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PDBsum entry 1npp
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protein ligands Protein-protein interface(s) links
Transcription PDB id
1npp

 

 

 

 

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Contents
Protein chains
244 a.a. *
Ligands
IPA ×2
Waters ×858
* Residue conservation analysis
PDB id:
1npp
Name: Transcription
Title: Crystal structure of aquifex aeolicus nusg in p2(1)
Structure: Transcription antitermination protein nusg. Chain: a, b, c, d. Engineered: yes
Source: Aquifex aeolicus. Organism_taxid: 63363. Gene: nusg or aq_1931. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.00Å     R-factor:   0.219     R-free:   0.279
Authors: J.R.Knowlton,M.Bubunenko,M.Andrykovitch,W.Guo,K.M.Routzahn,D.S.Waugh, D.L.Court,X.Ji
Key ref:
J.R.Knowlton et al. (2003). A spring-loaded state of NusG in its functional cycle is suggested by X-ray crystallography and supported by site-directed mutants. Biochemistry, 42, 2275-2281. PubMed id: 12600194 DOI: 10.1021/bi0272508
Date:
18-Jan-03     Release date:   11-Mar-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O67757  (NUSG_AQUAE) -  Transcription termination/antitermination protein NusG from Aquifex aeolicus (strain VF5)
Seq:
Struc: 		248 a.a.
244 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1021/bi0272508 Biochemistry 42:2275-2281 (2003)
PubMed id: 12600194  
 
 
A spring-loaded state of NusG in its functional cycle is suggested by X-ray crystallography and supported by site-directed mutants.
J.R.Knowlton, M.Bubunenko, M.Andrykovitch, W.Guo, K.M.Routzahn, D.S.Waugh, D.L.Court, X.Ji.
 
  ABSTRACT  
 
Transcription factor NusG is present in all prokaryotes, and orthologous proteins have also been identified in yeast and humans. NusG contains a 27-residue KOW motif, found in ribosomal protein L24 where it interacts with rRNA. NusG in Escherichia coli (EcNusG) is an essential protein and functions as a regulator of Rho-dependent transcription termination, phage lambda N and rRNA transcription antitermination, and phage HK022 Nun termination. Relative to EcNusG, Aquifex aeolicus NusG (AaNusG) and several other bacterial NusG proteins contain a variable insertion sequence of approximately 70 residues in the central region of the molecule. Recently, crystal structures of AaNusG in space groups P2(1) and I222 have been reported; the authors conclude that there are no conserved dimers among the contacting molecules in the crystals [Steiner, T., Kaiser, J. T., Marinkovic, S., Huber, R., and Wahl, M. C. (2002) EMBO J. 21, 4641-4653]. We have independently determined the structures of AaNusG also in two crystal forms, P2(1) and C222(1), and surprisingly found that AaNusG molecules form domain-swapped dimers in both crystals. Additionally, polymerization is also observed in the P2(1) crystal. A unique "ball-and-socket" junction dominates the intermolecular interactions within both oligomers. We believe that this interaction is a clue to the function of the molecule and propose a spring-loaded state in the functional cycle of NusG. The importance of the ball-and-socket junction for the function of NusG is supported by the functional analysis of site-directed mutants.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21187417 B.J.Klein, D.Bose, K.J.Baker, Z.M.Yusoff, X.Zhang, and K.S.Murakami (2011).
RNA polymerase and transcription elongation factor Spt4/5 complex structure.
  Proc Natl Acad Sci U S A, 108, 546-550.
PDB code: 3p8b
21345171 B.M.Burmann, U.Scheckenhofer, K.Schweimer, and P.Rösch (2011).
Domain interactions of the transcription-translation coupling factor Escherichia coli NusG are intermolecular and transient.
  Biochem J, 435, 783-789.  
21386817 F.W.Martinez-Rucobo, S.Sainsbury, A.C.Cheung, and P.Cramer (2011).
Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity.
  EMBO J, 30, 1302-1310.
PDB code: 3qqc
20639538 A.Sevostyanova, and I.Artsimovitch (2010).
Functional analysis of Thermus thermophilus transcription factor NusG.
  Nucleic Acids Res, 38, 7432-7445.  
20413501 B.M.Burmann, K.Schweimer, X.Luo, M.C.Wahl, B.L.Stitt, M.E.Gottesman, and P.Rösch (2010).
A NusE:NusG complex links transcription and translation.
  Science, 328, 501-504.
PDB code: 2kvq
19013248 D.Zhang, J.Tözsér, and D.S.Waugh (2009).
Molecular cloning, overproduction, purification and biochemical characterization of the p39 nsp2 protease domains encoded by three alphaviruses.
  Protein Expr Purif, 64, 89-97.  
19500594 R.A.Mooney, K.Schweimer, P.Rösch, M.Gottesman, and R.Landick (2009).
Two structurally independent domains of E. coli NusG create regulatory plasticity via distinct interactions with RNA polymerase and regulators.
  J Mol Biol, 391, 341-358.
PDB codes: 2jvv 2k06
18649350 G.S.Stein, J.R.Davie, J.R.Knowlton, and S.K.Zaidi (2008).
Nuclear microenvironments and cancer.
  J Cell Biochem, 104, 1949-1952.  
18786404 G.Shaw, J.Gan, Y.N.Zhou, H.Zhi, P.Subburaman, R.Zhang, A.Joachimiak, D.J.Jin, and X.Ji (2008).
Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription.
  Structure, 16, 1417-1427.
PDB codes: 3dmq 6bog
19000817 M.Guo, F.Xu, J.Yamada, T.Egelhofer, Y.Gao, G.A.Hartzog, M.Teng, and L.Niu (2008).
Core structure of the yeast spt4-spt5 complex: a conserved module for regulation of transcription elongation.
  Structure, 16, 1649-1658.  
17198710 A.P.Korepanov, G.M.Gongadze, M.B.Garber, D.L.Court, and M.G.Bubunenko (2007).
Importance of the 5 S rRNA-binding ribosomal proteins for cell viability and translation in Escherichia coli.
  J Mol Biol, 366, 1199-1208.  
17724015 A.Schwartz, E.Margeat, A.R.Rahmouni, and M.Boudvillain (2007).
Transcription termination factor rho can displace streptavidin from biotinylated RNA.
  J Biol Chem, 282, 31469-31476.  
17434131 G.A.Belogurov, M.N.Vassylyeva, V.Svetlov, S.Klyuyev, N.V.Grishin, D.G.Vassylyev, and I.Artsimovitch (2007).
Structural basis for converting a general transcription factor into an operon-specific virulence regulator.
  Mol Cell, 26, 117-129.
PDB code: 2oug
17277072 M.Bubunenko, T.Baker, and D.L.Court (2007).
Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli.
  J Bacteriol, 189, 2844-2853.  
18073113 M.Kuratani, Y.Yoshikawa, Y.Bessho, K.Higashijima, T.Ishii, R.Shibata, S.Takahashi, K.Yutani, and S.Yokoyama (2007).
Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine.
  Structure, 15, 1642-1653.
PDB codes: 2e21 2e89
17384193 S.Phadtare, T.Kazakov, M.Bubunenko, D.L.Court, T.Pestova, and K.Severinov (2007).
Transcription antitermination by translation initiation factor IF1.
  J Bacteriol, 189, 4087-4093.  
15596505 A.Merlino, M.A.Ceruso, L.Vitagliano, and L.Mazzarella (2005).
Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A.
  Biophys J, 88, 2003-2012.  
15090525 H.D.Carter, V.Svetlov, and I.Artsimovitch (2004).
Highly divergent RfaH orthologs from pathogenic proteobacteria can substitute for Escherichia coli RfaH both in vivo and in vitro.
  J Bacteriol, 186, 2829-2840.  
15162485 P.Reay, K.Yamasaki, T.Terada, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2004).
Structural and sequence comparisons arising from the solution structure of the transcription elongation factor NusG from Thermus thermophilus.
  Proteins, 56, 40-51.
PDB codes: 1nz8 1nz9
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 code is shown on the right.

 

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