Bu Kang
- Department of Life Science, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
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18
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Rho SH, Park HH, Kang GB, Im YJ, Kang MS, Lim BK, Seong IS, Seol J, Chung CH, Wang J, Eom SH. Crystal structure ofBacillus subtilis CodW, a noncanonical HslV-like peptidase with an impaired catalytic apparatus. Proteins 2008; 71:1020-6. [DOI: 10.1002/prot.21758] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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19
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Lee JH, Kang GB, Lim HH, Jin KS, Kim SH, Ree M, Park CS, Kim SJ, Eom SH. Crystal structure of the GluR0 ligand-binding core from Nostoc punctiforme in complex with L-glutamate: structural dissection of the ligand interaction and subunit interface. J Mol Biol 2007; 376:308-16. [PMID: 18164033 DOI: 10.1016/j.jmb.2007.10.081] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 10/20/2007] [Accepted: 10/23/2007] [Indexed: 11/26/2022]
Abstract
GluR0 from Nostoc punctiforme (NpGluR0) is a bacterial homologue of the ionotropic glutamate receptor (iGluR). We have solved the crystal structure of the ligand-binding core of NpGluR0 in complex with l-glutamate at a resolution of 2.1 A. The structure exhibits a noncanonical ligand interaction and two distinct subunit interfaces. The side-chain guanidium group of Arg80 forms a salt bridge with the gamma-carboxyl group of bound L-glutamate: in GluR0 from Synechocystis (SGluR0) and other iGluRs, the equivalent residues are Asn or Thr, which cannot form a similar interaction. We suggest that the local positively charged environment and the steric constraint created by Arg80 mediate the selectivity of L-glutamate binding by preventing the binding of positively charged and hydrophobic amino acids. In addition, the NpGluR0 ligand-binding core forms a new subunit interface in which the two protomers are arranged differently than the known iGluR and SGluR0 dimer interfaces. The significance of there being two different dimer interfaces was investigated using analytical ultracentrifugation analysis.
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Affiliation(s)
- Jun Hyuck Lee
- Department of Life Science, Cell Dynamics Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju 500-712, Republic of Korea
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20
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Cho JH, Ko KM, Singaruvelu G, Lee W, Kang GB, Rho SH, Park BJ, Yu JR, Kagawa H, Eom SH, Kim DH, Ahnn J. Functional importance of polymerization and localization of calsequestrin in C. elegans. J Cell Sci 2007; 120:1551-8. [PMID: 17405817 DOI: 10.1242/jcs.001016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dual roles of calsequestrin (CSQ-1) being the Ca2+ donor and Ca2+ acceptor make it an excellent Ca2+-buffering protein within the sarcoplasmic reticulum (SR). We have isolated and characterized a calsequestrin (csq-1)-null mutant in Caenorhabditis elegans. To our surprise, this mutant csq-1(jh109) showed no gross defects in muscle development or function but, however, is highly sensitive to perturbation of Ca2+ homeostasis. By taking advantage of the viable null mutant, we investigated the domains of CSQ-1 that are important for polymerization and cellular localization, and required for its correct buffering functions. In transgenic animals rescued with various CSQ-1 constructs, the in vivo patterns of polymerization and localization of several mutated calsequestrins were observed to correlate with the structure-function relationship. Our results suggest that polymerization of CSQ-1 is essential but not sufficient for correct cellular localization and function of CSQ-1. In addition, direct interaction between CSQ-1 and the ryanodine receptor (RyR) was found for the first time, suggesting that the cellular localization of CSQ-1 in C. elegans is indeed modulated by RyR through a physical interaction.
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Affiliation(s)
- Jeong Hoon Cho
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju, 500-712, Korea.
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21
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Kim MK, Cho MK, Song HE, Kim D, Park BH, Lee JH, Kang GB, Kim SH, Im YJ, Lee DS, Eom SH. Crystal structure of UDP-N-acetylenolpyruvylglucosamine reductase (MurB) from Thermus caldophilus. Proteins 2007; 66:751-4. [PMID: 17120230 DOI: 10.1002/prot.21174] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mun-Kyoung Kim
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
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22
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Lee JH, Im YJ, Bae J, Kim D, Kim MK, Kang GB, Lee DS, Eom SH. Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation. Biochem Biophys Res Commun 2006; 350:1044-9. [PMID: 17045964 DOI: 10.1016/j.bbrc.2006.09.151] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Accepted: 09/28/2006] [Indexed: 11/22/2022]
Abstract
Phosphoglycerate kinase (PGK) is a key glycolytic enzyme that catalyzes the reversible transfer of a phosphate from 1,3-bisphosphoglycerate to ADP to form 3-phosphoglycerate and ATP in the presence of magnesium. During catalysis, a conformational change occurs that brings the N- and C-domains of PGK closer together. Here we present the 1.8A crystal structure of unliganded PGK from Thermus caldophilus (Tca). Comparison of the structure of TcaPGK (open conformation) with that of Thermotoga maritima (Tma) PGK (closed conformation) revealed that the conformational change reflects a change in the interaction between the domains. We identified Arg148 as a key residue involved in open-to-closed transition. The open conformation of TcaPGK is stabilized by an interdomain salt bridge between Arg148 and Glu375. The binding of 3-PG (or maybe 1,3-BPG) disrupts this salt bridge and, in ternary complex, the formation of new salt bridge between Arg60 and Asp197 stabilizes the closed conformation.
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Affiliation(s)
- Jun Hyuck Lee
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
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23
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Kim MK, Lee JH, Kim H, Park SJ, Kim SH, Kang GB, Lee YS, Kim JB, Kim KK, Suh SW, Eom SH. Crystal structure of visfatin/pre-B cell colony-enhancing factor 1/nicotinamide phosphoribosyltransferase, free and in complex with the anti-cancer agent FK-866. J Mol Biol 2006; 362:66-77. [PMID: 16901503 DOI: 10.1016/j.jmb.2006.06.082] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2006] [Revised: 06/28/2006] [Accepted: 06/29/2006] [Indexed: 01/24/2023]
Abstract
Visfatin/pre-B cell colony-enhancing factor 1 (PBEF)/nicotinamide phosphoribosyltransferase (NAmPRTase) is a multifunctional protein having phosphoribosyltransferase, cytokine and adipokine activities. Originally isolated as a cytokine promoting the differentiation of B cell precursors, it was recently suggested to act as an insulin analog via the insulin receptor. Here, we describe the first crystal structure of visfatin in three different forms: apo and in complex with either nicotinamide mononucleotide (NMN) or the NAmPRTase inhibitor FK-866 which was developed as an anti-cancer agent, interferes with NAD biosynthesis, showing a particularly high specificity for NAmPRTase. The crystal structures of the complexes with either NMN or FK-866 show that the enzymatic active site of visfatin is optimized for nicotinamide binding and that the nicotinamide-binding site is important for inhibition by FK-866. Interestingly, visfatin mimics insulin signaling by binding to the insulin receptor with an affinity similar to that of insulin and does not share the binding site with insulin on the insulin receptor. To predict binding sites, the potential interaction patches of visfatin and the L1-CR-L2 domain of insulin receptor were generated and analyzed. Although the relationship between the insulin-mimetic property and the enzymatic function of visfatin has not been clearly established, our structures raise the intriguing possibility that the glucose metabolism and the NAD biosynthesis are linked by visfatin.
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Affiliation(s)
- Mun-Kyoung Kim
- Department of Life Science, Gwangju Institute of Science & Technology, Gwangju 500-712, Korea
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24
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Lee JH, Bae J, Kim D, Choi Y, Im YJ, Koh S, Kim JS, Kim MK, Kang GB, Hong SI, Lee DS, Eom SH. Stereoselectivity of fructose-1,6-bisphosphate aldolase in Thermus caldophilus. Biochem Biophys Res Commun 2006; 347:616-25. [PMID: 16843441 DOI: 10.1016/j.bbrc.2006.06.139] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Accepted: 06/21/2006] [Indexed: 10/24/2022]
Abstract
It was recently established that fructose-1,6-bisphosphate (FBP) aldolase (FBA) and tagatose-1,6-bisphosphate (TBP) aldolase (TBA), two class II aldolases, are highly specific for the diastereoselective synthesis of FBP and TBP from glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP), respectively. In this paper, we report on a FBA from the thermophile Thermus caldophilus GK24 (Tca) that produces both FBP and TBP from C(3) substrates. Moreover, the FBP:TBP ratio could be adjusted by manipulating the concentrations of G3P and DHAP. This is the first native FBA known to show dual diastereoselectivity among the FBAs and TBAs characterized thus far. To explain the behavior of this enzyme, the X-ray crystal structure of the Tca FBA in complex with DHAP was determined at 2.2A resolution. It appears that as a result of alteration of five G3P binding residues, the substrate binding cavity of Tca FBA has a greater volume than those in the Escherichia coli FBA-phosphoglycolohydroxamate (PGH) and TBA-PGH complexes. We suggest that this steric difference underlies the difference in the diastereoselectivities of these class II aldolases.
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Affiliation(s)
- Jun Hyuck Lee
- Department of Life Science, Gwangju Institute of Science and Technology, Republic of Korea
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25
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Lee JH, Na Y, Song HE, Kim D, Park BH, Rho SH, Im YJ, Kim MK, Kang GB, Lee DS, Eom SH. Crystal structure of the apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: A basis for the substrate-induced conformational changes. Proteins 2006; 64:1078-82. [PMID: 16779845 DOI: 10.1002/prot.20927] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jun Hyuck Lee
- Department of Life Science, Gwangju Institute of Science & Technology, Gwangju, Korea
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26
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Affiliation(s)
- Gil Bu Kang
- Department of Life Science, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
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27
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Lee JH, Kim SY, Rho SH, Im YJ, Kim YR, Kim MK, Kang GB, Rhee JH, Eom SH. Crystallization and preliminary X-ray crystallographic analysis of PAS factor from Vibrio vulnificus. Mol Cells 2005; 20:361-3. [PMID: 16404150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
Plasmid Achromobacter secretion (PAS) factor is a putative secretion factor that induces the secretion of periplasmic proteins. PAS factor from Vibrio vulnificus was crystallized at 294 K by the hanging drop vapor-diffusion method. It was isolated as a monomer during the purification procedures. The native crystal belongs to the F222 space group with unit cell parameters a=56.1, b=74.4, c=80.0 A, a=b=g=90 degrees. The crystal was soaked in cryoprotectant containing 1 M NaBr for 1 h for MAD phasing. The diffraction limit of the Br-MAD data set was 1.9 A using synchrotron X-ray irradiation at beam line BL-18B at the Photon Factory, Japan.
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Affiliation(s)
- Jun Hyuck Lee
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
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28
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Lee JH, Yang ST, Rho SH, Im YJ, Kim SY, Kim YR, Kim MK, Kang GB, Kim JI, Rhee JH, Eom SH. Crystal structure and functional studies reveal that PAS factor from Vibrio vulnificus is a novel member of the saposin-fold family. J Mol Biol 2005; 355:491-500. [PMID: 16318855 DOI: 10.1016/j.jmb.2005.10.074] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Revised: 10/25/2005] [Accepted: 10/27/2005] [Indexed: 12/01/2022]
Abstract
PAS factor is a novel putative bacterial secretion factor thought to induce secretion of periplasmic proteins. We solved the crystal structure of PAS factor from Vibrio vulnificus at 1.8A resolution and found it to be comprised of five alpha helices that form an antiparallel bundle with an up-and-down topology, and to adopt the saposin-fold characteristic of a family of proteins that bind to membranes and lipids. PAS factor lacks the disulfide bridge characteristic of mammalian saposin-fold proteins; in fact, it shows no sequence homology with mammalian proteins. Nevertheless, the molecular architectures are similar, and the shared propensity for membrane interaction suggests strongly that PAS factor is another member of the saposin-fold family. Analysis of the CD spectra showed that PAS factor binds to membranes directly, while measurement of calcein dye leakage showed that PAS factor interacts strongly with liposomes composed of anionic phospholipids, making them leaky, but binds very weakly with liposomes composed of zwitterionic phospholipids. Moreover, by analyzing tryptophan fluorescence emission from four single-tryptophan mutants (V10W, T22W, F35W, and L70W), we identified the putative phospholipid-binding site of PAS factor. The resultant membrane destabilization likely mediates secretion of periplasmic proteins required for the in vivo survival and pathogenesis of V.vulnificus.
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Affiliation(s)
- Jun Hyuck Lee
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
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29
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Lee JH, Park SJ, Rho SH, Im YJ, Kim MK, Kang GB, Eom SH. Crystallization and preliminary X-ray crystallographic analysis of the GluR0 ligand-binding core from Nostoc punctiforme. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:1020-2. [PMID: 16511224 PMCID: PMC1978126 DOI: 10.1107/s1744309105034329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Accepted: 10/24/2005] [Indexed: 12/31/2022]
Abstract
GluR0 from Nostoc punctiforme (NpGluR0) is a bacterial homologue of the ionotropic glutamate receptor. The ligand-binding core of NpGluR0 was crystallized at 294 K using the hanging-drop vapour-diffusion method. The L-glutamate-complexed crystal belongs to space group C222(1), with unit-cell parameters a = 78.0, b = 145.1, c = 132.1 A. The crystals contain three subunits in the asymmetric unit, with a VM value of 2.49 A3 Da(-1). The diffraction limit of the L-glutamate complex data set was 2.1 A using synchrotron X-ray radiation at beamline BL-4A of the Pohang Accelerator Laboratory (Pohang, Korea).
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Affiliation(s)
- Jun Hyuck Lee
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Soo Jeong Park
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Seong-Hwan Rho
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Young Jun Im
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Mun-Kyoung Kim
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Gil Bu Kang
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Soo Hyun Eom
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
- Correspondence e-mail:
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30
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Im YJ, Na Y, Kang GB, Rho SH, Kim MK, Lee JH, Chung CH, Eom SH. The active site of a lon protease from Methanococcus jannaschii distinctly differs from the canonical catalytic Dyad of Lon proteases. J Biol Chem 2004; 279:53451-7. [PMID: 15456757 DOI: 10.1074/jbc.m410437200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATP-dependent Lon proteases catalyze the degradation of various regulatory proteins and abnormal proteins within cells. Methanococcus jannaschii Lon (Mj-Lon) is a homologue of Escherichia coli Lon (Ec-Lon) but has two transmembrane helices within its N-terminal ATPase domain. We solved the crystal structure of the proteolytic domain of Mj-Lon using multiwavelength anomalous dispersion, refining it to 1.9-angstroms resolution. The structure displays an overall fold conserved in the proteolytic domain of Ec-Lon; however, the active site shows uniquely configured catalytic Ser-Lys-Asp residues that are not seen in Ec-Lon, which contains a catalytic dyad. In Mj-Lon, the C-terminal half of the beta4-alpha2 segment is an alpha-helix, whereas it is a beta-strand in Ec-Lon. Consequently, the configurations of the active sites differ due to the formation of a salt bridge between Asp-547 and Lys-593 in Mj-Lon. Moreover, unlike Ec-Lon, Mj-Lon has a buried cavity in the region of the active site containing three water molecules, one of which is hydrogen-bonded to catalytic Ser-550. The geometry and environment of the active site residues in Mj-Lon suggest that the charged Lys-593 assists in lowering the pK(a) of the Ser-550 hydroxyl group via its electrostatic potential, and the water in the cavity acts as a proton acceptor during catalysis. Extensive sequence alignment and comparison of the structures of the proteolytic domains clearly indicate that Lon proteases can be classified into two groups depending on active site configuration and the presence of DGPSA or (D/E)GDSA consensus sequences, as represented by Ec-Lon and Mj-Lon.
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Affiliation(s)
- Young Jun Im
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
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Im YJ, Lee JH, Park SH, Park SJ, Rho SH, Kang GB, Kim E, Eom SH. Crystal structure of the Shank PDZ-ligand complex reveals a class I PDZ interaction and a novel PDZ-PDZ dimerization. J Biol Chem 2003; 278:48099-104. [PMID: 12954649 DOI: 10.1074/jbc.m306919200] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Shank/proline-rich synapse-associated protein family of multidomain proteins is known to play an important role in the organization of synaptic multiprotein complexes. For instance, the Shank PDZ domain binds to the C termini of guanylate kinase-associated proteins, which in turn interact with the guanylate kinase domain of postsynaptic density-95 scaffolding proteins. Here we describe the crystal structures of Shank1 PDZ in its peptide free form and in complex with the C-terminal hexapeptide (EAQTRL) of guanylate kinase-associated protein (GKAP1a) determined at 1.8- and 2.25-A resolutions, respectively. The structure shows the typical class I PDZ interaction of PDZ-peptide complex with the consensus sequence -X-(Thr/Ser)-X-Leu. In addition, Asp-634 within the Shank1 PDZ domain recognizes the positively charged Arg at -1 position and hydrogen bonds, and salt bridges between Arg-607 and the side chains of the ligand at -3 and -5 positions contribute further to the recognition of the peptide ligand. Remarkably, whether free or complexed, Shank1 PDZ domains form dimers with a conserved beta B/beta C loop and N-terminal beta A strands, suggesting a novel model of PDZ-PDZ homodimerization. This implies that antiparallel dimerization through the N-terminal beta A strands could be a common configuration among PDZ dimers. Within the dimeric structure, the two-peptide binding sites are arranged so that the N termini of the bound peptide ligands are in close proximity and oriented toward the 2-fold axis of the dimer. This configuration may provide a means of facilitating dimeric organization of PDZ-target assemblies.
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Affiliation(s)
- Young Jun Im
- Department of Life Science, Kwangju Institute of Science and Technology, Gwangju 500-712, South Korea
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Abstract
The ubiquitous NAD(+) synthetase catalyzes the key step in the biosynthesis of nicotinamide adenine dinucleotide. NH3-dependent NAD(+) synthetase from Helicobacter pylori was purified to homogeneity and crystallized using PEG 1500 as a precipitant. The crystal diffracted up to a resolution of 2.3+ and was found to belong to space group C2 with unit cell dimensions of a = 93.8, b = 48.3, c = 64.2 A and alpha = gamma = 90, beta = 110.0 degrees.
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Affiliation(s)
- Gil Bu Kang
- Department of Life Science, Kwangju Institute of Science and Technology (K-JIST), Gwangju 500-712, Korea
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Kim MK, Kim YS, Rho SH, Im YJ, Lee JH, Kang GB, Eom SH. Crystallization and preliminary X-ray crystallographic analysis of quinolinate phosphoribosyltransferase of Helicobacter pylori. Acta Crystallogr D Biol Crystallogr 2003; 59:1265-6. [PMID: 12832780 DOI: 10.1107/s0907444903009053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2003] [Accepted: 04/22/2003] [Indexed: 11/10/2022]
Abstract
Quinolinic acid phosphoribosyltransferase (NadC; EC 2.4.2.19) is the key enzyme of NAD(+) biosynthesis in both prokaryotes and eukaryotes. NadC catalyzes the decarboxylation of quinolinic acid (QA) to produce nicotinic acid mononucleotide (NAMN), an intermediate in NAD synthesis. NadCs of Helicobacter pylori appeared to be a hexamer during the purification procedure. Three different complexes of NadC, with QA, NAMN and phthalic acid (PA), an analogue of QA, were crystallized at 294 +/- 1 K using the hanging-drop vapour-diffusion method. The QA complex crystal was found to belong to space group P4(1)2(1)2, with unit-cell parameters a = b = 148.8, c = 145.7 A, alpha = beta = gamma = 90 degrees. Diffraction data were collected from the NadC-substrate and NadC-substrate analogue complexes to resolutions of 2.3 A (QA), 2.8 A (PA) and 3.3 A (NAMN) using synchrotron X-ray radiation.
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Affiliation(s)
- Mun-Kyoung Kim
- Department of Life Science, Kwangju Institute of Science and Technology, Gwangju 500-712, South Korea
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Kim MK, Song HE, Kim YS, Rho SH, Im YJ, Lee JH, Kang GB, Eom SH. Crystallization and preliminary X-ray crystallographic analysis of orotate phosphoribosyltransferase from Helicobacter pylori. Mol Cells 2003; 15:361-3. [PMID: 12872993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Orotic acid phosphoribosyltransferase (PyrE) (EC 2.4.2.10) is a key enzyme in de novo uridine monophosphate (UMP) biosynthesis. It catalyzes the reaction between orotic acid and 5-phosphoribosyl-1-pyrophosphate (PRPP) to yield orotidine monophosphate (OMP), which is transformed to uridine monophosphate by decarboxylation. H. pylori PyrE was crystallized at 294 +/- 1 K by the hanging drop vapor-diffusion method. The crystals belong to the space group P2(1)2(1)2(1) with unit-cell dimensions a = 95.8, b = 104.9, c = 281.1 A, alpha = beta = gamma = 90 degrees. A set of diffraction data was collected to 3.29 A resolution using synchrotron X-ray radiation.
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Affiliation(s)
- Mun-Kyoung Kim
- Department of Life Science, Kwangju Institute of Science and Technology, Gwangju 500-712, Korea
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Lee JH, Im YJ, Rho SH, Park SH, Kang GB, Cho SJ, Kim TY, Shin HJ, Lee DS, Eom SH. Crystallization and preliminary X-ray crystallographic studies of phosphoglycerate kinase from Thermus caldophilus. Mol Cells 2003; 15:370-2. [PMID: 12872995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
We report the purification and crystallization of phosphoglycerate kinase from Thermus caldophilus (Tca). The enzyme crystallizes in the P2(1)2(1)2(1) space group (cell dimensions a = 65.1, b = 71.3, c = 80.2 A), with one molecule in the asymmetric unit. A complete set of diffraction data was collected from an orthorhombic crystal up to 1.8 A resolution.
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Affiliation(s)
- Jun Hyuck Lee
- Department of Life Science, Kwangju Institute of Science and Technology, Gwangju 500-712, Korea
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Im YJ, Park SH, Rho SH, Lee JH, Kang GB, Sheng M, Kim E, Eom SH. Crystal structure of GRIP1 PDZ6-peptide complex reveals the structural basis for class II PDZ target recognition and PDZ domain-mediated multimerization. J Biol Chem 2003; 278:8501-7. [PMID: 12493751 DOI: 10.1074/jbc.m212263200] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PDZ domains bind to short segments within target proteins in a sequence-specific fashion. Glutamate receptor-interacting protein (GRIP)/ABP family proteins contain six to seven PDZ domains and interact via the sixth PDZ domain (class II) with the C termini of various proteins including liprin-alpha. In addition the PDZ456 domain mediates the formation of homo- and heteromultimers of GRIP proteins. To better understand the structural basis of peptide recognition by a class II PDZ domain and PDZ-mediated multimerization, we determined the crystal structures of the GRIP1 PDZ6 domain alone and in complex with a synthetic C-terminal octapeptide of human liprin-alpha at resolutions of 1.5 and 1.8 A, respectively. Remarkably, unlike other class II PDZ domains, Ile-736 at alphaB5 rather than conserved Leu-732 at alphaB1 makes a direct hydrophobic contact with the side chain of the Tyr at the -2 position of the ligand. Moreover, the peptide-bound structure of PDZ6 shows a slight reorientation of helix alphaB, indicating that the second hydrophobic pocket undergoes a conformational adaptation to accommodate the bulkiness of the Tyr side chain, and forms an antiparallel dimer through an interface located at a site distal to the peptide-binding groove. This configuration may enable formation of GRIP multimers and efficient clustering of GRIP-binding proteins.
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Affiliation(s)
- Young Jun Im
- Department of Life Science, Kwangju Institute of Science and Technology, Gwangju 500-712, South Korea
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Fan M, Xu Y, Zhang HY, Ren HZ, Kang GB, Wang YJ, Chen H. [Identification of quantitative trait loci associated with fruit traits in watermelon [Citullus lanantus (Thanb) Mansf] and analysis of their genetic effects]. Yi Chuan Xue Bao 2001; 27:902-10. [PMID: 11192435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
In this study, we mapped and characterized quantitative trait loci (QTL) affecting watermelon fruit traits. A total of 118 F2 progenies derived from the cross 97103 (which is a cultivar with higher total soluble solids concentration, thin rind, susceptible to Fusarium wilt disease) x PI296341(which is a wild germplasm with lower total soluble solids concentration, thick rind, resistant to Fusarium wilt disease) were used to construct a 96-markers map in watermelon. By using interval mapping 4 QTLs for total soluble solids concentration, 5 QTLs for hardness of rind, 2 QTLs for thickness of rind, 3 QTLs for weight of simple fruit, and 6 QTLs for weight of one thousand grain seeds were identified. In addition, the explained variations, additive effects and dominance effects for all detected QTLs were analyzed.
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Affiliation(s)
- M Fan
- College of Horticulture, China Agricultural University, Beijing 100094, China
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Xu Y, Zhang HY, Kang GB, Wang YJ, Chen H. [Studies of molecular marker-assisted-selection for resistance to Fusarium wilt in watermelon (Citrullus lanatus) breeding]. Yi Chuan Xue Bao 2000; 27:151-7. [PMID: 10887683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The RAPD marker OPP01/700 proved to be linked to the Fusarium wilt resistant gene in watermelon wild germplasm PI296341 was cloned and sequenced, and transferred into a SCAR marker. The linked marker was tested to be one copy by Southern blotting. The technique of detection of the SCAR-amplified products was simplified. These techniques were applied in selecting resistant plants in F3 of the introgression of the disease resistant gene. It is the first report in this field of transfer ring a RAPD marker linked to disease resistance gene into SCAR marker, and establishing the technique of molecular marker-assisted-selection for breeding Fusarium wilt resistance cultivars.
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Affiliation(s)
- Y Xu
- National Engineering Research Center for Vegetable, Beijing, China
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