4iht | pdb_00004iht

Crystal Structure of BenM_DBD/benA site 1 DNA Complex

spinqualitylabelsall models 4iht, resolution 3.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4iht is a 8 chain structure with sequence from Acinetobacter baylyi ADP1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function BENM_ACIAD Positive regulator of the ben and cat genes for benzoate degradation. BenM is necessary for ben gene expression but not for expression of the cat genes, which can be regulated by CatM. Binds to the inducers cis,cis-muconate and benzoate. Publication Abstract from PubMed LysR-type transcriptional regulators (LTTRs) play critical roles in metabolism and constitute the largest family of bacterial regulators. To understand protein-DNA interactions, atomic structures of the DNA-binding domain and linker-helix regions of a prototypical LTTR, BenM, were determined by X-ray crystallography. BenM structures with and without bound DNA reveal a set of highly conserved amino acids that interact directly with DNA bases. At the N-terminal end of the recognition helix (alpha3) of a winged-helix-turn-helix DNA-binding motif, several residues create hydrophobic pockets (Pro30, Pro31 and Ser33). These pockets interact with the methyl groups of two thymines in the DNA-recognition motif and its complementary strand, T-N11-A. This motif usually includes some dyad symmetry, as exemplified by a sequence that binds two subunits of a BenM tetramer (ATAC-N7-GTAT). Gln29 forms hydrogen bonds to adenine in the first position of the recognition half-site (ATAC). Another hydrophobic pocket defined by Ala28, Pro30 and Pro31 interacts with the methyl group of thymine, complementary to the base at the third position of the half-site. Arg34 interacts with the complementary base of the 3' position. Arg53, in the wing, provides AT-tract recognition in the minor groove. For DNA recognition, LTTRs use highly conserved interactions between amino acids and nucleotide bases as well as numerous less-conserved secondary interactions. The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N11-A sequence motif by LysR-type transcriptional regulators.,Alanazi AM, Neidle EL, Momany C Acta Crystallogr D Biol Crystallogr. 2013 Oct;69(Pt 10):1995-2007. doi:, 10.1107/S0907444913017320. Epub 2013 Sep 20. PMID:24100318 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Transcriptional activator 3D structures

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