Summary for 1MKM
| Entry DOI | 10.2210/pdb1mkm/pdb |
| Descriptor | IclR transcriptional regulator, ZINC ION, FORMIC ACID, ... (4 entities in total) |
| Functional Keywords | structural genomics, winged helix-turn-helix, psi, protein structure initiative, midwest center for structural genomics, mcsg, transcription |
| Biological source | Thermotoga maritima |
| Total number of polymer chains | 2 |
| Total formula weight | 57068.88 |
| Authors | Kim, Y.,Zhang, R.G.,Joachimiak, A.,Skarina, T.,Edwards, A.,Savchenko, A.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2002-08-29, release date: 2002-09-11, Last modification date: 2024-02-14) |
| Primary citation | Zhang, R.G.,Kim, Y.,Skarina, T.,Beasley, S.,Laskowski, R.,Arrowsmith, C.,Edwards, A.,Joachimiak, A.,Savchenko, A. Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family. J.Biol.Chem., 277:19183-19190, 2002 Cited by PubMed 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. PubMed: 11877432DOI: 10.1074/jbc.M112171200 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.2 Å) |
Structure validation
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