Int. J. Mol. Sci. 2012, 13(7), 8578-8596; doi:10.3390/ijms13078578
Article

Molecular Cloning and 3D Structure Modeling of APEX1, DNA Base Excision Repair Enzyme from the Camel, Camelus dromedarius

1 Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia 2 Department of Molecular Biology, Genetic Engineering Division, National Research Center, Dokki, Cairo 12311, Egypt 3 Department of Zoology, College of Science, King Saud University, P.O. Box 22452, Riyadh 11459, Saudi Arabia 4 Protein Research Chair Lab, Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia 5 Genome Research Chair Lab, Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia 6 Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, P.O. Box 832, Alexandria 21526, Egypt
* Author to whom correspondence should be addressed.
Received: 28 March 2012; in revised form: 15 June 2012 / Accepted: 27 June 2012 / Published: 10 July 2012
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Abstract: The domesticated one-humped camel, Camelus dromedarius, is one of the most important animals in the Arabian Desert. It is exposed most of its life to both intrinsic and extrinsic genotoxic factors that are known to cause gross DNA alterations in many organisms. Ionic radiation and sunlight are known producers of Reactive Oxygen Species (ROS), one of the causes for DNA lesions. The damaged DNA is repaired by many enzymes, among of them Base Excision Repair enzymes, producing the highly mutagenic apurinic/apyrimidinicsites (AP sites). Therefore, recognition of AP sites is fundamental to cell/organism survival. In the present work, the full coding sequence of a putative cAPEX1 gene was amplified for the first time from C. dromedarius by RT-PCR and cloned (NCBI accession number are HM209828 and ADJ96599 for nucleotides and amino acids, respectively). cDNA sequencing was deduced to be 1041 nucleotides, of which 954 nucleotides encode a protein of 318 amino acids, similar to the coding region of the APEX1 gene and the protein from many other species. The calculated molecular weight and isoelectric point of cAPEX1 using Bioinformatics tools was 35.5 kDa and 8.11, respectively. The relative expressions of cAPEX1 in camel kidney, spleen, lung and testis were examined using qPCR and compared with that of the liver using a 18S ribosomal subunit as endogenous control. The highest level of cAPEX1 transcript was found in the testis; 325% higher than the liver, followed by spleen (87%), kidney (20%) and lung (5%), respectively. The cAPEX1 is 94%–97% similar to their mammalian counterparts. Phylogenetic analysis revealed that cAPEX1 is grouped together with that of S. scrofa. The predicted 3D structure of cAPEX1 has similar folds and topology with the human (hAPEX1). The root-mean-square deviation (rmsd) between cAPEX1 and hAPEX1 was 0.582 and the Q-score was 0.939.
Keywords: Ape1/Ref-1/APEX1; 3D structure modeling; DNA repair; BER; cloning; molecular characterization; qPCR; one-humped camel

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MDPI and ACS Style

Ataya, F.S.; Fouad, D.; Malik, A.; Saeed, H.M. Molecular Cloning and 3D Structure Modeling of APEX1, DNA Base Excision Repair Enzyme from the Camel, Camelus dromedarius. Int. J. Mol. Sci. 2012, 13, 8578-8596.

AMA Style

Ataya FS, Fouad D, Malik A, Saeed HM. Molecular Cloning and 3D Structure Modeling of APEX1, DNA Base Excision Repair Enzyme from the Camel, Camelus dromedarius. International Journal of Molecular Sciences. 2012; 13(7):8578-8596.

Chicago/Turabian Style

Ataya, Farid Shokry; Fouad, Dalia; Malik, Ajamaluddin; Saeed, Hesham Mahmoud. 2012. "Molecular Cloning and 3D Structure Modeling of APEX1, DNA Base Excision Repair Enzyme from the Camel, Camelus dromedarius." Int. J. Mol. Sci. 13, no. 7: 8578-8596.

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