Sequence-specific 1H, 13C, 15N resonance assignments of the carboxyterminal
domain of the transcription factor NusA from E.coli

Escherichia coli N utilization substance (339-495)

Sequence-specific 1H, 13C, 15N resonance assignments and secondary structure of the carboxyterminal domain of the E. coli transcription factor NusA.

The crystal structure of Thermotoga maritima NusA, a transcription factor
involved in pausing, termination, and antitermination processes, reveals a
four-domain, rod-shaped molecule. An N-terminal alpha/beta portion, a
five-stranded beta-barrel (S1 domain), and two K-homology (KH) modules create a
continuous spine of positive electrostatic potential, suitable for nonspecific
mRNA attraction. Homology models suggest how, in addition, specific mRNA
regulatory sequences can be recognized by the S1 and KH motifs. An arrangement
of multiple S1 and KH domains mediated by highly conserved residues is seen,
creating an extended RNA binding surface, a paradigm for other proteins with
similar domain arrays. Structural and mutational analyses indicate that the
motifs cooperate, modulating strength and specificity of RNA binding.

Worbs et. al.
An extended RNA binding surface through arrayed S1 and KH domains in transcription factor NusA.
Mol Cell. 2001 Jun;7(6):1177-89.

An extended RNA binding surface through arrayed S1 and KH domains in transcription factor NusA.

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.

Gopal et. al.
Crystal structure of the transcription elongation/anti-termination factor NusA from Mycobacterium
tuberculosis at 1.7 A resolution.
J Mol Biol. 2001 Dec 14;314(5):1087-95.

Crystal structure of the transcription elongation/anti-termination factor NusA from Mycobacterium tuberculosis at 1.7 A resolution.

The Escherichia coli NusA protein modulates pausing, termination, and
antitermination by associating with the transcribing RNA polymerase core
enzyme. NusA can be covalently cross-linked to nascent RNA within a
transcription complex, but does not bind RNA on its own. We have found that
deletion of the 79 carboxy-terminal amino acids of the 495-amino-acid NusA
protein allows NusA to bind RNA in gel mobility shift assays. The
carboxy-terminal domain (CTD) of the alpha subunit of RNA polymerase, as well
as the bacteriophage lambda N gene antiterminator protein, bind to
carboxy-terminal regions of NusA and enable full-length NusA to bind RNA.
Binding of NusA to RNA in the presence of alpha or N involves an amino-terminal
S1 homology region that is otherwise inactive in full-length NusA. The
interaction of the alpha-CTD with full-length NusA stimulates termination. N
may prevent termination by inducing NusA to interact with N utilization (nut)
site RNA rather than RNA near the 3' end of the nascent transcript. Sequence
analysis showed that the alpha-CTD contains a modified helix-hairpin-helix
motif (HhH), which is also conserved in the carboxy-terminal regions of some
eubacterial NusA proteins. These HhH motifs may mediate protein-protein
interactions in NusA and the alpha-CTD.

Mah et. al.
The alpha subunit of E. coli RNA polymerase activates RNA binding by NusA.
Genes Dev. 2000 Oct 15;14(20):2664-75.

The alpha subunit of E. coli RNA polymerase activates RNA binding by NusA.

Escherichia coli N utilization substance A (339-495)

transcription termination-antitermination factor NusA [Escherichia coli O157:H7 str. Sakai]

transcription termination/antitermination L factor [Escherichia coli str. K-12 substr. W3110]

N utilization substance protein A [Escherichia coli SE11]

transcription termination/antitermination L factor NusA [Escherichia coli O26:H11 str. 11368]

transcription termination/antitermination L factor NusA [Escherichia coli O103:H2 str. 12009]

unnamed protein product [Escherichia coli]

Transcription elongation protein nusA [Escherichia coli LF82]

transcription termination/antitermination L factor [Escherichia coli BL21(DE3)]

transcription termination/antitermination L factor [Escherichia fergusonii ATCC 35469]

transcription termination/antitermination L factor [Escherichia coli IAI1]

L factor [Escherichia coli str. K-12 substr. MG1655]

transcription termination/antitermination L factor [Escherichia coli str. K-12 substr. MG1655]

transcription pausing; L factor [Escherichia coli O157:H7 str. EDL933]

transcription pausing; L factor [Shigella flexneri 2a str. 301]

N utilization substance protein A [Escherichia coli CFT073]

transcription elongation factor NusA [Escherichia coli O157:H7 str. EDL933]

transcription elongation factor NusA [Escherichia coli O157:H7 str. Sakai]

transcription elongation factor NusA [Shigella flexneri 2a str. 301]

transcription elongation factor NusA [Escherichia coli CFT073]

RecName: Full=Transcription termination/antitermination protein NusA; AltName: Full=N utilization substance protein A; AltName:

RecName: Full=Transcription termination/antitermination protein NusA [Escherichia coli CFT073]

RecName: Full=Transcription termination/antitermination protein NusA [Escherichia coli O157:H7]

RecName: Full=Transcription termination/antitermination protein NusA [Shigella flexneri]

B.A. Johnson, Merck, Whitehouse Station, NJ, USA