PDBsum entry 1hh2

Transcription regulation

PDB id

1hh2

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Contents

			Protein chain

					344 a.a. *

			Waters ×357

* Residue conservation analysis

PDB id:

1hh2

Links

Name:

Transcription regulation

Title:

Crystal structure of nusa from thermotoga maritima

Structure:

N utilization substance protein a. Chain: p. Synonym: nusa. Engineered: yes

Source:

Thermotoga maritima. Organism_taxid: 2336. Gene: nusa. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.10Å

R-factor:

0.244

R-free:

0.319

Authors:

M.Worbs,G.P.Bourenkov,H.D.Bartunik,R.Huber,M.C.Wahl

Key ref:

M.Worbs et al. (2001). An extended RNA binding surface through arrayed S1 and KH domains in transcription factor NusA. Mol Cell, 7, 1177-1189. PubMed id: 11430821 DOI: 10.1016/S1097-2765(01)00262-3

Date:

18-Dec-00

Release date:

19-Oct-01

PROCHECK

	Headers

	References

Protein chain

Q9X298 (Q9X298_THEMA) - Transcription termination/antitermination protein NusA from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: Struc:					344 a.a. 344 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.?

[IntEnz] [ExPASy] [KEGG] [BRENDA]

DOI no: 10.1016/S1097-2765(01)00262-3	Mol Cell 7:1177-1189 (2001)
PubMed id: 11430821

An extended RNA binding surface through arrayed S1 and KH domains in transcription factor NusA.
M.Worbs, G.P.Bourenkov, H.D.Bartunik, R.Huber, M.C.Wahl.

ABSTRACT

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.

Selected figure(s)



	Figure 4. Figure 4. Domain Stacking(a) Closeup of the interactions between S1 and KH1. The view is from the back of Figure 1b, with S1 at the left and KH1 at the right.(b) Details of the KH1–KH2 contacts. The view is from the left in Figure 1b, with KH1 rotated to the left and KH2 to the right. Absolutely conserved residues involved in the interactions are labeled		Figure 5. Figure 5. KH Arrays(a) Arrangement of the NusA KH domains via opposite poles. The view is from the bottom right of Figure 1b.(b) Ribbon diagram of the same region with a KH1-bound RNA hairpin rotated vert, similar 90° counterclockwise about the longitudinal axis. The prime RNA binding peptides as deduced from Figure 3 are labeled (red). Additional contacts through KH2 are in green.(c) Crystal contacts of two NOVA KH3·RNA complexes. The bottom KH domains in (a) and (c) are in approximately the same orientation

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21036867

K.B.Cook, H.Kazan, K.Zuberi, Q.Morris, and T.R.Hughes (2011).
RBPDB: a database of RNA-binding specificities.

Nucleic Acids Res, 39, D301-D308.

20920266

M.Naville, and D.Gautheret (2010).
Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation.

Genome Biol, 11, R97.

19515940

S.Prasch, M.Jurk, R.S.Washburn, M.E.Gottesman, B.M.Wöhrl, and P.Rösch (2009).
RNA-binding specificity of E. coli NusA.

Nucleic Acids Res, 37, 4736-4742.

18465893

O.Paliy, S.M.Gargac, Y.Cheng, V.N.Uversky, and A.K.Dunker (2008).
Protein disorder is positively correlated with gene expression in Escherichia coli.

J Proteome Res, 7, 2234-2245.

19111659

X.Luo, H.H.Hsiao, M.Bubunenko, G.Weber, D.L.Court, M.E.Gottesman, H.Urlaub, and M.C.Wahl (2008).
Structural and functional analysis of the E. coli NusB-S10 transcription antitermination complex.

Mol Cell, 32, 791-802.

PDB codes:

3d3b 3d3c

17159918

A.Oddone, E.Lorentzen, J.Basquin, A.Gasch, V.Rybin, E.Conti, and M.Sattler (2007).
Structural and biochemical characterization of the yeast exosome component Rrp40.

EMBO Rep, 8, 63-69.

PDB code:

2ja9

17473849

B.M.Lunde, C.Moore, and G.Varani (2007).
RNA-binding proteins: modular design for efficient function.

Nat Rev Mol Cell Biol, 8, 479-490.

17277442

H.Tanaka, T.Umehara, K.Inaka, S.Takahashi, R.Shibata, Y.Bessho, M.Sato, S.Sugiyama, E.Fusatomi, T.Terada, M.Shirouzu, S.Sano, M.Motohara, T.Kobayashi, T.Tanaka, A.Tanaka, and S.Yokoyama (2007).
Crystallization of the archaeal transcription termination factor NusA: a significant decrease in twinning under microgravity conditions.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 69-73.

PDB code:

2cy1

17502377

S.Kyzer, K.S.Ha, R.Landick, and M.Palangat (2007).
Direct versus limited-step reconstitution reveals key features of an RNA hairpin-stabilized paused transcription complex.

J Biol Chem, 282, 19020-19028.

17420252

Y.Abe, T.Jo, Y.Matsuda, C.Matsunaga, T.Katayama, and T.Ueda (2007).
Structure and function of DnaA N-terminal domains: specific sites and mechanisms in inter-DnaA interaction and in DnaB helicase loading on oriC.

J Biol Chem, 282, 17816-17827.

PDB code:

2e0g

16407194

C.R.Ramos, C.L.Oliveira, I.L.Torriani, and C.C.Oliveira (2006).
The Pyrococcus exosome complex: structural and functional characterization.

J Biol Chem, 281, 6751-6759.

16428607

N.H.Chmiel, D.C.Rio, and J.A.Doudna (2006).
Distinct contributions of KH domains to substrate binding affinity of Drosophila P-element somatic inhibitor protein.

RNA, 12, 283-291.

15987884

A.Eisenmann, S.Schwarz, S.Prasch, K.Schweimer, and P.Rösch (2005).
The E. coli NusA carboxy-terminal domains are structurally similar and show specific RNAP- and lambdaN interaction.

Protein Sci, 14, 2018-2029.

PDB codes:

1wcl 1wcn

16193062

B.Beuth, S.Pennell, K.B.Arnvig, S.R.Martin, and I.A.Taylor (2005).
Structure of a Mycobacterium tuberculosis NusA-RNA complex.

EMBO J, 24, 3576-3587.

PDB codes:

2asb 2atw

15670167

I.Pozdnyakova, and L.Regan (2005).
New insights into Fragile X syndrome. Relating genotype to phenotype at the molecular level.

FEBS J, 272, 872-878.

16237005

L.M.Stickney, J.S.Hankins, X.Miao, and G.A.Mackie (2005).
Function of the conserved S1 and KH domains in polynucleotide phosphorylase.

J Bacteriol, 187, 7214-7221.

15720542

S.Borukhov, J.Lee, and O.Laptenko (2005).
Bacterial transcription elongation factors: new insights into molecular mechanism of action.

Mol Microbiol, 55, 1315-1324.

15365170

I.Bonin, R.Mühlberger, G.P.Bourenkov, R.Huber, A.Bacher, G.Richter, and M.C.Wahl (2004).
Structural basis for the interaction of Escherichia coli NusA with protein N of phage lambda.

Proc Natl Acad Sci U S A, 101, 13762-13767.

PDB code:

1u9l

15159542

K.B.Arnvig, S.Pennell, B.Gopal, and M.J.Colston (2004).
A high-affinity interaction between NusA and the rrn nut site in Mycobacterium tuberculosis.

Proc Natl Acad Sci U S A, 101, 8325-8330.

12592003

A.Ramos, D.Hollingworth, and A.Pastore (2003).
The role of a clinically important mutation in the fold and RNA-binding properties of KH motifs.

RNA, 9, 293-298.

14621988

D.H.Shin, H.H.Nguyen, J.Jancarik, H.Yokota, R.Kim, and S.H.Kim (2003).
Crystal structure of NusA from Thermotoga maritima and functional implication of the N-terminal domain.

Biochemistry, 42, 13429-13437.

PDB code:

1l2f

12888498

H.Meka, G.Daoust, K.B.Arnvig, F.Werner, P.Brick, and S.Onesti (2003).
Structural and functional homology between the RNAP(I) subunits A14/A43 and the archaeal RNAP subunits E/F.

Nucleic Acids Res, 31, 4391-4400.

12403469

A.Git, and N.Standart (2002).
The KH domains of Xenopus Vg1RBP mediate RNA binding and self-association.

RNA, 8, 1319-1333.

12167155

E.Nudler, and M.E.Gottesman (2002).
Transcription termination and anti-termination in E. coli.

Genes Cells, 7, 755-768.

11809881

J.A.Chekanova, J.A.Dutko, I.S.Mian, and D.A.Belostotsky (2002).
Arabidopsis thaliana exosome subunit AtRrp4p is a hydrolytic 3'-->5' exonuclease containing S1 and KH RNA-binding domains.

Nucleic Acids Res, 30, 695-700.

12198166

T.Steiner, J.T.Kaiser, S.Marinkoviç, R.Huber, and M.C.Wahl (2002).
Crystal structures of transcription factor NusG in light of its nucleic acid- and protein-binding activities.

EMBO J, 21, 4641-4653.

PDB codes:

1m1g 1m1h

11953318

Y.Yang, N.Declerck, X.Manival, S.Aymerich, and M.Kochoyan (2002).
Solution structure of the LicT-RNA antitermination complex: CAT clamping RAT.

EMBO J, 21, 1987-1997.

PDB code:

1l1c

11835484

A.G.Murzin, and A.Bateman (2001).
CASP2 knowledge-based approach to distant homology recognition and fold prediction in CASP4.

Proteins, (), 76-85.

11741548

F.Todone, P.Brick, F.Werner, R.O.Weinzierl, and S.Onesti (2001).
Structure of an archaeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex.

Mol Cell, 8, 1137-1143.

PDB code:

1go3

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.