In silico identification and characterization of 1-Aminocyclopropane-1- Carboxylate deaminase from Phytophthora sojae

Journal of Molecular Modeling

Volumn 18, Issue 9, 2012, Pages 4101-4111

  Singh, Nidhi ^a   Kashyap, Sudhanshu ^a  

^a ICAR NATIONAL BUREAU OF AGRICULTURALLY IMPORTANT MICROORGANISMS   (India)

Author keywords

Active site; Docking; ESTs; Homo tetramer; Modeller; Phytopthora sojae

Indexed keywords

1 AMINOCYCLOPROPANECARBOXYLATE DEAMINASE; DEAMINASE; UNCLASSIFIED DRUG;

ARTICLE; BIOINFORMATICS; CHEMICAL ANALYSIS; CHEMICAL REACTION; GEOMETRY; MICROBIAL IDENTIFICATION; MOLECULAR DOCKING; NONHUMAN; PHYTOPHTHORA; PHYTOPHTHORA SOJAE; PREDICTION; PRIORITY JOURNAL; RAMACHANDRAN PLOT ANALYSIS;

AMINO ACID SEQUENCE; ASPERGILLUS FUMIGATUS; BASE SEQUENCE; CARBON-CARBON LYASES; COMPUTATIONAL BIOLOGY; EXPRESSED SEQUENCE TAGS; INTERNET; LIGANDS; MOLECULAR DOCKING SIMULATION; PHYLOGENY; PHYTOPHTHORA; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN; SUBSTRATE SPECIFICITY;

PHYTOPHTHORA SOJAE; PSEUDOMONAS;

EID: 84867578433     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-012-1389-0     Document Type: Article

References (34)

1. Boller T (1991) Ethylene in pathogenasis and disease resistance. In: Mattoo AK, Suttle JC (ed) The plant hormone ethylene, CRC Press, pp 293-314
2. McKeon T, Yang SF (1987) Biosynthesis and metabolism of ethylene. In: Davies PJ (ed) Plant hormones and their role in plant growth and development. Martinus Nijhoff, Boston, pp 94-112
3. Madhaiyan M, Poonguzhali S, Sa T (2007) Characterization of 1-aminocyclopropane-1-carboxylate deaminase containing Methylobacterium spp. Isolated from rhizosphere soils of field-grown rice and regulation of ethylene levels in canola. Planta 226:867-876. doi:10.1007/s00425-007-0532-0
4. Glick BR, Karaturovic DM, Newell PC (1995) A novel procedure for rapid isolation of plant growth promoting Pseudomonads. Can J Microbiol 41:533-536. doi:10.1139/m95-070
5. Penrose DM, Glick BR (1997) Enzymes that regulate ethylene levels-1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, ACC synthase and ACC oxidase. Indian J Exp Biol 35:1-17
6. Glick BR, Penrose DM, Li J (1998) A model for the lowering of plant ethylene concentration by the plant growth promoting bacteria. J Theor Biol 190:63-68. doi:10.1006/jtbi.1997.0532
7. Sheehy RE, Honma M, YamadaM, Sasaki T,Martineau B, HiattWR (1991) Isolation, sequence, and expression in Escherichia coli of the Pseudomonas sp. Strain ACP gene encoding 1-aminocyclopropane-1-carboxylate deaminase. J Bacteriol 173:5260-5265
8. Klee HJ, Hayford MB, Kretzmer KA, Barry GF, Kishore GM (1991) Control of ethylene synthesis by expression of a bacterial enzyme in transgenic tomato plant. Plant Cell 3:1187-1193. doi:10.1105/ tpc.3.11.1187
9. Jacobson CB, Pasternak JJ, Glick BR (1994) Partial purification and characterization of ACC deaminase from the plant growth promoting rhizobacterium Pseudomonas putida GR12-2. Can J Microbiol 40:1019-1025. doi:10.1139/m94-162
10. Campbell BG, Thomson JA (1996) 1-Aminocyclopropane-1-carboxylate deaminase gene from Pseudomonas strains. FEMS Microbiol Lett 138:207-210. doi:10.1016/0378-1097(96)00108-5
11. Shah S, Li J, Moffatt BA, Glick BR (1998) Isolation and characterization of ACC deaminase gene from two different plant growth promoting rhizobacteria. Can J Microbiol 44:833-843. doi::10.1139/w98-074
12. Minami R, Uchiyama K, Murakami T, Kawai J, Mikami K, Yamada T, Yokoi D, Ito H, Matsui H, Honma M (1998) Properties, sequence, and synthesis in Escherichia coli of 1-aminocyclopropane-1-carboxylate deaminase from Hensula saturnus. J Biochem 123:1112-1118
13. Jia YJ, Kakuta Y, Sugawara M, Igarashi T, Oki N, Kisaki M, Shoji T, Kanetuna Y, Horita T, Matsui H, Honma M (1999) Synthesis and degradation of 1-aminocyclopropane-1-carboxylic acid by Penicillium citrinum. Biosci Biotechanol Biochem 63:542-549. doi:10.1271/bbb.63.542
14. Kumar S, Dudley J, Nei M, Tamura K (2008) MEGA: Biologistcentric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299-306
15. Sali A, Potterton L, Yuan F, van Vlijmen H, Karplus M (1995) Evaluation of comparative protein modeling by MODELLER. Protein 23:318-326. doi:10.1002/prot.340230306
16. Laskowski RA, MacArtur MW, Moss DS, Thrnton JM (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Cryst 26:283-291. doi:10.1107/ S0021889892009944
17. Vriend G (1990) WHAT IF: A molecular modeling and drug designing program. J Mol Graph 8:52-56
18. Karthikeyan S, Zhou Q, Zhao Z, Kao CL, Tao Z, Robinson H, Liu HW, Zhang H (2004) Structural analysis of Pseudomonas 1-aminocyclopropane-1-carboxylate deaminase complexes: Insight into the mechanism of a unique pyridoxal-5'- phosphate dependent cyclopropane ring-opening reaction. Biochemistry 43:13328-13339. doi:10.1021/bi048878g
19. Duhovny DS, Inbar Y, Nussinov R, Wolfson HJ (2005) PatchDock and SymmDock: Servers for rigid and symmetric docking. Nucleic Acid Res 33:W363-W367. doi:10.1093/nar/gki481
20. Qutob D, Hraber PT, Sobral BWS, Gijzen M (2000) Comparative analysis of expressed sequences in Phytophthora sojae. Plant Physiol 123:243-253. doi:10.1104/pp.104.055624
21. Trudy A, Tripathy S, Smith BM, Arredondo FD, Zhou L, Li H, Chibucos MC, Qutob D, Gijzen M, Mao C, Sobral BWS, Waugh ME, Mitchell TK, Dean RA, Tyler BM (2007) Expressed sequence tags from Phytophthora sojae reveal genes specific to development and infection. Mol Plant Microb Interact 20:781-793. doi:10.1094/ MPMI-20-7-0781
22. Takai D, Jones PA (2002) Comprehensive analysis of CpG islands in human chromosomes 21 and 22. PNAS 99:3740-3745. doi:10.1073/pnas.052410099
23. Knogge W (1996) Fungal infections of plants. Plant Cell 8:1711-1722. doi:10.1105/tpc.8.10.1711
24. Collmer A, Badel JL, Charkowski AO, Deng WL, Fouts DE, Ramos AR, Rehm AH, Anderson DM, Schneewind O, van Dijk K, Alfano JR (2000) Pseudomonas syringae Hrp type III secretion system and effector proteins. PNAS 97:8770-8777
25. Staskawicz BJ, Mudgett MB, Dangl JL, Galan JE (2001) Common and contrasting themes of plant and animal diseases. Science 292:2285-2289. doi:10.1126/science.1062013
26. Huitema E, Bos JIB, Tian M, Win J, Waugh ME, Kamoun S (2004) Linking sequence to phenotype in Phytophthora-plant interactions. Trends Microbiol 12:193-200. doi:10.1016/j. tim.2004.02.008
27. Kamoun S (2006) A catalogue of the effector secretome of plant pathogenic oomycetes. Annu Rev Phytopathol 44:2.1-2.20. doi:10.1146/annurev.phyto.44. 070505.143436
28. Ose T, Fujino A, Yao M, Natanabe N, Honma M, Tanaka I (2003) Reaction intermediate structure of 1-aminocyclopropane-1-carboxylate deaminase. J Biol Chem 278:41069-41076. doi:10.1074/jbc. M305865200
29. Mehta PK, Christen P (1998) In: Purich DL (ed) Advances in enzymology and related areas of molecular biology. Wiley, New York, pp 129-184
30. Grishin NV, Phillips MA, Goldsmith EJ (1995) Modeling of the spatial structure of eukaryotic ornithine decarboxylases. Protein Sci 4:1291-1304. doi:10.1002/pro.5560040705
31. Burkhard P, Rao GS, Hohenester E, Schnackerz KD, Cook PF, Jansonius JN (1998) Three-dimensional structure of O-acetylserine sulfhydrylase from Salmonella typhimurium. J Mol Biol 283:121-133
32. Gallagher DT, Gilliland GL, Xiao G, Zondlo J, Fisher KE, Chinchilla D, Eisenstein E (1998) Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase. Structure 6:465-475. doi:10.1016/S0969-2126(98) 00048-3
33. Rhee S, Miles EW, Davies DR (1998) Cryocrystallography of a true substrate, indole-3-glycerol phosphate, bound to a mutant (RD60N) tryptophan synthase R2â2 complex reveals the correct orientation of active site RGlu49. J Biol Chem 273:8553-8555
34. Weyand M, Schlichting I (1999) Crystal structure of wildtype tryptophan synthase complexed with the natural substrate indole-3-glycerol phosphate. Biochemistry 38:16469-16480. doi:10.1021/ bi9920533