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protein dna_rna Protein-protein interface(s) links
DNA binding protein/DNA PDB id
1p71
Jmol
Contents
Protein chains
94 a.a. *
DNA/RNA
Waters ×196
* Residue conservation analysis
PDB id:
1p71
Name: DNA binding protein/DNA
Title: Anabaena hu-DNA corcrystal structure (tr3)
Structure: 5'-d( Tp Gp Cp Tp Tp Ap Tp Cp Ap Ap Tp Tp Tp Gp T Ap Cp C)-3'. Chain: c, d. Engineered: yes. DNA-binding protein hu. Chain: a, b. Engineered: yes
Source: Synthetic: yes. Other_details: chemically synthesized DNA. Anabaena sp.. Organism_taxid: 1167. Gene: hup or hana or asr3935. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
1.90Å     R-factor:   0.246     R-free:   0.288
Authors: K.S.Swinger,K.M.Lemberg,Y.Zhang,P.A.Rice
Key ref: K.K.Swinger et al. (2003). Flexible DNA bending in HU-DNA cocrystal structures. Embo J, 22, 3749-3760. PubMed id: 12853489 DOI: 10.1093/emboj/cdg351
Date:
30-Apr-03     Release date:   13-May-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P05514  (DBH_NOSS1) -  DNA-binding protein HU
Seq:
Struc: 		94 a.a.
94 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     chromosome condensation   2 terms 
  Biochemical function     DNA binding     1 term  

 

 
DOI no: 10.1093/emboj/cdg351 Embo J 22:3749-3760 (2003)
PubMed id: 12853489  
 
 
Flexible DNA bending in HU-DNA cocrystal structures.
K.K.Swinger, K.M.Lemberg, Y.Zhang, P.A.Rice.
 
  ABSTRACT  
 
HU and IHF are members of a family of prokaryotic proteins that interact with the DNA minor groove in a sequence-specific (IHF) or non-specific (HU) manner to induce and/or stabilize DNA bending. HU plays architectural roles in replication initiation, transcription regulation and site-specific recombination, and is associated with bacterial nucleoids. Cocrystal structures of Anabaena HU bound to DNA (1P71, 1P78, 1P51) reveal that while underlying proline intercalation and asymmetric charge neutralization mechanisms of DNA bending are similar for IHF and HU, HU stabilizes different DNA bend angles ( approximately 105-140 degrees ). The two bend angles within a single HU complex are not coplanar, and the resulting dihedral angle is consistent with negative supercoiling. Comparison of HU-DNA and IHF-DNA structures suggests that sharper bending is correlated with longer DNA binding sites and smaller dihedral angles. An HU-induced bend may be better modeled as a hinge, not a rigid bend. The ability to induce or stabilize varying bend angles is consistent with HU's role as an architectural cofactor in many different systems that may require differing geometries.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21097894 J.S.Graham, R.C.Johnson, and J.F.Marko (2011).
Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA.
  Nucleic Acids Res, 39, 2249-2259.  
20861000 M.Firczuk, M.Wojciechowski, H.Czapinska, and M.Bochtler (2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
  Nucleic Acids Res, 39, 744-754.
PDB code: 3ndh
20936276 N.Garnier, K.Loth, F.Coste, R.Augustyniak, V.Nadan, C.Damblon, and B.Castaing (2011).
An alternative flexible conformation of the E. coli HUβ₂ protein: structural, dynamics, and functional aspects.
  Eur Biophys J, 40, 117-129.  
20497998 B.Xiao, R.C.Johnson, and J.F.Marko (2010).
Modulation of HU-DNA interactions by salt concentration and applied force.
  Nucleic Acids Res, 38, 6176-6185.  
20723754 D.A.Koster, A.Crut, S.Shuman, M.A.Bjornsti, and N.H.Dekker (2010).
Cellular strategies for regulating DNA supercoiling: a single-molecule perspective.
  Cell, 142, 519-530.  
21078128 F.Paquet, K.Loth, H.Meudal, F.Culard, D.Genest, and G.Lancelot (2010).
Refined solution structure and backbone dynamics of the archaeal MC1 protein.
  FEBS J, 277, 5133-5145.  
20010798 M.Berger, A.Farcas, M.Geertz, P.Zhelyazkova, K.Brix, A.Travers, and G.Muskhelishvili (2010).
Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU.
  EMBO Rep, 11, 59-64.  
19910373 M.S.Medrano, P.F.Policastro, T.G.Schwan, and J.Coburn (2010).
Interaction of Borrelia burgdorferi Hbb with the p66 promoter.
  Nucleic Acids Res, 38, 414-427.  
  20824060 S.Kumar, A.A.Sardesai, D.Basu, K.Muniyappa, and S.E.Hasnain (2010).
DNA clasping by mycobacterial HU: the C-terminal region of HupB mediates increased specificity of DNA binding.
  PLoS One, 5, 0.  
19474339 G.Zheng, X.J.Lu, and W.K.Olson (2009).
Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures.
  Nucleic Acids Res, 37, W240-W246.  
19194530 J.Oberto, S.Nabti, V.Jooste, H.Mignot, and J.Rouviere-Yaniv (2009).
The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction.
  PLoS ONE, 4, e4367.  
19236006 N.T.Sebastian, E.M.Bystry, N.A.Becker, and L.J.Maher (2009).
Enhancement of DNA flexibility in vitro and in vivo by HMGB box A proteins carrying box B residues.
  Biochemistry, 48, 2125-2134.  
19332822 R.Teras, J.Jakovleva, and M.Kivisaar (2009).
Fis negatively affects binding of Tn4652 transposase by out-competing IHF from the left end of Tn4652.
  Microbiology, 155, 1203-1214.  
20365029 S.M.Rappaport, and Y.Rabin (2009).
Bending affects entropy of semiflexible polymers: Application to protein-DNA complexes.
  Phys Rev E Stat Nonlin Soft Matter Phys, 80, 052801.  
19561077 T.J.Moriarty, and G.Chaconas (2009).
Identification of the determinant conferring permissive substrate usage in the telomere resolvase, ResT.
  J Biol Chem, 284, 23293-23301.  
18515342 A.Mukherjee, A.O.Sokunbi, and A.Grove (2008).
DNA protection by histone-like protein HU from the hyperthermophilic eubacterium Thermotoga maritima.
  Nucleic Acids Res, 36, 3956-3968.  
18096614 D.Kamashev, A.Balandina, A.K.Mazur, P.B.Arimondo, and J.Rouviere-Yaniv (2008).
HU binds and folds single-stranded DNA.
  Nucleic Acids Res, 36, 1026-1036.  
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.  
18657548 J.Koh, R.M.Saecker, and M.T.Record (2008).
DNA binding mode transitions of Escherichia coli HU(alphabeta): evidence for formation of a bent DNA--protein complex on intact, linear duplex DNA.
  J Mol Biol, 383, 324-346.  
18413230 J.Zimmerman, and L.J.Maher (2008).
Transient HMGB protein interactions with B-DNA duplexes and complexes.
  Biochem Biophys Res Commun, 371, 79-84.  
18439894 K.W.Mouw, S.J.Rowland, M.M.Gajjar, M.R.Boocock, W.M.Stark, and P.A.Rice (2008).
Architecture of a serine recombinase-DNA regulatory complex.
  Mol Cell, 30, 145-155.
PDB code: 2r0q
18586040 L.Czapla, D.Swigon, and W.K.Olson (2008).
Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations.
  J Mol Biol, 382, 353-370.  
18515834 N.A.Becker, J.D.Kahn, and L.J.Maher (2008).
Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation.
  Nucleic Acids Res, 36, 4009-4021.  
18764298 S.M.Rappaport, and Y.Rabin (2008).
Model of DNA bending by cooperative binding of proteins.
  Phys Rev Lett, 101, 038101.  
17268506 A.Travers, and G.Muskhelishvili (2007).
A common topology for bacterial and eukaryotic transcription initiation?
  EMBO Rep, 8, 147-151.  
17360520 F.Guo, and S.Adhya (2007).
Spiral structure of Escherichia coli HUalphabeta provides foundation for DNA supercoiling.
  Proc Natl Acad Sci U S A, 104, 4309-4314.
PDB code: 2o97
17097674 K.K.Swinger, and P.A.Rice (2007).
Structure-based analysis of HU-DNA binding.
  J Mol Biol, 365, 1005-1016.
PDB code: 2ht0
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
17981466 M.Kucej, and R.A.Butow (2007).
Evolutionary tinkering with mitochondrial nucleoids.
  Trends Cell Biol, 17, 586-592.  
17553830 N.A.Becker, J.D.Kahn, and L.J.Maher (2007).
Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli.
  Nucleic Acids Res, 35, 3988-4000.  
17259223 T.Sarkar, I.Vitoc, I.Mukerji, and N.V.Hud (2007).
Bacterial protein HU dictates the morphology of DNA condensates produced by crowding agents and polyamines.
  Nucleic Acids Res, 35, 951-961.  
17916578 Y.W.Kow, B.Imhoff, B.Weiss, D.C.Hung, A.A.Hindoyan, R.M.Story, and S.D.Goodman (2007).
Escherichia coli HU protein has a role in the repair of abasic sites in DNA.
  Nucleic Acids Res, 35, 6672-6680.  
16981705 D.A.Hiller, and J.J.Perona (2006).
Positively charged C-terminal subdomains of EcoRV endonuclease: contributions to DNA binding, bending, and cleavage.
  Biochemistry, 45, 11453-11463.
PDB code: 2ge5
17200598 J.Stavans, and A.Oppenheim (2006).
DNA-protein interactions and bacterial chromosome architecture.
  Phys Biol, 3, R1-10.  
16553879 S.J.Rowland, M.R.Boocock, and W.M.Stark (2006).
DNA bending in the Sin recombination synapse: functional replacement of HU by IHF.
  Mol Microbiol, 59, 1730-1743.  
17124171 S.V.Kuznetsov, S.Sugimura, P.Vivas, D.M.Crothers, and A.Ansari (2006).
Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF.
  Proc Natl Acad Sci U S A, 103, 18515-18520.  
15841342 A.M.Kropinski, M.Hayward, M.D.Agnew, and K.F.Jarrell (2005).
The genome of BCJA1c: a bacteriophage active against the alkaliphilic bacterium, Bacillus clarkii.
  Extremophiles, 9, 99.  
15685225 A.Travers, and G.Muskhelishvili (2005).
DNA supercoiling - a global transcriptional regulator for enterobacterial growth?
  Nat Rev Microbiol, 3, 157-169.  
16099644 A.Travers, and G.Muskhelishvili (2005).
Bacterial chromatin.
  Curr Opin Genet Dev, 15, 507-514.  
15653643 C.Y.Chen, T.P.Ko, T.W.Lin, C.C.Chou, C.J.Chen, and A.H.Wang (2005).
Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d.
  Nucleic Acids Res, 33, 430-438.
PDB codes: 1wto 1wtp 1wtq 1wtr 1wtv 1wtw 1wtx 1xyi
15921535 J.D.Hackett, T.E.Scheetz, H.S.Yoon, M.B.Soares, M.F.Bonaldo, T.L.Casavant, and D.Bhattacharya (2005).
Insights into a dinoflagellate genome through expressed sequence tag analysis.
  BMC Genomics, 6, 80.  
15883182 L.M.Parsons, F.Liu, and J.Orban (2005).
HU-alpha binds to the putative double-stranded DNA mimic HI1450 from Haemophilus influenzae.
  Protein Sci, 14, 1684-1687.  
15988757 M.Thanbichler, S.C.Wang, and L.Shapiro (2005).
The bacterial nucleoid: a highly organized and dynamic structure.
  J Cell Biochem, 96, 506-521.  
15843682 R.T.Dame, J.van Mameren, M.S.Luijsterburg, M.E.Mysiak, A.Janićijević, G.Pazdzior, P.C.van der Vliet, C.Wyman, and G.J.Wuite (2005).
Analysis of scanning force microscopy images of protein-induced DNA bending using simulations.
  Nucleic Acids Res, 33, e68.  
15853876 R.T.Dame (2005).
The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin.
  Mol Microbiol, 56, 858-870.  
15950878 S.Semsey, K.Virnik, and S.Adhya (2005).
A gamut of loops: meandering DNA.
  Trends Biochem Sci, 30, 334-341.  
15118104 J.van Noort, S.Verbrugge, N.Goosen, C.Dekker, and R.T.Dame (2004).
Dual architectural roles of HU: formation of flexible hinges and rigid filaments.
  Proc Natl Acad Sci U S A, 101, 6969-6974.  
15123801 K.D.Corbett, R.K.Shultzaberger, and J.M.Berger (2004).
The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold.
  Proc Natl Acad Sci U S A, 101, 7293-7298.
PDB code: 1suu
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.  
14651642 R.Guo, H.Xue, and L.Huang (2003).
Ssh10b, a conserved thermophilic archaeal protein, binds RNA in vivo.
  Mol Microbiol, 50, 1605-1615.  
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.