Homology modeling of Ferredoxin-nitrite reductase from Arabidopsis thaliana

Kherraz, Karim; Kherraz, Khaled; Kameli, A.

doi:10.6026/97320630006115

Cited by 13 publications

(10 citation statements)

References 13 publications

(16 reference statements)

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“…In leaf, electrons excited by sunlight are the ultimate source of reducing equivalents in plants. Electron flow generated from the photosystems is used to reduce Fd, which in turn can be used for reduction of NADP to NADPH by FNR, for reduction of thiodoxins (Trx) by ferredoxin:thioredoxinreductase (FTR), for reduction of nitrite to ammonium by ferredoxin-nitrite reductase (NiR) [ 13 ] and for reduction of 2-oxoglutarate and glutamate to two glutamines by glutamate synthase (GOGAT). In the leaves and roots of the OE lines, there were no changes in the transcript abundance of four Fd genes, two FTR genes, nine Trx genes ( Trx f1-2, m1-4, Trx x, Trx y1-2 ), or most enzymes regulated by Trx (GAPD1-3, SBPase, PRK, RCA, NADP-MDH) (Additional file 8 b) [ 14 ].…”

Section: Resultsmentioning

confidence: 99%

Global transcriptome analysis of AtPAP2 - overexpressing Arabidopsisthalianawith elevated ATP

et al. 2013

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BackgroundAtPAP2 is a purple acid phosphatase that is targeted to both chloroplasts and mitochondria. Over-expression (OE) lines of AtPAP2 grew faster, produced more seeds, and contained higher leaf sucrose and glucose contents. The present study aimed to determine how high energy status affects leaf and root transcriptomes.ResultsATP and ADP levels in the OE lines are 30-50% and 20-50% higher than in the wild-type (WT) plants. Global transcriptome analyses indicated that transcriptional regulation does play a role in sucrose and starch metabolism, nitrogen, potassium and iron uptake, amino acids and secondary metabolites metabolism when there is an ample supply of energy. While the transcript abundance of genes encoding protein components of photosystem I (PS I), photosystem II (PS II) and light harvesting complex I (LHCI) were unaltered, changes in transcript abundance for genes encoding proteins of LHCII are significant. The gene expressions of most enzymes of the Calvin cycle, glycolysis and the tricarboxylic acid (TCA) cycle were unaltered, as these enzymes are known to be regulated by light/redox status or allosteric modulation by the products (e.g. citrate, ATP/ADP ratio), but not at the level of transcription.ConclusionsAtPAP2 overexpression resulted in a widespread reprogramming of the transcriptome in the transgenic plants, which is characterized by changes in the carbon, nitrogen, potassium, and iron metabolism. The fast-growing AtPAP2 OE lines provide an interesting tool for studying the regulation of energy system in plant.

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Section: Resultsmentioning

confidence: 99%

Global transcriptome analysis of AtPAP2 - overexpressing Arabidopsisthalianawith elevated ATP

et al. 2013

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“…The PDB Sum server was employed for evaluation by comparing the geometry and stereo chemical parameters ( r 0 , θ andΦ) quality of predicted models. A large number of literature related homology modeling were also found to use the PROCHECK for screening the best model . Further Ramachandran plot used to evaluate the values of the dihedral angels agree with the values of allowed conformation for protein backbones.…”

Section: Resultsmentioning

confidence: 99%

Serine protease identification (in vitro) and molecular structure predictions (in silico) from a phytopathogenic fungus,Alternaria solani

Chandrasekaran

Chandrasekar

et al. 2013

J. Basic Microbiol.

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Serine proteases are involved in an enormous number of biological processes. The present study aims at characterizing three‐dimensional (3D) molecular architecture of serine proteases from early blight pathogen, Alternaria solani that are hypothesized to be markers of phytopathogenicity. A serine protease was purified to homogeneity and MALDI‐TOF‐MS/MS analysis revealed that protease produced by A. solani belongs to alkaline serine proteases (AsP). AsP is made up of 403 amino acid residues with molecular weight of 42.1 kDa (Isoelectric point – 6.51) and its molecular formula was C1859H2930N516O595S4. AsP structure model was built based on its comparative homology with serine protease using the program, MODELER. AsP had 16 β‐sheets and 10 α‐helices, with Ser350 (G347–G357), Asp158 (D158–H169), and His193 (H193–G203) in separate turn/coil structures. Biological metal binding region situated near 6th‐helix and His193 residue is responsible for metal binding site. Also, calcium ion (Ca2+) is coordinated by the carboxyl groups of Lys84, Ile85, Lys86, Asp87, Phe88, Ala89, Ala90 (K84–A90) for first Ca2+ binding site and carbonyl oxygen atom of Lys244, Gly245, Arg246, Thr247, Lys248, Lys249, and Ala250 (K244–A250), for second Ca2+ binding site. Moreover, Ramachandran plot analysis of protein residues falling into most favored secondary structures were determined (83.3%). The predicted molecular 3D structural model was further verified using PROCHECK, ERRAT, and VADAR servers to confirm the geometry and stereo‐chemical parameters of the molecular structural design. The functional analysis of AsP 3D molecular structure predictions familiar in the current study may provide a new perspective in the understanding and identification of antifungal protease inhibitor designing.

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“…In this study, the primary sequence identity between Mt CMPK (target) and E.coli CMPK indicates that ~40% sequence identity (Figure 2). Medium accuracy model, obtained with a template-target sequence identity of 30-50% [20]. The sequence analysis result based on BLASTp, there were 220 amino acids only 88 amino acids had been matched.…”

Section: Resultsmentioning

confidence: 99%

Insight from the structural molecular model of cytidylate kinase from Mycobacterium tuberculosis

Verma

Singh

2013

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Mycobacterium tuberculosis is a gram-positive bacterium causes tuberculosis in human. H37Rv strain is a pathogenic strain utilized for tuberculosis research. The cytidylate mono-phosphate (CMP) kinase of Mycobacterium tuberculosis belongs to the family nucleoside mono-phosphate kinase (NMK), this enzyme is required for the bacterial growth. Therefore, it is important to study the structural and functional features of this enzyme in the control of the disease. Hence, we developed the structural molecular model of the CMP kinase protein from Mycobacterium tuberculosis by homology modeling using the software MODELLER (9v10). Based on sequence similarity with protein of known structure (template) of Mycobacterium smegmatis (PDB ID: 3R20) was chosen from protein databank (PDB) by using BLASTp. The energy of constructed models was minimized and the qualities of the models were evaluated by PROCHECK and VERRIFY-3D. Resulted Ramachandran plot analysis showed that conformations for 100.00% of amino acids residues are within the most favored regions. A possible homologous deep cleft active site was identified in the Model using CASTp program. Amino acid composition and polarity of that protein was observed by CLC-Protein Workbench tool. Expasy's Prot-param server and CYC_REC tool were used for physiochemical and functional characterization of the protein. Studied of secondary structure of that protein was carried out by computational program, ProFunc. The structure is finally submitted in Protein Model Database. The predicted model permits initial inferences about the unexplored 3D structure of the CMP kinase and may be promote in relational designing of molecules for structure-function studies.

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Homology modeling of Ferredoxin-nitrite reductase from Arabidopsis thaliana

Cited by 13 publications

References 13 publications

Global transcriptome analysis of AtPAP2 - overexpressing Arabidopsisthalianawith elevated ATP

Global transcriptome analysis of AtPAP2 - overexpressing Arabidopsisthalianawith elevated ATP

Serine protease identification (in vitro) and molecular structure predictions (in silico) from a phytopathogenic fungus,Alternaria solani

Insight from the structural molecular model of cytidylate kinase from Mycobacterium tuberculosis

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