title: Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.
abstract: Members of the IclR family of transcription regulators modulate signal-dependent expression of genes involved in carbon metabolism in bacteria and archaea. The Thermotoga maritima TM0065 gene codes for a protein (TM-IclR) that is homologous to the IclR family. We have determined the crystal structure of TM-IclR at 2.2 A resolution using MAD phasing and synchrotron radiation. The protein is composed of two domains: the N-terminal DNA-binding domain contains the winged helix-turn-helix motif, and the C-terminal presumed regulatory domain is involved in binding signal molecule. In a proposed signal-binding site, a bound Zn(2+) ion was found. In the crystal, TM-IclR forms a dimer through interactions between DNA-binding domains. In the dimer, the DNA-binding domains are 2-fold related, but the dimer is asymmetric with respect to the orientation of signal-binding domains. Crystal packing analysis showed that TM-IclR dimers form a tetramer through interactions exclusively by signal-binding domains. A model is proposed for binding of IclR-like factors to DNA, and it suggests that signal-dependent transcription regulation is accomplished by affecting an oligomerization state of IclR and therefore its affinity for DNA target.
authors.affiliation: Biosciences Division and Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, USA.
authors.forename: Rong-Guang
authors.initials: RG
authors.lastname: Zhang
authors.forename: Youngchang
authors.initials: Y
authors.lastname: Kim
authors.forename: Tatiana
authors.initials: T
authors.lastname: Skarina
authors.forename: Steven
authors.initials: S
authors.lastname: Beasley
authors.forename: Roman
authors.initials: R
authors.lastname: Laskowski
authors.forename: Cheryl
authors.initials: C
authors.lastname: Arrowsmith
authors.forename: Aled
authors.initials: A
authors.lastname: Edwards
authors.forename: Andrzej
authors.initials: A
authors.lastname: Joachimiak
authors.forename: Alexei
authors.initials: A
authors.lastname: Savchenko
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D004269:DNA, Bacterial / Q000378:metabolism; D029968:Escherichia coli Proteins; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D012097:Repressor Proteins / Q000737:chemistry* / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D020124:Thermotoga maritima / Q000378:metabolism*; D014157:Transcription Factors
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D012097:Repressor Proteins; D014157:Transcription Factors; C067479:IclR protein, E coli