Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

Comparative and ab initio three dimensional models of the carboxy terminal domain of the lambda repressor and their use to build intact repressor tetramer models bound to adjacent operator sites

Among two alternative models for residues 93-236 of the lambda repressor predicted, one (1gfx) has been partly built based on the UmuD' crystal structure. A second model (1lmd) containing a six-stranded jelly roll has been built ab initio by using secondary structure prediction, circular dichroism spectra of several C-terminal fragments, cysteine reactivity, autocleavage properties, and exploring possible protein folds compatible with these. The two models differ in the arrangement of the constituent beta strands, though extremely similar in secondary structure. The comparative model 1gfx shows 1.24 Angstrom RMS deviation from the crystal structure 1f39 for fragment 136-236. Part of the region previously called a hinge contains two small alpha helices as part of the C-domain in both theoretical models. Monomer-monomer interactions at the same operator site are stabilized by exposed hydrophobic side chains in beta strands while cooperative interactions are mostly confined to beta6 and adjacent residues in both models. Mutational data, existence of a two-fold axis relating two C-domains within a dimer, together with minimization of DNA distortion between adjacent operator sites allow us to roughly position the C-domain with respect to the N-domain for both 1gfx and 1lmd. We argue why the dimerization and tetramerization inferred in the crystal structure 1f39 cannot be true in vivo.

  1. Chattopadhyaya, R., Ghosh, K. & Namboodiri, V. M. H. (2000) Model of LexA Repressor Dimer Bound to recA Operator, JBSD, 18, 181-197.
  2. Ghosh, K. & Chattopadhyaya, R. (2001) Papain does not cleave operator-bound lambda repressor : structural characterization of the carboxy terminal domain and the hinge, JBSD, 18, 557-567.

Rajagopal Chattopadhyaya* and Kaushik Ghosh

Department of Biochemistry, Bose Institute, P-1/12, C. I. T. Scheme VIIM, Calcutta 700054, INDIA * Author to whom correspondence should be addressed. Phone 91-33-337-9544 ext 327, fax 91-33-334-3886; e-mail :raja@boseinst.ernet.in
PDB accession numbers for the lambda repressor comparative model in RCSB001477 (1gfx) processed June 22, 2000, ab initio model in RCSB000598 (1lmd) processed March 9, 1999, our related model of LexA repressor in RCSB000408 (1qaa) processed February 2, 1999.