spacer
spacer
Go to PDB code: 
protein links
Gene regulating protein PDB id
1r69
Jmol
Contents
Protein chain
63 a.a. *
Waters ×34
* Residue conservation analysis
PDB id:
1r69
Name: Gene regulating protein
Title: Structure of the amino-terminal domain of phage 434 repressor at 2.0 angstroms resolution
Structure: Repressor protein ci. Chain: a. Engineered: yes
Source: Phage 434. Organism_taxid: 10712
Resolution:
2.00Å     R-factor:   0.193    
Authors: A.Mondragon,S.Subbiah,S.C.Alamo,M.Drottar,S.C.Harrison
Key ref: A.Mondragón et al. (1989). Structure of the amino-terminal domain of phage 434 repressor at 2.0 A resolution. J Mol Biol, 205, 189-200. PubMed id: 2926803 DOI: 10.1016/0022-2836(89)90375-6
Date:
08-Dec-88     Release date:   15-Oct-89    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P16117  (RPC1_BP434) -  Repressor protein CI (Fragment)
Seq:
Struc: 		95 a.a.
63 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     DNA binding     2 terms  

 

 
DOI no: 10.1016/0022-2836(89)90375-6 J Mol Biol 205:189-200 (1989)
PubMed id: 2926803  
 
 
Structure of the amino-terminal domain of phage 434 repressor at 2.0 A resolution.
A.Mondragón, S.Subbiah, S.C.Almo, M.Drottar, S.C.Harrison.
 
  ABSTRACT  
 
The crystal structure of the amino-terminal domain of phage 434 repressor has been solved using molecular replacement methods and refined to an R-factor of 19.3% against data to 2.0 A resolution. The protein comprises five short alpha-helices. Two of these form a helix-turn-helix motif, very similar to those found in related proteins. The protein is remarkably similar to the Cro protein from the same phage.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19602149 S.Gebhard, A.Gaballa, J.D.Helmann, and G.M.Cook (2009).
Direct stimulus perception and transcription activation by a membrane-bound DNA binding protein.
  Mol Microbiol, 73, 482-491.  
19548767 T.Bereau, and M.Deserno (2009).
Generic coarse-grained model for protein folding and aggregation.
  J Chem Phys, 130, 235106.  
18780355 Z.Cao, Z.Lin, J.Wang, and H.Liu (2009).
Refining the description of peptide backbone conformations improves protein simulations using the GROMOS 53A6 force field.
  J Comput Chem, 30, 645-660.  
18042675 M.C.Reddy, K.Gokulan, W.R.Jacobs, T.R.Ioerger, and J.C.Sacchettini (2008).
Crystal structure of Mycobacterium tuberculosis LrpA, a leucine-responsive global regulator associated with starvation response.
  Protein Sci, 17, 159-170.
PDB code: 2qz8
18369196 M.S.Dubrava, W.M.Ingram, S.A.Roberts, A.Weichsel, W.R.Montfort, and M.H.Cordes (2008).
N15 Cro and lambda Cro: orthologous DNA-binding domains with completely different but equally effective homodimer interfaces.
  Protein Sci, 17, 803-812.
PDB code: 2hin
18410248 R.Das, and D.Baker (2008).
Macromolecular modeling with rosetta.
  Annu Rev Biochem, 77, 363-382.  
16186494 K.McLuskey, S.Cameron, F.Hammerschmidt, and W.N.Hunter (2005).
Structure and reactivity of hydroxypropylphosphonic acid epoxidase in fosfomycin biosynthesis by a cation- and flavin-dependent mechanism.
  Proc Natl Acad Sci U S A, 102, 14221-14226.
PDB codes: 2bnm 2bnn 2bno
15359276 S.Rumpel, A.Razeto, C.M.Pillar, V.Vijayan, A.Taylor, K.Giller, M.S.Gilmore, S.Becker, and M.Zweckstetter (2004).
Structure and DNA-binding properties of the cytolysin regulator CylR2 from Enterococcus faecalis.
  EMBO J, 23, 3632-3642.
PDB code: 1utx
15062080 T.Newlove, J.H.Konieczka, and M.H.Cordes (2004).
Secondary structure switching in Cro protein evolution.
  Structure, 12, 569-581.
PDB code: 1rzs
12945054 H.Fan, and A.E.Mark (2003).
Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study.
  Proteins, 53, 111-120.  
12598646 K.R.LeFevre, and M.H.Cordes (2003).
Retroevolution of lambda Cro toward a stable monomer.
  Proc Natl Acad Sci U S A, 100, 2345-2350.  
11924737 J.L.Klepeis, and C.A.Floudas (2002).
Ab initio prediction of helical segments in polypeptides.
  J Comput Chem, 23, 245-266.  
11297428 H.Matsuno, K.Niikura, and Y.Okahata (2001).
Design and characterization of asparagine- and lysine-containing alanine-based helical peptides that bind selectively to A.T base pairs of oligonucleotides immobilized on a 27 mhz quartz crystal microbalance.
  Biochemistry, 40, 3615-3622.  
11076539 D.V.Laurents, S.Corrales, M.Elías-Arnanz, P.Sevilla, M.Rico, and S.Padmanabhan (2000).
Folding kinetics of phage 434 Cro protein.
  Biochemistry, 39, 13963-13973.  
10894750 E.R.Zinser, and R.Kolter (2000).
Prolonged stationary-phase incubation selects for lrp mutations in Escherichia coli K-12.
  J Bacteriol, 182, 4361-4365.  
10707026 K.Steinmetzer, A.Hillisch, J.Behlke, and S.Brantl (2000).
Transcriptional repressor CopR: structure model-based localization of the deoxyribonucleic acid binding motif.
  Proteins, 38, 393-406.  
10429210 J.Ruiz-Sanz, A.Simoncsits, I.Törö, S.Pongor, P.L.Mateo, and V.V.Filimonov (1999).
A thermodynamic study of the 434-repressor N-terminal domain and of its covalently linked dimers.
  Eur J Biochem, 263, 246-253.  
  10452612 S.Padmanabhan, M.A.Jiménez, and M.Rico (1999).
Folding propensities of synthetic peptide fragments covering the entire sequence of phage 434 Cro protein.
  Protein Sci, 8, 1675-1688.  
10223291 S.Y.Chung, and S.Subbiah (1999).
Validation of NMR side-chain conformations by packing calculations.
  Proteins, 35, 184-194.  
  9521100 N.N.Alexandrov, and R.Luethy (1998).
Alignment algorithm for homology modeling and threading.
  Protein Sci, 7, 254-258.  
9235002 A.L.Lomize, and H.I.Mosberg (1997).
Thermodynamic model of secondary structure for alpha-helical peptides and proteins.
  Biopolymers, 42, 239-269.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
9032054 M.A.Kercher, P.Lu, and M.Lewis (1997).
Lac repressor-operator complex.
  Curr Opin Struct Biol, 7, 76-85.  
8880931 H.Wako, M.Tachikawa, and A.Ogawa (1996).
A comparative study of dynamic structures between phage 434 Cro and repressor proteins by normal mode analysis.
  Proteins, 26, 72-80.  
  8631721 Y.Hashimoto, A.Q.Khan, and T.Ezaki (1996).
Positive autoregulation of vipR expression in ViaB region-encoded Vi antigen of Salmonella typhi.
  J Bacteriol, 178, 1430-1436.  
  7663342 C.Mumenthaler, and W.Braun (1995).
Predicting the helix packing of globular proteins by self-correcting distance geometry.
  Protein Sci, 4, 863-871.  
  8535237 J.R.Desjarlais, and T.M.Handel (1995).
De novo design of the hydrophobic cores of proteins.
  Protein Sci, 4, 2006-2018.  
  8563626 S.Y.Chung, and S.Subbiah (1995).
The use of side-chain packing methods in modeling bacteriophage repressor and cro proteins.
  Protein Sci, 4, 2300-2309.  
  8590003 T.E.Strzelecka, G.M.Clore, and A.M.Gronenborn (1995).
The solution structure of the Mu Ner protein reveals a helix-turn-helix DNA recognition motif.
  Structure, 3, 1087-1095.
PDB codes: 1neq 1ner
8183927 J.U.Bowie, and D.Eisenberg (1994).
An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function.
  Proc Natl Acad Sci U S A, 91, 4436-4440.  
  7987224 T.Liu, E.F.DeRose, and G.P.Mullen (1994).
Determination of the structure of the DNA binding domain of gamma delta resolvase in solution.
  Protein Sci, 3, 1286-1295.
PDB codes: 1res 1ret
  8003958 Z.S.Hendsch, and B.Tidor (1994).
Do salt bridges stabilize proteins? A continuum electrostatic analysis.
  Protein Sci, 3, 211-226.  
  8318894 D.P.Yee, and K.A.Dill (1993).
Families and the structural relatedness among globular proteins.
  Protein Sci, 2, 884-899.  
  8467791 H.M.Weir, P.J.Kraulis, C.S.Hill, A.R.Raine, E.D.Laue, and J.O.Thomas (1993).
Structure of the HMG box motif in the B-domain of HMG1.
  EMBO J, 12, 1311-1319.
PDB codes: 1hme 1hmf
15335781 S.Subbiah, D.V.Laurents, and M.Levitt (1993).
Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core.
  Curr Biol, 3, 141-148.  
1584772 D.Neri, G.Wider, and K.Wüthrich (1992).
Complete 15N and 1H NMR assignments for the amino-terminal domain of the phage 434 repressor in the urea-unfolded form.
  Proc Natl Acad Sci U S A, 89, 4397-4401.  
  1607010 D.Neri, G.Wider, and K.Wüthrich (1992).
1H, 15N and 13C NMR assignments of the 434 repressor fragments 1-63 and 44-63 unfolded in 7 M urea.
  FEBS Lett, 303, 129-135.  
1470680 M.Billeter (1992).
Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals.
  Q Rev Biophys, 25, 325-377.  
1409566 R.Baumeister, G.Müller, B.Hecht, and W.Hillen (1992).
Functional roles of amino acid residues involved in forming the alpha-helix-turn-alpha-helix operator DNA binding motif of Tet repressor from Tn10.
  Proteins, 14, 168-177.  
2041776 R.Grandori, and C.Sander (1991).
Identification by computer sequence analysis of transcriptional regulator proteins in Dictyostelium discoideum and Serratia marcescens.
  Nucleic Acids Res, 19, 2359-2362.  
2408042 H.C.Pace, P.Lu, and M.Lewis (1990).
lac repressor: crystallization of intact tetramer and its complexes with inducer and operator DNA.
  Proc Natl Acad Sci U S A, 87, 1870-1873.  
1967983 M.P.Kamps, C.Murre, X.H.Sun, and D.Baltimore (1990).
A new homeobox gene contributes the DNA binding domain of the t(1;19) translocation protein in pre-B ALL.
  Cell, 60, 547-555.  
2672451 R.G.Brennan, and B.W.Matthews (1989).
Structural basis of DNA-protein recognition.
  Trends Biochem Sci, 14, 286-290.  
2572329 Y.Q.Qian, M.Billeter, G.Otting, M.Müller, W.J.Gehring, and K.Wüthrich (1989).
The structure of the Antennapedia homeodomain determined by NMR spectroscopy in solution: comparison with prokaryotic repressors.
  Cell, 59, 573-580.  
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.