1mkm

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[[Image:1mkm.gif|left|200px]]<br /><applet load="1mkm" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1mkm, resolution 2.20&Aring;" />
 
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'''CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA ICLR'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA ICLR==
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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.
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<StructureSection load='1mkm' size='340' side='right'caption='[[1mkm]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1mkm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1jmr 1jmr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MKM FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mkm OCA], [https://pdbe.org/1mkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mkm RCSB], [https://www.ebi.ac.uk/pdbsum/1mkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mkm ProSAT], [https://www.topsan.org/Proteins/MCSG/1mkm TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9WXS0_THEMA Q9WXS0_THEMA]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mk/1mkm_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1mkm ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1MKM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] with <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=FMT:'>FMT</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 1JMR. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MKM OCA].
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*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family., Zhang RG, Kim Y, Skarina T, Beasley S, Laskowski R, Arrowsmith C, Edwards A, Joachimiak A, Savchenko A, J Biol Chem. 2002 May 24;277(21):19183-90. Epub 2002 Mar 4. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11877432 11877432]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Thermotoga maritima]]
[[Category: Thermotoga maritima]]
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[[Category: Edwards, A.]]
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[[Category: Edwards A]]
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[[Category: Joachimiak, A.]]
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[[Category: Joachimiak A]]
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[[Category: Kim, Y.]]
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[[Category: Kim Y]]
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[[Category: MCSG, Midwest Center for Structural Genomics.]]
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[[Category: Savchenko A]]
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[[Category: Savchenko, A.]]
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[[Category: Skarina T]]
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[[Category: Skarina, T.]]
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[[Category: Zhang RG]]
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[[Category: Zhang, R G.]]
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[[Category: FMT]]
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[[Category: ZN]]
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[[Category: mcsg]]
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[[Category: midwest center for structural genomics]]
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[[Category: protein structure initiative]]
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[[Category: psi]]
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[[Category: structural genomics]]
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[[Category: winged helix-turn-helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:56:08 2008''
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Current revision

CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA ICLR

PDB ID 1mkm

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