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DNA-binding protein PDB id
1huu
Jmol
Contents
Protein chains
80 a.a. *
74 a.a. *
Waters ×271
* Residue conservation analysis
PDB id:
1huu
Name: DNA-binding protein
Title: DNA-binding protein hu from bacillus stearothermophilus
Structure: Protein hu. Chain: a, b, c. Synonym: bsb, ns
Source: Geobacillus stearothermophilus. Organism_taxid: 1422
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.193     R-free:   0.213
Authors: S.W.White,I.Tanaka,K.Appelt,K.S.Wilson
Key ref: S.W.White et al. (1989). A protein structural motif that bends DNA. Proteins, 5, 281-288. PubMed id: 2508086 DOI: 10.1002/prot.340050405
Date:
06-Jul-98     Release date:   13-Jan-99    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A3H0  (DBH_GEOSE) -  DNA-binding protein HU
Seq:
Struc: 		90 a.a.
80 a.a.
Protein chains
Pfam   ArchSchema ?
P0A3H0  (DBH_GEOSE) -  DNA-binding protein HU
Seq:
Struc: 		90 a.a.
74 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     chromosome condensation   1 term 
  Biochemical function     DNA binding     1 term  

 

 
DOI no: 10.1002/prot.340050405 Proteins 5:281-288 (1989)
PubMed id: 2508086  
 
 
A protein structural motif that bends DNA.
S.W.White, K.Appelt, K.S.Wilson, I.Tanaka.
 
  ABSTRACT  
 
The prokaryotic protein HU, integration host factor (IHF) from Escherichia coli, and transcription factor 1 (TF1) from bacteriophage SPO1 are closely related molecules. Biochemical results suggest that the role of these proteins is to bind and bend DNA. From the high-resolution structure of HU, we propose a model for this interaction with DNA. Crucial amino acid differences between the proteins can be rationalized in terms of their different specific functions.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20026582 G.Witz, and A.Stasiak (2010).
DNA supercoiling and its role in DNA decatenation and unknotting.
  Nucleic Acids Res, 38, 2119-2133.  
18818867 F.Orfaniotou, P.Tzamalis, A.Thanassoulas, E.Stefanidi, A.Zees, E.Boutou, M.Vlassi, G.Nounesis, and C.E.Vorgias (2009).
The stability of the archaeal HU histone-like DNA-binding protein from Thermoplasma volcanium.
  Extremophiles, 13, 1.  
18663012 E.V.Ram, R.Naik, M.Ganguli, and S.Habib (2008).
DNA organization by the apicoplast-targeted bacterial histone-like protein of Plasmodium falciparum.
  Nucleic Acids Res, 36, 5061-5073.  
18187505 J.M.Chen, H.Ren, J.E.Shaw, Y.J.Wang, M.Li, A.S.Leung, V.Tran, N.M.Berbenetz, D.Kocíncová, C.M.Yip, J.M.Reyrat, and J.Liu (2008).
Lsr2 of Mycobacterium tuberculosis is a DNA-bridging protein.
  Nucleic Acids Res, 36, 2123-2135.  
17244195 K.W.Mouw, and P.A.Rice (2007).
Shaping the Borrelia burgdorferi genome: crystal structure and binding properties of the DNA-bending protein Hbb.
  Mol Microbiol, 63, 1319-1330.
PDB code: 2np2
15264235 A.J.Heck, and R.H.Van Den Heuvel (2004).
Investigation of intact protein complexes by mass spectrometry.
  Mass Spectrom Rev, 23, 368-389.  
15102446 K.K.Swinger, and P.A.Rice (2004).
IHF and HU: flexible architects of bent DNA.
  Curr Opin Struct Biol, 14, 28-35.  
15322284 K.Wojtuszewski, and I.Mukerji (2004).
The HU-DNA binding interaction probed with UV resonance Raman spectroscopy: structural elements of specificity.
  Protein Sci, 13, 2416-2428.  
12809494 D.Serban, J.M.Benevides, and G.J.Thomas (2003).
HU protein employs similar mechanisms of minor-groove recognition in binding to different B-DNA sites: demonstration by Raman spectroscopy.
  Biochemistry, 42, 7390-7399.  
12649443 D.Serban, S.F.Arcineigas, C.E.Vorgias, and G.J.Thomas (2003).
Structure and dynamics of the DNA-binding protein HU of B. stearothermophilus investigated by Raman and ultraviolet-resonance Raman spectroscopy.
  Protein Sci, 12, 861-870.  
12853489 K.K.Swinger, K.M.Lemberg, Y.Zhang, and P.A.Rice (2003).
Flexible DNA bending in HU-DNA cocrystal structures.
  EMBO J, 22, 3749-3760.
PDB codes: 1p51 1p71 1p78
12198167 B.N.Wardleworth, R.J.Russell, S.D.Bell, G.L.Taylor, and M.F.White (2002).
Structure of Alba: an archaeal chromatin protein modulated by acetylation.
  EMBO J, 21, 4654-4662.
PDB codes: 1h0x 1h0y
11327882 K.Wojtuszewski, M.E.Hawkins, J.L.Cole, and I.Mukerji (2001).
HU binding to DNA: evidence for multiple complex formation and DNA bending.
  Biochemistry, 40, 2588-2598.  
10715001 M.A.Ross, and P.Setlow (2000).
The Bacillus subtilis HBsu protein modifies the effects of alpha/beta-type, small acid-soluble spore proteins on DNA.
  J Bacteriol, 182, 1942-1948.  
10561602 A.Miyamoto, M.Usui, N.Yamasaki, N.Yamada, E.Kuwano, I.Tanaka, and M.Kimura (1999).
Role of the N-terminal region of ribosomal protein S7 in its interaction with 16S rRNA which binds to the concavity formed by the beta-ribbon arm and the alpha-helix.
  Eur J Biochem, 266, 591-598.  
10508175 D.Kamashev, A.Balandina, and J.Rouviere-Yaniv (1999).
The binding motif recognized by HU on both nicked and cruciform DNA.
  EMBO J, 18, 5434-5444.  
  10386888 H.Vis, C.M.Dobson, and C.V.Robinson (1999).
Selective association of protein molecules followed by mass spectrometry.
  Protein Sci, 8, 1368-1370.  
10483709 S.Takashima, and K.Yamaoka (1999).
The electric dipole moment of DNA-binding HU protein calculated by the use of an NMR database.
  Biophys Chem, 80, 153-163.  
10089311 S.W.White, K.S.Wilson, K.Appelt, and I.Tanaka (1999).
The high-resolution structure of DNA-binding protein HU from Bacillus stearothermophilus.
  Acta Crystallogr D Biol Crystallogr, 55, 801-809.  
9685334 S.Kawamura, Y.Abe, T.Ueda, K.Masumoto, T.Imoto, N.Yamasaki, and M.Kimura (1998).
Investigation of the structural basis for thermostability of DNA-binding protein HU from Bacillus stearothermophilus.
  J Biol Chem, 273, 19982-19987.  
9148920 A.Grove, M.L.Figueiredo, A.Galeone, L.Mayol, and E.P.Geiduschek (1997).
Twin hydroxymethyluracil-A base pair steps define the binding site for the DNA-binding protein TF1.
  J Biol Chem, 272, 13084-13087.  
  9331418 B.T.Wimberly, S.W.White, and V.Ramakrishnan (1997).
The structure of ribosomal protein S7 at 1.9 A resolution reveals a beta-hairpin motif that binds double-stranded nucleic acids.
  Structure, 5, 1187-1198.
PDB code: 1rss
  9098077 J.Pérez-Martín, and V.De Lorenzo (1997).
Coactivation in vitro of the sigma54-dependent promoter Pu of the TOL plasmid of Pseudomonas putida by HU and the mammalian HMG-1 protein.
  J Bacteriol, 179, 2757-2760.  
9032059 P.A.Rice (1997).
Making DNA do a U-turn: IHF and related proteins.
  Curr Opin Struct Biol, 7, 86-93.  
9218807 T.Aki, and S.Adhya (1997).
Repressor induced site-specific binding of HU for transcriptional regulation.
  EMBO J, 16, 3666-3674.  
  9032076 T.Ellenberger, and A.Landy (1997).
A good turn for DNA: the structure of integration host factor bound to DNA.
  Structure, 5, 153-157.  
8646783 B.D.Lavoie, G.S.Shaw, A.Millner, and G.Chaconas (1996).
Anatomy of a flexer-DNA complex inside a higher-order transposition intermediate.
  Cell, 85, 761-771.  
8875823 E.C.van Geerestein-Ujah, M.Mariani, H.Vis, R.Boelens, and R.Kaptein (1996).
Use of graph theory for secondary structure recognition and sequential assignment in heteronuclear (13C, 15N) NMR spectra: application to HU protein from Bacillus stearothermophilus.
  Biopolymers, 39, 691-707.  
  8670817 K.S.Pai, D.E.Bussiere, F.Wang, C.A.Hutchison, S.W.White, and D.Bastia (1996).
The structure and function of the replication terminator protein of Bacillus subtilis: identification of the 'winged helix' DNA-binding domain.
  EMBO J, 15, 3164-3173.  
  8576073 L.B.Pedersen, S.Birkelund, A.Holm, S.Ostergaard, and G.Christiansen (1996).
The 18-kilodalton Chlamydia trachomatis histone H1-like protein (Hc1) contains a potential N-terminal dimerization site and a C-terminal nucleic acid-binding domain.
  J Bacteriol, 178, 994.  
9101760 R.Boelens, H.Vis, C.E.Vorgias, K.S.Wilson, and R.Kaptein (1996).
Structure and dynamics of the DNA binding protein HU from Bacillus stearothermophilus by NMR spectroscopy.
  Biopolymers, 40, 553-559.  
  8892836 R.Calb, A.Davidovitch, S.Koby, H.Giladi, D.Goldenberg, H.Margalit, A.Holtel, K.Timmis, J.M.Sanchez-Romero, V.de Lorenzo, and A.B.Oppenheim (1996).
Structure and function of the Pseudomonas putida integration host factor.
  J Bacteriol, 178, 6319-6326.  
7625690 A.Klug (1995).
Gene regulatory proteins and their interaction with DNA.
  Ann N Y Acad Sci, 758, 143-160.  
7852372 J.C.Alonso, F.Weise, and F.Rojo (1995).
The Bacillus subtilis histone-like protein Hbsu is required for DNA resolution and DNA inversion mediated by the beta recombinase of plasmid pSM19035.
  J Biol Chem, 270, 2938-2945.  
  8521829 J.E.Mueller, D.Smith, M.Bryk, and M.Belfort (1995).
Intron-encoded endonuclease I-TevI binds as a monomer to effect sequential cleavage via conformational changes in the td homing site.
  EMBO J, 14, 5724-5735.  
  7601841 J.Pérez-Martín, and V.de Lorenzo (1995).
The sigma 54-dependent promoter Ps of the TOL plasmid of Pseudomonas putida requires HU for transcriptional activation in vivo by XylR.
  J Bacteriol, 177, 3758-3763.  
7629095 L.Zulianello, P.van Ulsen, P.van de Putte, and N.Goosen (1995).
Participation of the flank regions of the integration host factor protein in the specificity and stability of DNA binding.
  J Biol Chem, 270, 17902-17907.  
8597113 V.L.Hsu, X.Jia, and D.R.Kearns (1995).
Multidimensional NMR spectroscopy of DNA-binding proteins: structure and function of a transcription factor.
  Toxicol Lett, 82, 577-589.  
  8139553 A.Andrianopoulos, and W.E.Timberlake (1994).
The Aspergillus nidulans abaA gene encodes a transcriptional activator that acts as a genetic switch to control development.
  Mol Cell Biol, 14, 2503-2515.  
  8113176 L.Andera, and E.P.Geiduschek (1994).
Determinants of affinity and mode of DNA binding at the carboxy terminus of the bacteriophage SPO1-encoded type II DNA-binding protein, TF1.
  J Bacteriol, 176, 1364-1373.  
  7925279 R.Freire, M.Salas, and J.M.Hermoso (1994).
A new protein domain for binding to DNA through the minor groove.
  EMBO J, 13, 4353-4360.  
8404814 D.E.Lewis, and J.Carey (1993).
Analysis of trp repressor-DNA interactions using gel electrophoresis.
  Electrophoresis, 14, 713-719.  
8290347 F.A.Palida, C.Hale, and K.U.Sprague (1993).
Transcription of a silkworm tRNA(cAla) gene is directed by two AT-rich upstream sequence elements.
  Nucleic Acids Res, 21, 5875-5881.  
8223641 H.Welfle, R.Misselwitz, K.Welfle, H.Schindelin, A.S.Scholtz, and U.Heinemann (1993).
Conformations and conformational changes of four Phe-->Trp variants of the DNA-binding histone-like protein, HBsu, from Bacillus subtilis studied by circular dichroism and fluorescence spectroscopy.
  Eur J Biochem, 217, 849-856.  
  8508775 M.J.Haykinson, and R.C.Johnson (1993).
DNA looping and the helical repeat in vitro and in vivo: effect of HU protein and enhancer location on Hin invertasome assembly.
  EMBO J, 12, 2503-2512.  
8346553 M.Serrano, M.Salas, and J.M.Hermoso (1993).
Multimeric complexes formed by DNA-binding proteins of low sequence specificity.
  Trends Biochem Sci, 18, 202-206.  
  1480106 D.Lane, P.Prentki, and M.Chandler (1992).
Use of gel retardation to analyze protein-nucleic acid interactions.
  Microbiol Rev, 56, 509-528.  
1330326 D.Thanos, and T.Maniatis (1992).
The high mobility group protein HMG I(Y) is required for NF-kappa B-dependent virus induction of the human IFN-beta gene.
  Cell, 71, 777-789.  
  1425583 E.Bonnefoy, and J.Rouvière-Yaniv (1992).
HU, the major histone-like protein of E. coli, modulates the binding of IHF to oriC.
  EMBO J, 11, 4489-4496.  
  1531459 E.C.Lee, L.M.Hales, R.I.Gumport, and J.F.Gardner (1992).
The isolation and characterization of mutants of the integration host factor (IHF) of Escherichia coli with altered, expanded DNA-binding specificities.
  EMBO J, 11, 305-313.  
1551385 H.Welfle, R.Misselwitz, K.Welfle, N.Groch, and U.Heinemann (1992).
Salt-dependent and protein-concentration-dependent changes in the solution structure of the DNA-binding histone-like protein, HBsu, from Bacillus subtilis.
  Eur J Biochem, 204, 1049-1055.  
15336020 J.W.Schwabe (1992).
DNA between the sheets.
  Curr Biol, 2, 661-663.  
1313943 K.Drlica (1992).
Control of bacterial DNA supercoiling.
  Mol Microbiol, 6, 425-433.  
1644313 P.M.Padas, K.S.Wilson, and C.E.Vorgias (1992).
The DNA-binding protein HU from mesophilic and thermophilic bacilli: gene cloning, overproduction and purification.
  Gene, 117, 39-44.  
1961742 B.Toussaint, C.Bosc, P.Richaud, A.Colbeau, and P.M.Vignais (1991).
A mutation in a Rhodobacter capsulatus gene encoding an integration host factor-like protein impairs in vivo hydrogenase expression.
  Proc Natl Acad Sci U S A, 88, 10749-10753.  
1760847 D.B.Starr, and D.K.Hawley (1991).
TFIID binds in the minor groove of the TATA box.
  Cell, 67, 1231-1240.  
  2001682 E.Bonnefoy, and J.Rouvière-Yaniv (1991).
HU and IHF, two homologous histone-like proteins of Escherichia coli, form different protein-DNA complexes with short DNA fragments.
  EMBO J, 10, 687-696.  
  1825651 I.Mendelson, M.Gottesman, and A.B.Oppenheim (1991).
HU and integration host factor function as auxiliary proteins in cleavage of phage lambda cohesive ends by terminase.
  J Bacteriol, 173, 1670-1676.  
1647556 M.E.Churchill, and A.A.Travers (1991).
Protein motifs that recognize structural features of DNA.
  Trends Biochem Sci, 16, 92-97.  
1923761 M.Katouzian-Safadi, B.Laine, F.Chartier, J.Y.Cremet, D.Belaiche, P.Sautiere, and M.Charlier (1991).
Determination of the DNA-interacting region of the archaebacterial chromosomal protein MC1. Photocrosslinks with 5-bromouracil-substituted DNA.
  Nucleic Acids Res, 19, 4937-4941.  
  2556263 M.E.Churchill, and M.Suzuki (1989).
'SPKK' motifs prefer to bind to DNA at A/T-rich sites.
  EMBO J, 8, 4189-4195.  
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.