2it0
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 2it0 |SIZE=350|CAPTION= <scene name='initialview01'>2it0</scene>, resolution 2.600Å | |PDB= 2it0 |SIZE=350|CAPTION= <scene name='initialview01'>2it0</scene>, resolution 2.600Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= IdeR,dtxR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis]) | |GENE= IdeR,dtxR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1fx7|1FX7]], [[1u8r|1U8R]], [[2isy|2ISY]], [[2isz|2ISZ]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2it0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2it0 OCA], [http://www.ebi.ac.uk/pdbsum/2it0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2it0 RCSB]</span> | ||
}} | }} | ||
| Line 30: | Line 33: | ||
[[Category: Wisedchaisri, G.]] | [[Category: Wisedchaisri, G.]] | ||
[[Category: Wu, M.]] | [[Category: Wu, M.]] | ||
| - | [[Category: ACT]] | ||
| - | [[Category: NI]] | ||
[[Category: dna-binding protein]] | [[Category: dna-binding protein]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:48:08 2008'' |
Revision as of 00:48, 31 March 2008
| |||||||
| , resolution 2.600Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Gene: | IdeR,dtxR (Mycobacterium tuberculosis) | ||||||
| Related: | 1FX7, 1U8R, 2ISY, 2ISZ
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of a two-domain IdeR-DNA complex crystal form II
Overview
The iron-dependent regulator IdeR is a key transcriptional regulator of iron uptake in Mycobacterium tuberculosis. In order to increase our insight into the role of the SH3-like third domain of this essential regulator, the metal-binding and DNA-binding properties of two-domain IdeR (2D-IdeR) whose SH3-like domain has been truncated were characterized. The equilibrium dissociation constants for Co2+ and Ni2+ activation of 2D-IdeR for binding to the fxbA operator and the DNA-binding affinities of 2D-IdeR in the presence of excess metal ions were estimated using fluorescence spectroscopy. 2D-IdeR binds to fxbA operator DNA with similar affinity as full-length IdeR in the presence of excess metal ion. However, the Ni2+ concentrations required to activate 2D-IdeR for DNA binding appear to be smaller than that for full-length IdeR while the concentration of Co2+ required for activation remains the same. We have determined the crystal structures of Ni2+-activated 2D-IdeR at 1.96 A resolution and its double dimer complex with the mbtA-mbtB operator DNA in two crystal forms at 2.4 A and 2.6 A, the highest resolutions for DNA complexes for any structures of iron-dependent regulator family members so far. The 2D-IdeR-DNA complex structures confirm the specificity of Ser37 and Pro39 for thymine bases and suggest preferential contacts of Gln43 to cytosine bases of the DNA. In addition, our 2D-IdeR structures reveal a remarkable property of the TEV cleavage sequence remaining after removal of the C-terminal His6. This C-terminal tail promotes crystal contacts by forming a beta-sheet with the corresponding tail of neighboring subunits in two unrelated structures of 2D-IdeR, one with and one without DNA. The contact-promoting properties of this C-terminal TEV cleavage sequence may be beneficial for crystallizing other proteins.
About this Structure
2IT0 is a Single protein structure of sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA.
Reference
Crystal structures, metal activation, and DNA-binding properties of two-domain IdeR from Mycobacterium tuberculosis., Wisedchaisri G, Chou CJ, Wu M, Roach C, Rice AE, Holmes RK, Beeson C, Hol WG, Biochemistry. 2007 Jan 16;46(2):436-47. PMID:17209554
Page seeded by OCA on Mon Mar 31 03:48:08 2008
