Structural and docking studies of Leucaena leucocephala Cinnamoyl CoA reductase

Journal of Molecular Modeling

Volumn 17, Issue 3, 2011, Pages 533-541

  Prasad, Nirmal K ^a   Vindal, Vaibhav ^b   Kumar, Vikash ^a   Kabra, Ashish ^a   Phogat, Navneet ^a   Kumar, Manoj ^a  

^a GOA UNIVERSITY   (India)

^b UNIVERSITY OF HYDERABAD   (India)

Author keywords

Cinnamoyl CoA reductase; Docking; Feruloyl CoA; Leucaena leucocephala; Lignin biosynthesis

Indexed keywords

CINNAMOYL COENZYME A REDUCTASE; DIHYDROFLAVONOL 4 REDUCTASE; FERULOYL COENZYME A REDUCTASE; OXIDOREDUCTASE; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; ENZYME ENGINEERING; ENZYME MECHANISM; LEGUME; LEUCAENA LEUCOCEPHALA; MOLECULAR DOCKING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

ALDEHYDE OXIDOREDUCTASES; AMINO ACID SEQUENCE; CATALYTIC DOMAIN; FABACEAE; LIGNIN; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PLANT PROTEINS; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY;

LEUCAENA LEUCOCEPHALA; VITACEAE;

EID: 79954438347     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-010-0744-2     Document Type: Article

References (32)

1. L Li X Cheng S Lu T Nakatsubo T Umezawa VL Chiang 2005 Clarification of cinnamoyl co-enzyme a reductase catalysis in monolignol biosynthesis of aspen Plant Cell Physiol 46 1073 1082 10.1093/pcp/pci120 1:CAS:528: DC%2BD2MXmslGjsLo%3D (Pubitemid 41373471)
2. BR Thumma MF Nolan R Evans GF Moran 2005 Polymorphisms in Cinnamoyl CoA Reductase (CCR) are associated with variation in microfibril angle in eucalyptus spp Genetics 171 1257 1265 10.1534/genetics.105.042028 1:CAS:528: DC%2BD28Xjs1Kruw%3D%3D (Pubitemid 43234857)
3. E Lacombe S Hawkins JV Doorsselaere J Piquemal D Goffner, et al. 1997 Cinnamoyl CoA reductase, the first committed enzyme of the lignin branch biosynthetic pathway: cloning, expression and phylogenetic relationships Plant J 11 429 441 10.1046/j.1365-313X.1997.11030429.x 1:CAS:528:DyaK2sXislagt7o%3D (Pubitemid 27158950)
4. V Lauvergeat P Rech A Jauneau C Guez P Coutos-Thevenot, et al. 2002 The vascular expression pattern directed by the Eucalyptus gunnii cinnamyl alcohol dehydrogenase Eg CAD2 promoter is conserved among woody and herbaceous plant species Plant Mol Biol 50 497 509 10.1023/A:1019817913604 1:CAS:528: DC%2BD38Xmt12rsbs%3D
5. M Baltas C Lapeyre F Bedos-Belval M Maturano P Saint-Aguet L Roussel H Duran J Grima-Pettenati 2005 Kinetic and inhibition studies of cinnamoyl-CoA reductase 1 from Arabidopsis thaliana Plant Physiol Biochem 43 746 753 10.1016/j.plaphy.2005.06.003 1:CAS:528:DC%2BD2MXhtFWhtr3L (Pubitemid 41454848)
6. RA Dixon F Chen D Guo K Parvathi 2001 The biosynthesis of monolignols: a 'metabolic grid', or independent pathways to guaiacyl and syringyl units Phytochemistry 57 1069 1084 10.1016/S0031-9422(01)00092-9 1:CAS:528: DC%2BD3MXks1Ojt74%3D (Pubitemid 32625584)
7. T Kawasaki H Koita T Nakatsubo K Hasegawa K Akabayashi H Akahashi K Umemura T Umezawa K Shimamoto 2006 Cinnamoyl-CoA reductase, a key enzyme in lignin biosynthesis, is an effector of small GTPase Rac in defense signaling in rice PNAS 103 230 235 10.1073/pnas.0509875103 1:CAS:528:DC%2BD28Xms12gsg%3D%3D (Pubitemid 43076132)
8. QH Ma 2007 Characterization of a cinnamoyl-CoA reductase that is associated with stem development in wheat J Exp Bot 58 2011 2021 10.1093/jxb/erm064 1:CAS:528:DC%2BD2sXosFeksb8%3D (Pubitemid 47216563)
9. B Moershbacher U Noll L Gorrichon HJ Reisener 1990 Specific inhibition of lignifications breaks hypersensitive resistance of wheat to stem rust Plant Physiol 93 465 470 10.1104/pp.93.2.465 (Pubitemid 120015505)
10. W Boerjan J Ralph M Baucher 2003 Lignin biosynthesis Annu Rev Plant Biol 54 519 546 10.1146/annurev.arplant.54.031902.134938 1:CAS:528: DC%2BD3sXntFSnsrg%3D (Pubitemid 37400004)
11. L Jones AR Ennos SR Turner 2001 Cloning and characterization of irregular xylem4 (irx4): A severely lignin-deficient mutant of Arabidopsis Plant J 26 205 216 10.1046/j.1365-313x.2001.01021.x 1:CAS:528:DC%2BD3MXkvVSnsrs%3D (Pubitemid 32540293)
12. T Luderitz H Grisebach 1981 Enzymic synthesis of lignin precursors. Comparison of cinnamoyl-CoA reductase and cinnamyl alcohol: NADP+ dehydrogenase from spruce (Picea abies L.) and soyabean (Glycine max L.) Eur J Biochem 119 115 124 10.1111/j.1432-1033.1981.tb05584.x 1:STN:280:DyaL387os1Kmuw%3D%3D
13. D Goffner MM Cambell C Campargue M Clastre G Borderies A Boudet AM Boudet 1994 Purification and characterization of cinnamoyl-coenzyme A: NADP oxidoreductase in Eucalyptus gunii Plant Physiol 106 625 632 1:CAS:528:DyaK2MXhslalsbc%3D
14. J Piquemal C Lapierre K Myton A O' Connel W Schuch J Grima-Pettenati AM Boudet 1998 Down-regulation of cinnamoyl- CoA reductase induces significant changes of lignin profiles in transgenic tobacco plants Plant J 13 71 83 10.1046/j.1365-313X.1998.00014.x 1:CAS:528:DyaK1cXhtVahsrk%3D (Pubitemid 28065691)
15. F Sarni C Grand AM Boudet 1984 Purification and properties of cinnamoyl-CoA reductase and cinnamyl alcohol dehydrogenase from poplar stems (Populus X euramerican) Eur J Biochem 139 259 265 10.1111/j.1432-1033.1984. tb08002.x 1:CAS:528:DyaL2cXhtFKru70%3D
16. H Meng WH Campbell 1998 Substrate profiles and expression of caffeoyl coenzyme A and caffeic acid O-methyltransferases in secondary xylem of aspen during seasonal development Plant Mol Biol 38 513 520 10.1023/A:1006071708728 1:CAS:528:DyaK1cXmtVSrtL4%3D (Pubitemid 28456104)
17. N Phogat, V Vindal, V Kumar, Krishna K Inampudi, Nirmal K Prasad (2010) Sequence analysis, in silico modeling and docking studies ofCaffeoyl CoA-O-methyltransferase of Populus trichopora. J Mol Model (In Press)
18. HM Berman J Westbrook Z Feng G Gilliland TN Bhat H Weissig IN Shindyalov PE Bourne 2000 The protein data bank Nucleic Acids Res 28 235 242 10.1093/nar/28.1.235 1:CAS:528:DC%2BD3cXhvVKjt7w%3D (Pubitemid 30047768)
19. MA Larkin G Blackshields NP Brown R Chenna PA McGettigan H McWilliam F Valentin IM Wallace A Wilm R Lopez JD Thompson TJ Gibson DG Higgins 2007 Clustal W and clustal X version 2.0 Bioinformatics 23 2947 2948 10.1093/bioinformatics/ btm404 1:CAS:528:DC%2BD2sXhtlaqsL%2FM (Pubitemid 350162903)
20. A Sali TL Blundell 1993 Comparative protein modelling by satisfaction of spatial restraints J Mol Biol 234 779 815 10.1006/jmbi.1993.1626 1:CAS:528:DyaK2cXnt1ylug%3D%3D (Pubitemid 24007801)
21. Eswar N, Marti-Renom MA, Webb B, Madhusudhan MS, Eramian D, Shen M, Pieper U, Sali A (2006) Comparative protein structure modeling with MODELLER. Current protocols in bioinformatics. Wiley, Suppl 15, 5.6.1-5.6.30
22. JC Phillips R Braun W Wang J Gumbart E Tajkhorshid E Villa C Chipot RD Skeel L Kale K Schulten 2005 Scalable molecular dynamics with NAMD J Comput Chem 26 1781 1802 10.1002/jcc.20289 1:CAS:528:DC%2BD2MXht1SlsbbJ (Pubitemid 43078511)
23. MacKerell AD Jr, Brooks B, Brooks CL III, Nilsson L, Roux B, Won Y, Karplus M (1998) CHARMM: The energy function and its parameterization with an overview of the program. In: Schleyer PVR et al. (eds) The encyclopedia of computational chemistry 1. Wiley, Chichester, pp 271-277
24. AD MacKerell Jr, et al. 1998 All-atom empirical potential for molecular modeling and dynamics studies of proteins J Phys Chem B 102 3586 3616 10.1021/jp973084f 1:CAS:528:DyaK1cXivVOlsb4%3D (Pubitemid 128576688)
25. L Willard A Ranjan H Zhang H Monzavi RF Boyko BD Sykes DS Wishart 2003 VADAR: a web server for quantitative evaluation of protein structure quality Nucleic Acids Res 31 3316 3319 10.1093/nar/gkg565 1:CAS:528:DC%2BD3sXltVWjtb8%3D (Pubitemid 37442148)
26. RA Laskowski MW MacArthur DS Moss JM Thornton 1993 PROCHECK: a program to check the stereochemical quality of protein structures J Appl Crystallogr 26 283 291 10.1107/S0021889892009944 1:CAS:528:DyaK3sXit12lurY%3D
27. J Dundas Z Ouyang J Tseng A Binkowski Y Turpaz J Liang 2006 CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues Nucleic Acids Res 34 W116 118 10.1093/nar/gkl282 1:CAS:528:DC%2BD28Xps1yhtrw%3D (Pubitemid 44529746)
28. G Jones P Willett RC Glen 1995 Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation J Mol Biol 245 43 53 10.1016/S0022-2836(95)80037-9 1:CAS:528:DyaK2MXjtVKlsbc%3D
29. G Jones P Willett RC Glen AR Leach R Taylor 1997 Development and validation of a genetic algorithm for flexible docking J Mol Biol 267 727 748 10.1006/jmbi.1996.0897 1:CAS:528:DyaK2sXis1KntLo%3D (Pubitemid 27170693)
30. ML Verdonk JC Cole MJC Hartshorn W Murray RD Taylor 2003 Improved protein-ligand docking using GOLD Proteins 52 609 623 10.1002/prot.10465 1:CAS:528:DC%2BD3sXmvFGrsLg%3D (Pubitemid 37034158)
31. Y Wang J Xiao TO Suzek J Zhang J Wang SH Bryant 2009 PubChem: a public information system for analyzing bioactivities of small molecules Nucleic Acids Res 6 1 11
32. A Pedretti L Villa G Vistoli 2004 VEGA - An open platform to develop chemo-bioinformatics applications, using plug-in architecture and script" programming" J Comput Aided Mater Des 18 167 173 10.1023/B:JCAM.0000035186. 90683.f2 1:CAS:528:DC%2BD2cXlsl2qt74%3D (Pubitemid 39069412)