PDBsum entry 1l1c

Transcription/RNA

PDB id

1l1c

Contents

			Protein chains

					55 a.a. *

			DNA/RNA

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Solution structure of the lict-Rna antitermination complex: cat clamping rat.

Authors

Y.Yang, N.Declerck, X.Manival, S.Aymerich, M.Kochoyan.

Ref.

EMBO J, 2002, 21, 1987-1997. [DOI no: 10.1093/emboj/21.8.1987]

PubMed id

11953318

Abstract

LicT is a bacterial regulatory protein able to prevent the premature arrest of transcription. When activated, LicT binds to a 29 base RNA hairpin overlapping a terminator located in the 5' mRNA leader region of the target genes. We have determined the solution structure of the LicT RNA-binding domain (CAT) in complex with its ribonucleic antiterminator (RAT) target by NMR spectroscopy (PDB 1L1C). CAT is a beta-stranded homodimer that undergoes no important conformational changes upon complex formation. It interacts, through mostly hydrophobic and stacking interactions, with the distorted minor groove of the hairpin stem that is interrupted by two asymmetric internal loops. Although different in sequence, these loops share sufficient structural analogy to be recognized similarly by symmetry-related elements of the protein dimer, leading to a quasi- symmetric structure reminiscent of that observed with dimeric transcription regulators bound to palindromic DNA. Sequence analysis suggests that this RNA- binding mode, where the RAT strands are clamped by the CAT dimer, is conserved in homologous systems.



	Figure 3. Figure 3 (A) Ensemble of NMR structures of the LicT-CAT−RAT complex showing the protein backbone (in red) with some of the interacting amino acid side chains (in yellow), and the RNA helix (phosphodiester backbone in purple and nucleotides in standard atom colours). (B) MOLSCRIPT (Kraulis, 1991) representation of the LicT-CAT dimer interacting with its RAT hairpin target. The two CAT monomers, each composed of a four-stranded antiparallel -sheet, are coloured in red and blue. Some important side chains interacting with the RNA are shown in ball-and-stick representation. The RNA phosphodiester backbone is shown in purple and the nucleotides are in standard atom colours. (C and D) Stereo views showing the pseudo-symmetric recognition of the RNA asymmetric internal loop 1 and loop 2, respectively, by each CAT monomer. The nucleotides forming loop 1 (the A3−A27 sheared pair and the bulged-out A26) and loop 2 (the U7−A9−G22 triplet and the bulged-out U8) are shown in ball-and-sticks as well as the neighbouring canonical base pairs (U4−A25 in loop 1, G6−C23 in loop 2). Relevant hydrogen bonds between protein and RNA residues are indicated as dotted lines.		Figure 5. Figure 5 GRASP (Nicholls et al., 1991) representations of the protein−RNA complex showing the symmetric role of the CAT monomers and the cavity on each side of the dimer receiving the bulged-out base in the RNA internal loop 1 (left side views) and loop 2 (right side views). In each case, the left and right side views showing the protein surface and the RNA backbone are rotated by 180° with respect to each other. (A) The protein monomers are coloured in red and blue as in Figure 3. Amino acid residues are labelled in black. The bulged-out bases are labelled in white. (B) The electrostatic surface potential as calculated for the free CAT dimer using GRASP. The amino acids lying in the minor groove of the RNA helix are essentially neutral. They are surrounded by two spines of basic residues, interacting with the phosphodiester backbone. (C) Conserved amino acids and nucleotides coloured as a function of their level of conservation among the LicT/SacY family. Strictly conserved amino acids within the AT family are coloured in dark blue, conserved residues in blue and others in green. Similarly, the nucleotides are coloured in red, orange, yellow and green as their level of conservation within the RAT sequences decreases.

PROCHECK

	Headers