PDBsum entry 1l2f

Go to PDB code: 
protein links
Transcription PDB id
Protein chain
344 a.a. *
Waters ×219
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Crystal structure of nusa from thermotoga maritima: a structure-based role of the n-terminal domain
Structure: N utilization substance protein a. Chain: a. Synonym: nusa. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.50Å     R-factor:   0.223     R-free:   0.298
Authors: D.H.Shin,H.H.Nguyen,J.Jancarik,H.Yokota,R.Kim,S.H.Kim, Berkeley Structural Genomics Center (Bsgc)
Key ref:
D.H.Shin et al. (2003). Crystal structure of NusA from Thermotoga maritima and functional implication of the N-terminal domain. Biochemistry, 42, 13429-13437. PubMed id: 14621988 DOI: 10.1021/bi035118h
20-Feb-02     Release date:   23-Sep-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9X298  (Q9X298_THEMA) -  N utilization substance protein A
344 a.a.
344 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     translational elongation   2 terms 
  Biochemical function     sequence-specific DNA binding transcription factor activity     3 terms  


DOI no: 10.1021/bi035118h Biochemistry 42:13429-13437 (2003)
PubMed id: 14621988  
Crystal structure of NusA from Thermotoga maritima and functional implication of the N-terminal domain.
D.H.Shin, H.H.Nguyen, J.Jancarik, H.Yokota, R.Kim, S.H.Kim.
We report the crystal structure of N-utilizing substance A protein (NusA) from Thermotoga maritima (TmNusA), a protein involved in transcriptional pausing, termination, and antitermination. TmNusA has an elongated rod-shaped structure consisting of an N-terminal domain (NTD, residues 1-132) and three RNA binding domains (RBD). The NTD consists of two subdomains, the globular head and the helical body domains, that comprise a unique three-dimensional structure that may be important for interacting with RNA polymerase. The globular head domain possesses a high content of negatively charged residues that may interact with the positively charged flaplike domain of RNA polymerase. The helical body domain is composed of a three-helix bundle that forms a hydrophobic core with the aid of two neighboring beta-strands. This domain shows structural similarity with one of the helical domains of sigma(70) factor from Escherichia coli. One side of the molecular surface shows positive electrostatic potential suitable for nonspecific RNA interaction. The RBD is composed of one S1 domain and two K-homology (KH) domains forming an elongated RNA binding surface. Structural comparison between TmNusA and Mycobacterium tuberculosis NusA reveals a possible hinge motion between NTD and RBD. In addition, a functional implication of the NTD in its interaction with RNA polymerase is discussed.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20179338 T.C.Terwilliger (2010).
Rapid model building of alpha-helices in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 268-275.  
20179339 T.C.Terwilliger (2010).
Rapid model building of beta-sheets in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 276-284.  
20179340 T.C.Terwilliger (2010).
Rapid chain tracing of polypeptide backbones in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 285-294.  
18996995 S.E.Cohen, V.G.Godoy, and G.C.Walker (2009).
Transcriptional modulator NusA interacts with translesion DNA polymerases in Escherichia coli.
  J Bacteriol, 191, 665-672.  
18757535 K.B.Arnvig, S.Zeng, S.Quan, A.Papageorge, N.Zhang, A.C.Villapakkam, and C.L.Squires (2008).
Evolutionary comparison of ribosomal operon antitermination function.
  J Bacteriol, 190, 7251-7257.  
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.  
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
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.  
15331784 D.H.Shin, Y.Lou, J.Jancarik, H.Yokota, R.Kim, and S.H.Kim (2004).
Crystal structure of YjeQ from Thermotoga maritima contains a circularly permuted GTPase domain.
  Proc Natl Acad Sci U S A, 101, 13198-13203.
PDB code: 1u0l
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.