메뉴 건너뛰기




Volumn 8, Issue 7, 2013, Pages

The Mode of Inhibitor Binding to Peptidyl-tRNA Hydrolase: Binding Studies and Structure Determination of Unbound and Bound Peptidyl-tRNA Hydrolase from Acinetobacter baumannii

Author keywords

[No Author keywords available]

Indexed keywords

ANTIINFECTIVE AGENT; CYTIDINE; HYDROLASE INHIBITOR; PEPTIDYL TRNA HYDROLASE; PEPTIDYL TRNA HYDROLASE INHIBITOR; RIBONUCLEASE; TRANSFER RNA; UNCLASSIFIED DRUG; URIDINE;

EID: 84879760460     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0067547     Document Type: Article
Times cited : (21)

References (45)
  • 1
    • 33747145161 scopus 로고    scopus 로고
    • Peptidyl tRNA hydrolase and its critical role in protein biosynthesis
    • Das G, Varshney U, (2006) Peptidyl tRNA hydrolase and its critical role in protein biosynthesis. Microbiology 152: 2191-2195.
    • (2006) Microbiology , vol.152 , pp. 2191-2195
    • Das, G.1    Varshney, U.2
  • 2
    • 11344289875 scopus 로고    scopus 로고
    • A physiological connection between tmRNA and peptidyl-tRNA hydrolase functions in Escherichia coli
    • Singh NS, Varshney U, (2004) A physiological connection between tmRNA and peptidyl-tRNA hydrolase functions in Escherichia coli. Nucleic Acids Res 32: 6028-6037.
    • (2004) Nucleic Acids Res , vol.32 , pp. 6028-6037
    • Singh, N.S.1    Varshney, U.2
  • 3
    • 33846085054 scopus 로고    scopus 로고
    • Mechanism of tRNA-dependent editing in translational quality control
    • Ling J, Roy H, Ibba M, (2007) Mechanism of tRNA-dependent editing in translational quality control. Proc Natl Acad Sci U S A 104: 72-78.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 72-78
    • Ling, J.1    Roy, H.2    Ibba, M.3
  • 4
    • 0030738859 scopus 로고    scopus 로고
    • Crystal structure at 1.2 Å resolution and active site mapping of Escherichia coli peptidyl-tRNA hydrolase
    • Schmitt E, Mechulam Y, Fromant M, Plateau P, Blanquet S, (1997) Crystal structure at 1.2 Å resolution and active site mapping of Escherichia coli peptidyl-tRNA hydrolase. EMBO J 16: 4760-4769.
    • (1997) EMBO J , vol.16 , pp. 4760-4769
    • Schmitt, E.1    Mechulam, Y.2    Fromant, M.3    Plateau, P.4    Blanquet, S.5
  • 5
    • 0018340811 scopus 로고
    • Accumulation of peptidyl tRNA is lethal to Escherichia coli
    • Menninger JR, (1979) Accumulation of peptidyl tRNA is lethal to Escherichia coli. J Bacteriol 137: 694-696.
    • (1979) J Bacteriol , vol.137 , pp. 694-696
    • Menninger, J.R.1
  • 6
    • 1542289663 scopus 로고    scopus 로고
    • Crystal structure of a human peptidyl-tRNA hydrolase reveals a new fold and suggests basis for a bifunctional activity
    • De-Pereda JM, Waas WF, Jan Y, Ruoslahti E, Schimmel P, et al. (2004) Crystal structure of a human peptidyl-tRNA hydrolase reveals a new fold and suggests basis for a bifunctional activity. J Biol Chem 279: 8111-8115.
    • (2004) J Biol Chem , vol.279 , pp. 8111-8115
    • De-Pereda, J.M.1    Waas, W.F.2    Jan, Y.3    Ruoslahti, E.4    Schimmel, P.5
  • 8
    • 0038410024 scopus 로고    scopus 로고
    • The epidemiology of multidrug-resistant Acinetobacter baumannii: does the community represent a reservoir?
    • Zeana C, Larson E, Sahni J, Bayuga SJ, Wu F, et al. (2003) The epidemiology of multidrug-resistant Acinetobacter baumannii: does the community represent a reservoir? Infect Control Hosp Epidemiol 24: 275-279.
    • (2003) Infect Control Hosp Epidemiol , vol.24 , pp. 275-279
    • Zeana, C.1    Larson, E.2    Sahni, J.3    Bayuga, S.J.4    Wu, F.5
  • 9
    • 71549130399 scopus 로고    scopus 로고
    • Acinetobacter: an old friend, but a new enemy J Hosp Infec
    • Towner KJ, (2009) Acinetobacter: an old friend, but a new enemy J Hosp Infec. 73: 355-363.
    • (2009) , vol.73 , pp. 355-363
    • Towner, K.J.1
  • 10
    • 84944657709 scopus 로고
    • Community acquired Acinetobacter calcoaceticus var anitratus pneumonia
    • Goodhart GL, Abrutyn E, Watson R, Root RK, Egert J, (1977) Community acquired Acinetobacter calcoaceticus var anitratus pneumonia. JAMA 238: 1516-1518.
    • (1977) JAMA , vol.238 , pp. 1516-1518
    • Goodhart, G.L.1    Abrutyn, E.2    Watson, R.3    Root, R.K.4    Egert, J.5
  • 11
    • 0036686040 scopus 로고    scopus 로고
    • Pandrug-resistant Acinetobacter baumannii causing nosocomial infections in a university hospital, Taiwan
    • Hsueh PR, Teng LJ, Chen CY, Chen WH, Yu C, et al. (2002) Pandrug-resistant Acinetobacter baumannii causing nosocomial infections in a university hospital, Taiwan. Emerg Infect Dis 8: 827-832.
    • (2002) Emerg Infect Dis , vol.8 , pp. 827-832
    • Hsueh, P.R.1    Teng, L.J.2    Chen, C.Y.3    Chen, W.H.4    Yu, C.5
  • 12
    • 80055023981 scopus 로고    scopus 로고
    • Multidrug-Resistant Acinetobacter spp.: Increasingly Problematic Nosocomial Pathogens
    • Lee K, Yong D, Jeong SH, Chong Y, (2011) Multidrug-Resistant Acinetobacter spp.: Increasingly Problematic Nosocomial Pathogens. Yonsei Med J 52: 879-891.
    • (2011) Yonsei Med J , vol.52 , pp. 879-891
    • Lee, K.1    Yong, D.2    Jeong, S.H.3    Chong, Y.4
  • 13
    • 62249105264 scopus 로고    scopus 로고
    • Treatment of multiresistant Acinetobacter baumannii infections
    • Pachon J, Vila J, (2009) Treatment of multiresistant Acinetobacter baumannii infections. Curr Opin Investig Drugs 10: 150-156.
    • (2009) Curr Opin Investig Drugs , vol.10 , pp. 150-156
    • Pachon, J.1    Vila, J.2
  • 14
    • 0033770897 scopus 로고    scopus 로고
    • Molecular surveillance of European Quinolone-resistant clinical isolates of Pseudomonas aeruginosa and Acinetobacter spp. using automated ribotyping
    • Brisse S, Milatovic D, Fluit AC, Kusters K, Toelstra A, et al. (2000) Molecular surveillance of European Quinolone-resistant clinical isolates of Pseudomonas aeruginosa and Acinetobacter spp. using automated ribotyping. J Clin Microbiol 38: 3636-3645.
    • (2000) J Clin Microbiol , vol.38 , pp. 3636-3645
    • Brisse, S.1    Milatovic, D.2    Fluit, A.C.3    Kusters, K.4    Toelstra, A.5
  • 15
    • 79953787256 scopus 로고    scopus 로고
    • Are we ready for novel detection methods to treat respiratory pathogens in hospital-acquired pneumonia?
    • Endimiani A, Hujer KM, Hujer AM, Kurz S, Jacobs MR, et al. (2011) Are we ready for novel detection methods to treat respiratory pathogens in hospital-acquired pneumonia? Clin Infect Dis 52: S373-S383.
    • (2011) Clin Infect Dis , vol.52
    • Endimiani, A.1    Hujer, K.M.2    Hujer, A.M.3    Kurz, S.4    Jacobs, M.R.5
  • 16
    • 0036159749 scopus 로고    scopus 로고
    • Community-acquired bacteremic Acinetobacter pneumonia in tropical Australia is caused by diverse strains of Acinetobacter baumannii, with carriage in the throat of at-risk groups
    • Anstey NM, Currie BJ, Hassell M, Palmer D, Dwyer B, et al. (2002) Community-acquired bacteremic Acinetobacter pneumonia in tropical Australia is caused by diverse strains of Acinetobacter baumannii, with carriage in the throat of at-risk groups. J Clin Microbiol 40: 685-686.
    • (2002) J Clin Microbiol , vol.40 , pp. 685-686
    • Anstey, N.M.1    Currie, B.J.2    Hassell, M.3    Palmer, D.4    Dwyer, B.5
  • 17
    • 0034796340 scopus 로고    scopus 로고
    • Severe community-acquired pneumonia due to Acinetobacter baumannii
    • Chen MZ, Hsueh PR, Lee LN, Yu CJ, Yang PC, et al. (2001) Severe community-acquired pneumonia due to Acinetobacter baumannii. Chest 120: 1072-1077.
    • (2001) Chest , vol.120 , pp. 1072-1077
    • Chen, M.Z.1    Hsueh, P.R.2    Lee, L.N.3    Yu, C.J.4    Yang, P.C.5
  • 19
    • 80052849429 scopus 로고    scopus 로고
    • Genomic Analysis of the Multidrug-Resistant Acinetobacter baumannii Strain MDR-ZJ06 Widely Spread in China
    • Zhou H, Zhang T, Yu D, Pi B, Yang Q, et al. (2011) Genomic Analysis of the Multidrug-Resistant Acinetobacter baumannii Strain MDR-ZJ06 Widely Spread in China. Antimicrob Agents Chemother 55: 4506-4512.
    • (2011) Antimicrob Agents Chemother , vol.55 , pp. 4506-4512
    • Zhou, H.1    Zhang, T.2    Yu, D.3    Pi, B.4    Yang, Q.5
  • 20
    • 84455161855 scopus 로고    scopus 로고
    • Colistin-resistant, lipopolysaccharide-deficient Acinetobacter baumannii responds to lipopolysaccharide loss through increased expression of genes involved in the synthesis and transport of lipoproteins, phospholipids, and poly-β-1,6-N-Acetylglucosamine
    • Henry R, Vithanage N, Harrison P, Seemann T, Coutts S, et al. (2012) Colistin-resistant, lipopolysaccharide-deficient Acinetobacter baumannii responds to lipopolysaccharide loss through increased expression of genes involved in the synthesis and transport of lipoproteins, phospholipids, and poly-β-1,6-N-Acetylglucosamine. Antimicrob Agents Chemother 56: 59-69.
    • (2012) Antimicrob Agents Chemother , vol.56 , pp. 59-69
    • Henry, R.1    Vithanage, N.2    Harrison, P.3    Seemann, T.4    Coutts, S.5
  • 21
    • 79955418678 scopus 로고    scopus 로고
    • In-Vitro Activity of Polymyxin B, Rifampicin, Tigecycline Alone and in Combination against Carbapenem-Resistant Acinetobacter baumannii in Singapore
    • Lim TP, Tan TY, Lee W, Sasikala S, Tan TT, et al. (2011) In-Vitro Activity of Polymyxin B, Rifampicin, Tigecycline Alone and in Combination against Carbapenem-Resistant Acinetobacter baumannii in Singapore. PLoS One 6: 184-185.
    • (2011) PLoS One , vol.6 , pp. 184-185
    • Lim, T.P.1    Tan, T.Y.2    Lee, W.3    Sasikala, S.4    Tan, T.T.5
  • 22
    • 34547683824 scopus 로고    scopus 로고
    • Structural plasticity and enzyme action: crystal structures of mycobacterium tuberculosis peptidyl-tRNA hydrolase
    • Selvaraj M, Roy S, Singh NS, Sangeetha R, Varshney U, et al. (2007) Structural plasticity and enzyme action: crystal structures of mycobacterium tuberculosis peptidyl-tRNA hydrolase. J Mol Biol 372: 186-193.
    • (2007) J Mol Biol , vol.372 , pp. 186-193
    • Selvaraj, M.1    Roy, S.2    Singh, N.S.3    Sangeetha, R.4    Varshney, U.5
  • 23
    • 84859702544 scopus 로고    scopus 로고
    • Crystal structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis reveals novel features related to enzyme dynamics
    • Kumar A, Singh N, Yadav R, Kumar RP, Sharma S, et al. (2012) Crystal structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis reveals novel features related to enzyme dynamics. Int J Biochem Mol Biol 23: 58-69.
    • (2012) Int J Biochem Mol Biol , vol.23 , pp. 58-69
    • Kumar, A.1    Singh, N.2    Yadav, R.3    Kumar, R.P.4    Sharma, S.5
  • 24
    • 84870862550 scopus 로고    scopus 로고
    • Recombinant production, crystallization and X-ray crystallographic structure determination of the peptidyl-tRNA hydrolase of Pseudomonas aeruginosa
    • Hughes RC, McFeeters H, Coates L, McFeeters RL, (2012) Recombinant production, crystallization and X-ray crystallographic structure determination of the peptidyl-tRNA hydrolase of Pseudomonas aeruginosa. Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1472-1476.
    • (2012) Acta Crystallogr Sect F Struct Biol Cryst Commun , vol.68 , pp. 1472-1476
    • Hughes, R.C.1    McFeeters, H.2    Coates, L.3    McFeeters, R.L.4
  • 25
    • 84869022853 scopus 로고    scopus 로고
    • Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase
    • Ito K, Murakami R, Mochizuki M, Qi H, Shimizu Y, et al. (2012) Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase. Nucleic Acids Res 40: 10521-10531.
    • (2012) Nucleic Acids Res , vol.40 , pp. 10521-10531
    • Ito, K.1    Murakami, R.2    Mochizuki, M.3    Qi, H.4    Shimizu, Y.5
  • 27
    • 33745931764 scopus 로고    scopus 로고
    • Binding interactions of pefloxacin mesylate with bovine lactoferrin and human serum albumin
    • Fan JC, Chen X, Wang Y, Fan CP, Shang ZC, (2006) Binding interactions of pefloxacin mesylate with bovine lactoferrin and human serum albumin. J Zhejiang Univ Sci B 7: 452-458.
    • (2006) J Zhejiang Univ Sci B , vol.7 , pp. 452-458
    • Fan, J.C.1    Chen, X.2    Wang, Y.3    Fan, C.P.4    Shang, Z.C.5
  • 28
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z, Minor W, (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307-326.
    • (1997) Methods Enzymol , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 29
    • 0014432781 scopus 로고
    • Solvent Content of Protein Crystals
    • Matthews BW, (1968) Solvent Content of Protein Crystals. J Mol Biol 33: 491-496.
    • (1968) J Mol Biol , vol.33 , pp. 491-496
    • Matthews, B.W.1
  • 31
    • 13244281317 scopus 로고    scopus 로고
    • Coot: model-building tools for molecular graphics
    • Emsley P, Cowtan K, (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr. 60: 2126-2132.
    • (2004) Acta Crystallogr D Biol Crystallogr , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 32
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones TA, Zou JY, Cowan SW, Kjeldgaard M, (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 47: 110-119.
    • (1991) Acta Crystallogr A , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 34
    • 3242886389 scopus 로고    scopus 로고
    • MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes
    • Davis IW, Murray LW, Richardson JS, Richardson DC, (2004) MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 1: 615-619.
    • (2004) Nucleic Acids Res , vol.1 , pp. 615-619
    • Davis, I.W.1    Murray, L.W.2    Richardson, J.S.3    Richardson, D.C.4
  • 36
    • 0001832403 scopus 로고
    • Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function
    • Chapman MS, (1995) Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function. Acta Crystallogr A Biol 51: 69-80.
    • (1995) Acta Crystallogr A Biol , vol.51 , pp. 69-80
    • Chapman, M.S.1
  • 37
    • 84860305929 scopus 로고    scopus 로고
    • Statistical quality indicators for electron-density maps
    • Tickle IJ, (2012) Statistical quality indicators for electron-density maps. Acta Crystallogr D Biol Crystallogr 68: 454-467.
    • (2012) Acta Crystallogr D Biol Crystallogr , vol.68 , pp. 454-467
    • Tickle, I.J.1
  • 38
    • 34548232365 scopus 로고    scopus 로고
    • Inference of macromolecular assemblies from crystalline state
    • Krissinel E, Henrick K, (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774-779.
    • (2007) J Mol Biol , vol.372 , pp. 774-779
    • Krissinel, E.1    Henrick, K.2
  • 39
    • 84875820731 scopus 로고    scopus 로고
    • First structural evidence of sequestration of mRNA cap structures by type 1 ribosome inactivating protein from Momordica balsamina
    • Kushwaha GS, Yamini S, Kumar M, Sinha M, Kaur P, et al. (2012) First structural evidence of sequestration of mRNA cap structures by type 1 ribosome inactivating protein from Momordica balsamina. Proteins 81: 896-905.
    • (2012) Proteins , vol.81 , pp. 896-905
    • Kushwaha, G.S.1    Yamini, S.2    Kumar, M.3    Sinha, M.4    Kaur, P.5
  • 40
    • 84862828902 scopus 로고    scopus 로고
    • Crystal structures of a type-1 ribosome inactivating protein from Momordica balsamina in the bound and unbound states
    • Kushwaha GS, Pandey N, Sinha M, Singh SB, Kaur P, et al. (2012) Crystal structures of a type-1 ribosome inactivating protein from Momordica balsamina in the bound and unbound states. Biochim Biophys Acta 1824: 679-691.
    • (2012) Biochim Biophys Acta , vol.1824 , pp. 679-691
    • Kushwaha, G.S.1    Pandey, N.2    Sinha, M.3    Singh, S.B.4    Kaur, P.5
  • 41
    • 84894892112 scopus 로고    scopus 로고
    • Crystal structures of the complexes of a group IIA phospholipase A2 with two natural anti-inflammatory agents, anisic acid, and atropine reveal a similar mode of binding
    • Singh N, Jabeen T, Pal A, Sharma S, Perbandt M, et al. (2008) Crystal structures of the complexes of a group IIA phospholipase A2 with two natural anti-inflammatory agents, anisic acid, and atropine reveal a similar mode of binding. Proteins 64: 80-100.
    • (2008) Proteins , vol.64 , pp. 80-100
    • Singh, N.1    Jabeen, T.2    Pal, A.3    Sharma, S.4    Perbandt, M.5
  • 42
    • 70349921112 scopus 로고    scopus 로고
    • Simultaneous inhibition of anti-coagulation and inflammation: crystal structure of phospholipase A2 complexed with indomethacin at 1.4 A resolution reveals the presence of the new common ligand-binding site
    • Singh N, Kumar RP, Kumar S, Sharma S, Mir R, et al. (2009) Simultaneous inhibition of anti-coagulation and inflammation: crystal structure of phospholipase A2 complexed with indomethacin at 1.4 A resolution reveals the presence of the new common ligand-binding site. J Mol Recognit 6: 437-445.
    • (2009) J Mol Recognit , vol.6 , pp. 437-445
    • Singh, N.1    Kumar, R.P.2    Kumar, S.3    Sharma, S.4    Mir, R.5
  • 43
    • 33644841098 scopus 로고    scopus 로고
    • Non-steroidal anti-inflammatory drugs as potent inhibitors of phospholipase A2: structure of the complex of phospholipase A2 with niflumic acid at 2.5 Angstroms resolution
    • Jabeen T, Singh N, Singh RK, Sharma S, Somvanshi RK, et al. (2005) Non-steroidal anti-inflammatory drugs as potent inhibitors of phospholipase A2: structure of the complex of phospholipase A2 with niflumic acid at 2.5 Angstroms resolution. Acta Crystallogr D Biol Crystallogr 12: 1579-1586.
    • (2005) Acta Crystallogr D Biol Crystallogr , vol.12 , pp. 1579-1586
    • Jabeen, T.1    Singh, N.2    Singh, R.K.3    Sharma, S.4    Somvanshi, R.K.5
  • 44
    • 17444413112 scopus 로고    scopus 로고
    • Aspirin induces its anti-inflammatory effects through its specific binding to phospholipase A2: crystal structure of the complex formed between phospholipase A2 and aspirin at 1.9 angstroms resolution
    • Singh RK, Ethayathulla AS, Jabeen T, Sharma S, Kaur P, et al. (2005) Aspirin induces its anti-inflammatory effects through its specific binding to phospholipase A2: crystal structure of the complex formed between phospholipase A2 and aspirin at 1.9 angstroms resolution. J Drug Target 2: 113-119.
    • (2005) J Drug Target , vol.2 , pp. 113-119
    • Singh, R.K.1    Ethayathulla, A.S.2    Jabeen, T.3    Sharma, S.4    Kaur, P.5
  • 45
    • 13244292170 scopus 로고    scopus 로고
    • Crystal structure of the complex formed between a group I phospholipase A2 and a naturally occurring fatty acid at 2.7 A resolution
    • Singh G, Jasti J, Saravanan K, Sharma S, Kaur P, et al. (2005) Crystal structure of the complex formed between a group I phospholipase A2 and a naturally occurring fatty acid at 2.7 A resolution. Protein Sci 2: 395-400.
    • (2005) Protein Sci , vol.2 , pp. 395-400
    • Singh, G.1    Jasti, J.2    Saravanan, K.3    Sharma, S.4    Kaur, P.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.