Sam-Yong Park Publications

65
Terada D, Kawai F, Noguchi H, Unzai S, Hasan I, Fujii Y, Park SY, Ozeki Y, Tame JRH:
Crystal structure of mytilec, a galactose-binding lectin from the mussel mytilus galloprovincialis with cytotoxicity against certain cancer cell types.
Sci Rep (2016) 6(28344):28344.
64
Ohki M, Sugiyama K, Kawai F, Tanaka H, Nihei Y, Unzai S, Takebe M, Matsunaga S, Adachi S, Shibayama N, Zhou Z et al:
Structural insight into photoactivation of an adenylate cyclase from a photosynthetic cyanobacterium.
Proc Natl Acad Sci U S A (2016) 113(24):6659-6664.
63
Yoshida H, Park SY, Oda T, Akiyoshi T, Sato M, Shirouzu M, Tsuda K, Kuwasako K, Unzai S, Muto Y, Urano T et al:
A novel 3' splice site recognition by the two zinc fingers in the u2af small subunit.
Genes Dev (2015) 29(15):1649-1660.
62
Hirano T, Sugiyama K, Sakaki Y, Hakamata W, Park SY, Nishio T:
Structure-based analysis of domain function of chitin oligosaccharide deacetylase from vibrio parahaemolyticus.
FEBS Lett (2015) 589(1):145-151.
61
Sugiyama K, Iyori M, Sawaguchi A, Akashi S, Tame JRH, Park SY, Yoshida S:
The crystal structure of the active domain of anopheles anti-platelet protein, a powerful anti-coagulant, in complex with an antibody.
J Biol Chem (2014) 289(23):16303-16312.
60
Shibayama N, Sugiyama K, Tame JRH, Park SY:
Capturing the hemoglobin allosteric transition in a single crystal form.
J Am Chem Soc (2014) 136(13):5097-5105.
59
Nishiyama T, Noguchi H, Yoshida H, Park SY, Tame JRH:
The structure of the deacetylase domain of escherichia coli pgab, an enzyme required for biofilm formation: A circularly permuted member of the carbohydrate esterase 4 family.
Acta Crystallogr D Biol Crystallogr (2013) 69(Pt 1):44-51.
58
Cho KJ, Lee JH, Hong KW, Kim SH, Park Y, Lee JY, Kang S, Kim S, Yang JH, Kim EK, Seok JH et al:
Insight into structural diversity of influenza virus haemagglutinin.
J Gen Virol (2013) 94(Pt 8):1712-1722.
57
Yoshida H, Kawai F, Obayashi E, Akashi S, Roper DI, Tame JRH, Park SY:
Crystal structures of penicillin-binding protein 3 (pbp3) from methicillin-resistant staphylococcus aureus in the apo and cefotaxime-bound forms.
J Mol Biol (2012) 423(3):351-364.
56
Noguchi H, Campbell KL, Ho C, Unzai S, Park SY, Tame JRH:
Structures of haemoglobin from woolly mammoth in liganded and unliganded states.
Acta Crystallogr D Biol Crystallogr (2012) 68(Pt 11):1441-1449.
55
Tachiwana H, Kagawa W, Shiga T, Osakabe A, Miya Y, Saito K, Hayashi-Takanaka Y, Oda T, Sato M, Park SY, Kimura H et al:
Crystal structure of the human centromeric nucleosome containing cenp-a.
Nature (2011) 476(7359):232-235.
54
Shibayama N, Sugiyama K, Park SY:
Structures and oxygen affinities of crystalline human hemoglobin c (beta6 glu->lys) in the r and r2 quaternary structures.
J Biol Chem (2011) 286(38):33661-33668.
53
Kawai F, Clarke TB, Roper DI, Han GJ, Hwang KY, Unzai S, Obayashi E, Park SY, Tame JRH:
Crystal structures of penicillin-binding proteins 4 and 5 from haemophilus influenzae.
J Mol Biol (2010) 396(3):634-645.
52
Nishimura K, Tajima N, Yoon YH, Park SY, Tame JRH:
Autotransporter passenger proteins: Virulence factors with common structural themes.
J Mol Med (Berl) (2010) 88(5):451-458.
51
Nishimura K, Yoon YH, Kurihara A, Unzai S, Luirink J, Park SY, Tame JRH:
Role of domains within the autotransporter hbp/tsh.
Acta Crystallogr D Biol Crystallogr (2010) 66(Pt 12):1295-1300.
50
Tajima N, Kawai F, Park SY, Tame JRH:
A novel intein-like autoproteolytic mechanism in autotransporter proteins.
J Mol Biol (2010) 402(4):645-656.
49
Watanabe M, Heddle JG, Kikuchi K, Unzai S, Akashi S, Park SY, Tame JRH:
The nature of the trap-anti-trap complex.
Proc Natl Acad Sci U S A (2009) 106(7):2176-2181.
48
Clarke TB, Kawai F, Park SY, Tame JRH, Dowson CG, Roper DI:
Mutational analysis of the substrate specificity of escherichia coli penicillin binding protein 4.
Biochemistry (2009) 48(12):2675-2683.
47
Akashi S, Watanabe M, Heddle JG, Unzai S, Park SY, Tame JRH:
Rna and protein complexes of trp rna-binding attenuation protein characterized by mass spectrometry.
Anal Chem (2009) 81(6):2218-2226.
46
Obayashi E, Yoshida H, Kawai F, Shibayama N, Kawaguchi A, Nagata K, Tame JRH, Park SY:
The structural basis for an essential subunit interaction in influenza virus rna polymerase.
Nature (2008) 454(7208):1127-1131.
45
Hiraki T, Shibayama N, Akashi S, Park SY:
Crystal structures of the clock protein ea4 from the silkworm bombyx mori.
J Mol Biol (2008) 377(3):630-635.
44
Addy C, Ohara M, Kawai F, Kidera A, Ikeguchi M, Fuchigami S, Osawa M, Shimada I, Park SY, Tame JRH, Heddle JG:
Nickel binding to nika: An additional binding site reconciles spectroscopy, calorimetry and crystallography.
Acta Crystallogr D Biol Crystallogr (2007) 63(Pt 2):221-229.
43
Hiraki T, Shibayama N, Yoon YH, Yun KM, Hamamoto T, Tame JRH, Park SY:
Crystallization and preliminary crystallographic studies of the metalloglycoprotein esterase a4 using a baculovirus expression system.
Acta Crystallogr Sect F Struct Biol Cryst Commun (2007) 63(Pt 9):734-736.
42
Izumi A, Rea D, Adachi T, Unzai S, Park SY, Roper DI, Tame JRH:
Structure and mechanism of hpcg, a hydratase in the homoprotocatechuate degradation pathway of escherichia coli.
J Mol Biol (2007) 370(5):899-911.
41
Nam KH, Kwon OY, Sugiyama K, Lee WH, Kim YK, Song HK, Kim EE, Park SY, Jeon H, Hwang KY:
Structural characterization of the photoswitchable fluorescent protein dronpa-c62s.
Biochem Biophys Res Commun (2007) 354(4):962-967.
40
Yoshizawa K, Mishima Y, Park SY, Heddle JG, Tame JRH, Iwahori K, Kobayashi M, Yamashita I:
Effect of n-terminal residues on the structural stability of recombinant horse l-chain apoferritin in an acidic environment.
J Biochem (2007) 142(6):707-713.
39
Yokoyama T, Neya S, Tsuneshige A, Yonetani T, Park SY, Tame JRH: R-state haemoglobin with low oxygen affinity:
Crystal structures of deoxy human and carbonmonoxy horse haemoglobin bound to the effector molecule l35.
J Mol Biol (2006) 356(3):790-801.
38
Park SY, Yokoyama T, Shibayama N, Shiro Y, Tame JRH:
1.25 a resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms.
J Mol Biol (2006) 360(3):690-701.
37
Kishida H, Unzai S, Roper DI, Lloyd A, Park SY, Tame JRH:
Crystal structure of penicillin binding protein 4 (dacb) from escherichia coli, both in the native form and covalently linked to various antibiotics.
Biochemistry (2006) 45(3):783-792.
36
Heddle JG, Yokoyama T, Yamashita I, Park SY, Tame JRH:
Rounding up: Engineering 12-membered rings from the cyclic 11-mer trap.
Structure (2006) 14(5):925-933.
35
Handa N, Terada T, Doi-Katayama Y, Hirota H, Tame JRH, Park SY, Kuramitsu S, Shirouzu M, Yokoyama S:
Crystal structure of a novel polyisoprenoid-binding protein from thermus thermophilus hb8.
Protein Sci (2005) 14(4):1004-1010.
34
Otto BR, Sijbrandi R, Luirink J, Oudega B, Heddle JG, Mizutani K, Park SY, Tame JRH:
Crystal structure of hemoglobin protease, a heme binding autotransporter protein from pathogenic escherichia coli.
J Biol Chem (2005) 280(17):17339-17345.
33
Piao S, Song YL, Kim JH, Park SY, Park JW, Lee BL, Oh BH, Ha NC:
Crystal structure of a clip-domain serine protease and functional roles of the clip domains.
Embo J (2005) 24(24):4404-4414.
32
Unzai S, Park SY, Tame JRH:
[crystal structure of heme binding protein, an autotransporter hemoglobin protease from pathogenic escherichia coli].
Tanpakushitsu Kakusan Koso (2005) 50(10 Suppl):1322-1327.
31
Yokoyama T, Chong KT, Miyazaki G, Morimoto H, Shih DT, Unzai S, Tame JRH, Park SY:
Novel mechanisms of ph sensitivity in tuna hemoglobin: A structural explanation of the root effect.
J Biol Chem (2004) 279(27):28632-28640.
30
Wada T, Shirouzu M, Terada T, Kamewari Y, Park SY, Tame JRH, Kuramitsu S, Yokoyama S:
Crystal structure of the conserved hypothetical protein tt1380 from thermus thermophilus hb8.
Proteins (2004) 55(3):778-780.
29
Park SY, Shibayama N, Hiraki T, Tame JRH:
Crystal structures of unliganded and half-liganded human hemoglobin derivatives cross-linked between lys 82beta1 and lys 82beta2.
Biochemistry (2004) 43(27):8711-8717.
28
Mizutani K, Machida Y, Unzai S, Park SY, Tame JRH:
Crystal structures of the catalytic domains of pseudouridine synthases rluc and rlud from escherichia coli.
Biochemistry (2004) 43(15):4454-4463.
27
Kishishita S, Tatsuguchi A, Ushikoshi-Nakayama R, Terada T, Kuramitsu S, Park SY, Tame JRH, Shirouzu M, Yokoyama S:
Crystal structure of a conserved hypothetical protein tt1751 from thermus thermophilus hb8.
Proteins (2004) 57(4):883-887.
26
Handa N, Terada T, Kamewari Y, Hamana H, Tame JRH, Park SY, Kinoshita K, Ota M, Nakamura H, Kuramitsu S, Shirouzu M et al:
Crystal structure of the conserved protein tt1542 from thermus thermophilus hb8.
Protein Sci (2003) 12(8):1621-1632.
25
Heddle J, Scott DJ, Unzai S, Park SY, Tame JRH:
Crystal structures of the liganded and unliganded nickel-binding protein nika from escherichia coli.
J Biol Chem (2003) 278(50):50322-50329.
24
Lee DS, Yamada A, Sugimoto H, Matsunaga I, Ogura H, Ichihara K, Adachi S, Park SY, Shiro Y:
Substrate recognition and molecular mechanism of fatty acid hydroxylation by cytochrome p450 from bacillus subtilis. Crystallographic, spectroscopic, and mutational studies.
J Biol Chem (2003) 278(11):9761-9767.
23
Nagano S, Shimada H, Tarumi A, Hishiki T, Kimata-Ariga Y, Egawa T, Suematsu M, Park SY, Adachi S, Shiro Y, Ishimura Y:
Infrared spectroscopic and mutational studies on putidaredoxin-induced conformational changes in ferrous co-p450cam.
Biochemistry (2003) 42(49):14507-14514.
22
Tawaramoto MS, Park SY, Tanaka Y, Nureki O, Kurumizaka H, Yokoyama S:
Crystal structure of the human centromere protein b (cenp-b) dimerization domain at 1.65-a resolution.
J Biol Chem (2003) 278(51):51454-51461.
21
Wada T, Kuzuyama T, Satoh S, Kuramitsu S, Yokoyama S, Unzai S, Tame JRH, Park SY:
Crystal structure of 4-(cytidine 5'-diphospho)-2-c-methyl-d-erythritol kinase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis.
J Biol Chem (2003) 278(32):30022-30027.
20
Wada T, Shirouzu M, Terada T, Ishizuka Y, Matsuda T, Kigawa T, Kuramitsu S, Park SY, Tame JRH, Yokoyama S:
Structure of a conserved coa-binding protein synthesized by a cell-free system.
Acta Crystallogr D Biol Crystallogr (2003) 59(Pt 7):1213-1218.
19
Kim HY, Heo YS, Kim JH, Park MH, Moon J, Kim E, Kwon D, Yoon J, Shin D, Jeong EJ, Park SY et al:
Molecular basis for the local conformational rearrangement of human phosphoserine phosphatase.
J Biol Chem (2002) 277(48):46651-46658.
18
Mito M, Chong KT, Miyazaki G, Adachi S, Park SY, Tame JRH, Morimoto H:
Crystal structures of deoxy- and carbonmonoxyhemoglobin f1 from the hagfish eptatretus burgeri.
J Biol Chem (2002) 277(24):21898-21905.
17
Park SY, Yamane K, Adachi S, Shiro Y, Weiss KE, Maves SA, Sligar SG:
Thermophilic cytochrome p450 (cyp119) from sulfolobus solfataricus: High resolution structure and functional properties.
J Inorg Biochem (2002) 91(4):491-501.
16
Shibayama N, Miura S, Tame JRH, Yonetani T, Park SY:
Crystal structure of horse carbonmonoxyhemoglobin-bezafibrate complex at 1.55-a resolution. A novel allosteric binding site in r-state hemoglobin.
J Biol Chem (2002) 277(41):38791-38796.
15
Shimizu H, Park SY, Shiro Y, Adachi S:
X-ray structure of nitric oxide reductase (cytochrome p450nor) at atomic resolution.
Acta Crystallogr D Biol Crystallogr (2002) 58(Pt 1):81-89.
14
Nakajima H, Honma Y, Tawara T, Kato T, Park SY, Miyatake H, Shiro Y, Aono S:
Redox properties and coordination structure of the heme in the co-sensing transcriptional activator cooa.
J Biol Chem (2001) 276(10):7055-7061.
13
Kikuchi A, Park SY, Miyatake H, Sun D, Sato M, Yoshida T, Shiro Y:
Crystal structure of rat biliverdin reductase.
Nat Struct Biol (2001) 8(3):221-225.
12
Denisov IG, Hung SC, Weiss KE, McLean MA, Shiro Y, Park SY, Champion PM, Sligar SG:
Characterization of the oxygenated intermediate of the thermophilic cytochrome p450 cyp119.
J Inorg Biochem (2001) 87(4):215-226.
11
Yamada S, Park SY, Shimizu H, Koshizuka Y, Kadokura K, Satoh T, Suruga K, Ogawa M, Isogai Y, Nishio T, Shiro Y et al:
Structure of cytochrome c6 from the red alga porphyra yezoensis at 1. 57 a resolution.
Acta Crystallogr D Biol Crystallogr (2000) 56(Pt 12):1577-1582.
10
Shimizu H, Obayashi E, Gomi Y, Arakawa H, Park SY, Nakamura H, Adachi S, Shoun H, Shiro Y:
Proton delivery in no reduction by fungal nitric-oxide reductase. Cryogenic crystallography, spectroscopy, and kinetics of ferric-no complexes of wild-type and mutant enzymes.
J Biol Chem (2000) 275(7):4816-4826.
9
Park SY, Yamane K, Adachi S, Shiro Y, Weiss KE, Sligar SG:
Crystallization and preliminary x-ray diffraction analysis of a cytochrome p450 (cyp119) from sulfolobus solfataricus.
Acta Crystallogr D Biol Crystallogr (2000) 56(Pt 9):1173-1175.
8
Obayashi E, Shimizu H, Park SY, Shoun H, Shiro Y:
Mutation effects of a conserved threonine (thr243) of cytochrome p450nor on its structure and function.
J Inorg Biochem (2000) 82(1-4):103-111.
7
Miyatake H, Mukai M, Park SY, Adachi S, Tamura K, Nakamura H, Nakamura K, Tsuchiya T, Iizuka T, Shiro Y:
Sensory mechanism of oxygen sensor fixl from rhizobium meliloti: Crystallographic, mutagenesis and resonance raman spectroscopic studies.
J Mol Biol (2000) 301(2):415-431.
6
Hishiki T, Shimada H, Nagano S, Egawa T, Kanamori Y, Makino R, Park SY, Adachi S, Shiro Y, Ishimura Y:
X-ray crystal structure and catalytic properties of thr252ile mutant of cytochrome p450cam: Roles of thr252 and water in the active center.
J Biochem (2000) 128(6):965-974.
5
Miyazaki G, Morimoto H, Yun KM, Park SY, Nakagawa A, Minagawa H, Shibayama N:
Magnesium(ii) and zinc(ii)-protoporphyrin ix's stabilize the lowest oxygen affinity state of human hemoglobin even more strongly than deoxyheme.
J Mol Biol (1999) 292(5):1121-1136.
4
Chu GC, Park SY, Shiro Y, Yoshida T, Ikeda-Saito M:
Crystallization and preliminary x-ray diffraction analysis of a recombinant bacterial heme oxygenase (hmu o) from corynebacterium diphtheriae.
J Struct Biol (1999) 126(2):171-174.
3
Park SY, Shimizu H, Adachi S, Shiro Y, Iizuka T, Nakagawa A, Tanaka I, Shoun H, Hori H:
Crystallization, preliminary diffraction and electron paramagnetic resonance studies of a single crystal of cytochrome p450nor. FEBS Lett (1997) 412(2):346-350.
2
Park SY, Shimizu H, Adachi S, Nakagawa A, Tanaka I, Nakahara K, Shoun H, Obayashi E, Nakamura H, Iizuka T, Shiro Y:
Crystal structure of nitric oxide reductase from denitrifying fungus fusarium oxysporum.
Nat Struct Biol (1997) 4(10):827-832.
1
Park SY, Nakagawa A, Morimoto H:
High-resolution crystal structure of magnesium (mgii)-iron (feii) hybrid hemoglobin with liganded beta subunits.
J Mol Biol (1996) 255(5):726-734.