PDBsum entry: 1per

Transcription/DNA

PDB-id

1per


	Asymmetric unit

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DNA/RNA

Waters ×40

* Residue conservation analysis

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		Biological unit, dimer (as deduced by PQS)

PDB id:

1per

Name:

Transcription/DNA

Title:

The complex between phage 434 repression DNA-binding domain and operator site or3: structural differences between consensus and non-consensus half-sites

Structure:

DNA (5'- d( Ap Ap Gp Tp Ap Cp Ap Gp Tp Tp Tp Tp Tp Cp Tp Tp G p Tp Ap T)-3'). Chain: a. Engineered: yes. DNA (5'- d( Tp Ap Tp Ap Cp Ap Ap Gp Ap Ap Ap Ap Ap Cp Tp Gp T p Ap Cp T)-3'). Chain: b.

Source:

Synthetic: yes. Phage 434. Organism_taxid: 10712

Biological unit:

Dimer (from PQS)

UniProt:

Chains L, R: P16117 (RPC1_BP434)

Seq:

95 a.a.

Struc:

63 a.a.

Key:		PfamA domain
		Secondary structure			CATH domain

Resolution:

2.50Å

R-factor:

0.187

Authors:

D.W.Rodgers,S.C.Harrison

Key ref:

D.W.Rodgers and S.C.Harrison (1993). The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites.. Structure, 1, 227-240. [PubMed id: 8081737] [DOI: 10.1016/0969-2126(93)90012-6]

Date:

09-Nov-93

Release date:

31-Jan-94

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Key reference

DOI no: 10.1016/0969-2126(93)90012-6 Structure 1:227-240 (1993)

PubMed id: 8081737

The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites.

D.W.Rodgers, S.C.Harrison.

ABSTRACT

BACKGROUND: The repressor of phage 434 binds to a set of operator sites as a homodimer. Its relative affinities for these sites determine the switch from lysogenic to lytic growth. The six 434 operator sites (OR1, OR2, OR3, OL1, OL2 and OL3) have a particularly simple organization; all are 14 base pairs long, with a conserved 5'-ACAA sequence symmetrically placed at either end, and a variable central six base pairs. OR3 is unique among naturally-occurring 434 operator sites in that it contains a non-consensus base pair, G.C, at the fourth position of the otherwise invariant 5'-ACAA sequence. Comparisons among structures of the 434 repressor DNA-binding domain, R1-69, bound to various operator sites, allow us to analyze differential specificity in regulatory complexes of this kind. RESULTS: We have determined the structure at 2.5 A resolution of a complex of R1-69 with DNA containing the OR3 site and compared it with previously studied complexes of R1-69 bound to OR1 and OR2. There are surprisingly extensive structural differences between the consensus and non-consensus half-sites of OR3 with respect to their interactions with R1-69, including a shift in the DNA backbone and a small rotation of the entire R1-69 monomer. CONCLUSIONS: Recognition of the base pair difference that is critical for the 434 regulatory switch involves a number of amino acid residues, not just the one or two side chains in direct contact with the G-C base pair. Moreover, the repressor imposes a somewhat altered DNA conformation on the non-consensus half-site.

Literature references that cite this PDB file's key reference

PubMed id Reference

17223787 A.S.Romanenkov, O.V.Kisil, T.S.Zatsepin, O.V.Iamskova, A.S.Kariagina, V.G.Metelev, T.S.Oretskaia, and E.A.Kubareva (2006).
DNA-methyltransferase SsoII as a bifunctional protein: features of the interaction with the promoter region of SsoII restriction-modification genes.

Biochemistry (Mosc), 71, 1341-1349.

17038333 N.B.Becker, L.Wolff, and R.Everaers (2006).
Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials.

Nucleic Acids Res, 34, 5638-5649.

12065400 C.G.Kalodimos, A.M.Bonvin, R.K.Salinas, R.Wechselberger, R.Boelens, and R.Kaptein (2002).
Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain.

EMBO J, 21, 2866-2876.

PDB code: 1l1m

11861910 Z.Morávek, S.Neidle, and B.Schneider (2002).
Protein and drug interactions in the minor groove of DNA.

Nucleic Acids Res, 30, 1182-1191.

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.

11438706 J.Hizver, H.Rozenberg, F.Frolow, D.Rabinovich, and Z.Shakked (2001).
DNA bending by an adenine--thymine tract and its role in gene regulation.

Proc Natl Acad Sci U S A, 98, 8490-8495.

PDB code: 1ilc

11526315 M.L.Coté, and M.M.Georgiadis (2001).
Structure of a pseudo-16-mer DNA with stacked guanines and two G-A mispairs complexed with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase.

Acta Crystallogr D Biol Crystallogr, 57, 1238-1250.

PDB code: 1i6j

10766954 D.C.Kombo, M.A.Young, and D.L.Beveridge (2000).
One nanosecond molecular dynamics simulation of the N-terminal domain of the lambda repressor protein.

Biopolymers, 53, 596-605.

11058965 J.Xu, and G.B.Koudelka (2000).
DNA sequence requirements for the activation of 434 P(RM) transcription by 434 repressor.

DNA Cell Biol, 19, 621-630.

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.

10329775 G.Savitha, and M.A.Viswamitra (1999).
An A-DNA structure with two independent duplexes in the asymmetric unit.

Acta Crystallogr D Biol Crystallogr, 55, 1136-1143.

PDB code: 414d

9727039 J.Xu, and G.B.Koudelka (1998).
DNA-based positive control mutants in the binding site sequence of 434 repressor.

J Biol Chem, 273, 24165-24172.

9518483 R.E.Dickerson (1998).
DNA bending: the prevalence of kinkiness and the virtues of normality.

Nucleic Acids Res, 26, 1906-1926.

10384325 W.Herr (1998).
The herpes simplex virus VP16-induced complex: mechanisms of combinatorial transcriptional regulation.

Cold Spring Harb Symp Quant Biol, 63, 599-607.

9251777 D.Kosztin, T.C.Bishop, and K.Schulten (1997).
Binding of the estrogen receptor to DNA. The role of waters.

Biophys J, 73, 557-570.

9153301 J.Chen, S.Pongor, and A.Simoncsits (1997).
Recognition of DNA by single-chain derivatives of the phage 434 repressor: high affinity binding depends on both the contacted and non-contacted base pairs.

Nucleic Acids Res, 25, 2047-2054.

9218422 M.Oda, K.Furukawa, K.Ogata, A.Sarai, S.Ishii, Y.Nishimura, and H.Nakamura (1997).
Investigation of the pyrimidine preference by the c-Myb DNA-binding domain at the initial base of the consensus sequence.

J Biol Chem, 272, 17966-17971.

9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.

Biopolymers, 44, 361-403.

9006933 R.Solano, A.Fuertes, L.Sánchez-Pulido, A.Valencia, and J.Paz-Ares (1997).
A single residue substitution causes a switch from the dual DNA binding specificity of plant transcription factor MYB.Ph3 to the animal c-MYB specificity.

J Biol Chem, 272, 2889-2895.

7836381 A.C.Bell, and G.B.Koudelka (1995).
How 434 repressor discriminates between OR1 and OR3. The influence of contacted and noncontacted base pairs.

J Biol Chem, 270, 1205-1212.

7716167 J.Janin (1995).
Elusive affinities.

Proteins, 21, 30-39.

7891704 M.A.Cleary, and W.Herr (1995).
Mechanisms for flexibility in DNA sequence recognition and VP16-induced complex formation by the Oct-1 POU domain.

Mol Cell Biol, 15, 2090-2100.

8749848 M.Suzuki, and M.Gerstein (1995).
Binding geometry of alpha-helices that recognize DNA.

Proteins, 23, 525-535.

7610037 M.Suzuki, and N.Yagi (1995).
Stereochemical basis of DNA bending by transcription factors.

Nucleic Acids Res, 23, 2083-2091.

7664086 N.D.Arbuckle, and B.Luisi (1995).
A recipe for specificity.

Nat Struct Biol, 2, 341-346.

7809040 M.Suzuki, and N.Yagi (1994).
DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families.

Proc Natl Acad Sci U S A, 91, 12357-12361.

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.