Biopolym. Cell. 2012; 28(1):68-74.
Cobaltand nickel-containing enzyme constructs from the sequences of methanogens
1Chellapandi P., 1Balachandramohan J.
  1. Department of Bioinformatics, School of Life Sciences,
    Bharathidasan University
    Tiruchirappalli-620024, Tamil Nadu, India


Aim. The conserved domain of sequences revealed in methanogens is considered for designing enzymes among which the attention has been focused on the metalloenzymes showing evolutionary significances. Methods. Molecular evolution, molecular modelling and molecular docking methods. Results. Molecular evolutionary hypothesis has been applied for designing cobalt-containing sirohydrocholine cobalt chelatase and nickel-containing coenzyme F420 non-reducing hydrogenase from conserved domains encompassing metaland substrate-binding sites. It was hypothesized that if any enzyme has similar or identical conserved domain in its catalytic region, the construct can bring similar catalytic activity. Using this approach, the region which covers such functional module has to be modeled for yielding enzyme constructs. The present approach has provided a high likelihood to design stable metalloenzyme constructs from the sequences of methanogens due to their low functional divergence. The resulted enzyme constructs have shown diverse reaction specificity and binding affinity with respective substrates. Conclusions. It seems to provide a new knowledge on understanding the catalytic competence as well as substrate-specificity of enzyme constructs. The resulted enzyme constructs could be experimentally reliable as the sequences originally driven from methanogenic archaea.
Keywords: molecular docking, metalloenzymes, conserved domains, molecular evolution, enzyme design, enzyme constructs


[1] Luetz S., Giver L., Lalonde J. Engineered enzymes for chemical production. Biotechnol. Bioeng 2008 101, N 4:647– 653.
[2] Alqueres S. M. C., Almeida R. V., Clementino M. M., Vieira R. P., Almeida W. I., Cardoso A. M., Martins O. B. Exploring the biotechnological applications in the archaeal domain. Braz. J. Microbiol 2007 38, N 3:398–405.
[3] Chellapandi P., Balachandramohan J. Molecular evolution-directed approach for designing of -methylaspartate mutase from the sequences of Haloarchaea. Int. J. Chem. Mod 2011 3, N 3:143–154.
[4] Schenk S., Weston S., Anders E. Computational studies on the mode of action of metalloenzymes – quantum chemistry connects molecular biology with chemistry. Berichte des IZWR 2003 2:1–18.
[5] Chellapandi P., Balachandramohan J. Molecular evolutiondirected approach for designing archaeal formyltetrahydrofolate ligase. Turk. J. Biochem 2011 36, N 2:122–136.
[6] Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997 25, N 24:4876–4882.
[7] Tamura K., Dudley J., Nei M., Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol 2007 24, N 8:1596–1599.
[8] Eswar N., John B., Mirkovic N., Fiser A., Ilyin V. A., Pieper U., Stuart A. C., Marti-Renom M. A., Madhusudhan M. S., Yerkovich B., Sali A. Tools for comparative protein structure modeling and analysis. Nucleic Acids Res 2003 31, N 13:3375–3380.
[9] Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997 25, N 17:3389–3402.
[10] Laskowski R. A., Watson J. D., Thornton J. M. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 2005 33, Web Server issue:W89–W93.
[11] Brindley A. A., Raux E., Leech H. K., Schubert H. L., Warren M. J. A story of chelatase evolution: identification and characterization of a small 13-15-kDa «ancestral» cobaltochelatase (CbiXS) in the archaea. J. Biol. Chem 2003 278, N 25:22388– 22395.
[12] Gerlt J. A., Babbitt P. C. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu. Rev. Biochem 2001 70:209– 246.
[13] Raux E., Thermes C., Heathcote P., Rambach A., Warren M. J. A role for Salmonella typhimurium cbiK in cobalamin (vitamin B12) and siroheme biosynthesis. J. Bacteriol 1997 179, N 10:3202–3212.
[14] Al-Karadaghi S., Franco R., Hansson M., Shelnutt J. A., Isaya G., Ferreira G. C. Chelatases: distort to select?. Trends Biochem. Sci 2006 31, N 3:135–142.
[15] Pisarchik A., Petri R., Schmidt-Dannert C. Probing the structural plasticity of an archaeal primordial cobaltochelatase CbiX (S). Protein Eng. Des. Sel 2007 20, N 6:257–265.
[16] Dailey H. A., Dailey T. A., Wu C. K., Medlock A. E., Wang K. F., Rose J. P., Wang B. C. Ferrochelatase at the millennium: structures, mechanisms and [2Fe-2S] clusters. Cell. Mol. Life Sci 2000 57, N 13–14:1909–1926.
[17] Leach M. R., Zhang J. W., Zamble D. B. The role of complex formation between the Escherichia coli hydrogenase accessory factors HypB and SlyD. J. Biol. Chem 2007 282, N 22:16177–16186.
[18] Pavlov M., Siegbahn P. E. M., Blomberg M. R. A., Crabtree R. H. Mechanism of H-H activation by nickel-iron hydrogenase. J. Am. Chem. Soc 1998 120, N 3:548–555.
[19] Chellapandi P. Molecular evolution of methanogens based on their metabolic facets. Front. Biol 2011.