PDBsum entry 1k0r

Transcription

PDB id

1k0r

Contents

			Protein chains

					326 a.a. *

			Ligands

					SO4 ×4

			Waters ×395

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of the transcription elongation/anti-Termination factor nusa from mycobacterium tuberculosis at 1.7 a resolution.

Authors

B.Gopal, L.F.Haire, S.J.Gamblin, E.J.Dodson, A.N.Lane, K.G.Papavinasasundaram, M.J.Colston, G.Dodson.

Ref.

J Mol Biol, 2001, 314, 1087-1095. [DOI no: 10.1006/jmbi.2000.5144]

PubMed id

11743725

Abstract

Mycobacterium tuberculosis is the cause of tuberculosis in humans, a disease that affects over a one-third of the world's population. This slow-growing pathogen has only one ribosomal RNA operon, thus making its transcriptional apparatus a fundamentally interesting target for drug discovery. NusA binds to RNA polymerase and modulates several of the ribosomal RNA transcriptional processes. Here, we report the crystal structure of NusA, and reveal that the molecule consists of four domains. They are organised as two distinct entities. The N-terminal domain (residues 1 to 99) that resembles the B chain of the Rad50cd ATP binding cassette-ATPase (ABC-ATPase) and a C-terminal module (residues 108 to 329) consisting of a ribosomal S1 protein domain followed by two K homology domains. The S1 and KH domains are tightly integrated together to form an extensive RNA-binding structure, but are flexibly tethered to the N-terminal domain. The molecule's surfaces and architecture provide insights into RNA and polymerase interactions and the mechanism of pause site discrimination. They also allow us to rationalize certain termination-defective and cold shock-sensitive mutations in the nusA gene that have been studied in Escherichia coli.



	Figure 1. Figure 1. (a) The N-terminal (green) , S1 (yellow), KH1 (blue) and KH2 (magenta) domains of NusA from M. tuberculosis represented as ribbons in two perpendicular orientations. The alpha-helices and strands are labelled according to the order in which they occur in the sequence. NusA can be regarded as being made up of two components, an N-terminal domain with a a[3]b[3] structure (comprising helices H1 to H3 and strands S1 to S3) linked to the C-terminal module which has a S1-like region (five-stranded beta-barrel S4-S8, with a turn of a 3[10]-helix H4) followed by two K homology domains, also with a[3]b[3] structure, KH1(H6-H8, S9-S11) and KH2 (H9-H11, S12-S14). (b) The NusA molecule with the residues H-bonded at the interfaces shown. The conserved residues are labelled. In this view the KH1 domain can be seen to form a wedge between the S1 and KH2 domains. (c) An enlarged view of the interfaces with KH1 at the centre. It shows the H-bonding networks around the partly buried Arg183 in S1 and Arg231 in KH1, and the completely buried Lys219 in KH1.		Figure 2. Figure 2. The structure of M. tuberculosis NusA is consistent with a nucleic acid binding protein. (a) Sequence comparison of NusA homologs. The secondary structure derived from M. tuberculosis NusA is shown under the sequence. The shaded regions refer to different structural motifs and are maintained in the structures shown in (b). It is interesting to compare the sequences of M. leprae and M. smegmatis NusA with that of M. tuberculosis in the C-terminal proline-rich region, in particular a poly(proline)stretch (PPPPPGQP) in M. tuberculosis NusA which is (PPCSAGQS) in M. leprae and (AP-VG-) in M. smegmatis. This poly(proline) sequence is totally absent in the other homologues. (b) Structural comparisons of the main motifs. The N-terminal domain of NusA compared to the B chain of the rad50cd ABC ATPase, the S1 domain compared to the solution structure of the S1 domain from polynucleotide phosphorylase, and the KH domain compared to the canonical KH domain from the nova KH3 structure.

PROCHECK

	Headers