PDBsum entry 3gfi

Transcription/DNA

PDB id

3gfi

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Contents

			Protein chains

					143 a.a. *

			DNA/RNA

			Waters ×154

* Residue conservation analysis

PDB id:

3gfi

Links

Name:

Transcription/DNA

Title:

Crystal structure of st1710 complexed with its promoter DNA

Structure:

146aa long hypothetical transcriptional regulator. Chain: a, c. Synonym: transcription regulator st1710. Engineered: yes. 5'-d( Tp Ap Ap Cp Ap Ap Tp Ap Gp Cp Ap Ap A)-3'. Chain: d. Engineered: yes. 5'-d( Tp Tp Gp Cp Tp Ap Tp Tp Gp T)-3'. Chain: e.

Source:

Sulfolobus tokodaii. Organism_taxid: 111955. Gene: st1710. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes

Resolution:

2.10Å

R-factor:

0.234

R-free:

0.280

Authors:

T.Kumarevel,T.Tanaka,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

T.Kumarevel et al. (2009). ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators. Nucleic Acids Res, 37, 4723-4735. PubMed id: 19509310

Date:

26-Feb-09

Release date:

25-Aug-09

PROCHECK

	Headers

	References

Protein chains

Q96ZY1 (Q96ZY1_SULTO) - MarR family transcriptional regulator from Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)

Seq: Struc:					146 a.a. 143 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

DNA/RNA chains

		T-A-A-C-A-A-T-A-G-C-A-A-A 13 bases
		T-T-G-C-T-A-T-T-G-T 10 bases

	Nucleic Acids Res 37:4723-4735 (2009)
PubMed id: 19509310

ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators.
T.Kumarevel, T.Tanaka, T.Umehara, S.Yokoyama.

ABSTRACT

ST1710, a member of the multiple antibiotic resistance regulator (MarR) family of regulatory proteins in bacteria and archaea, plays important roles in development of antibiotic resistance, a global health problem. Here, we present the crystal structure of ST1710 from Sulfolobus tokodaii strain 7 complexed with salicylate, a well-known inhibitor of MarR proteins and the ST1710 complex with its promoter DNA, refined to 1.8 and 2.10 A resolutions, respectively. The ST1710-DNA complex shares the topology of apo-ST1710 and MarR proteins, with each subunit containing a winged helix-turn-helix (wHtH) DNA binding motif. Significantly large conformational changes occurred upon DNA binding and in each of the dimeric monomers in the asymmetric unit of the ST1710-DNA complex. Conserved wHtH loop residues interacting with the bound DNA and mutagenic analysis indicated that R89, R90 and K91 were important for DNA recognition. Significantly, the bound DNA exhibited a new binding mechanism.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21432936

I.C.Perera, and A.Grove (2011).
MarR homologs with urate-binding signature.

Protein Sci, 20, 621-629.

20716550

I.C.Perera, and A.Grove (2010).
Molecular mechanisms of ligand-mediated attenuation of DNA binding by MarR family transcriptional regulators.

J Mol Cell Biol, 2, 243-254.

20421503

Y.M.Chang, W.Y.Jeng, T.P.Ko, Y.J.Yeh, C.K.Chen, and A.H.Wang (2010).
Structural study of TcaR and its complexes with multiple antibiotics from Staphylococcus epidermidis.

Proc Natl Acad Sci U S A, 107, 8617-8622.

PDB codes:

3kp2 3kp3 3kp4 3kp5 3kp6 3kp7

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 codes are shown on the right.