1g3y: Difference between revisions

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New page: left|200px<br /><applet load="1g3y" size="450" color="white" frame="true" align="right" spinBox="true" caption="1g3y, resolution 2.8Å" /> '''ARG80ALA DTXR'''<br /...
 
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[[Image:1g3y.jpg|left|200px]]<br /><applet load="1g3y" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1g3y, resolution 2.8&Aring;" />
'''ARG80ALA DTXR'''<br />


==Overview==
==ARG80ALA DTXR==
The diphtheria toxin repressor (DtxR) from Corynebacterium diphtheriae, regulates the expression of the gene on corynebacteriophages that encodes, diphtheria toxin (DT). Other genes regulated by DtxR include those that, encode proteins involved in siderophore-mediated iron uptake. DtxR, requires activation by divalent metals and holo-DtxR is a dimeric, regulator with two distinct metal-binding sites per three-domain monomer., At site 1, three side chains and a sulfate or phosphate anion are involved, in metal coordination. In the DtxR-DNA complex this anion is replaced by, the side chain of Glu170 provided by the third domain of the repressor. At, site 2 the metal ion is coordinated exclusively by constituents of the, polypeptide chain. In this paper, five crystal structures of three DtxR, variants focusing on residues Glu20, Arg80 and Cys102 are reported. The, resolution of these structures ranges from 2.3 to 2.8 A. The side chain of, Glu20 provided by the DNA-binding domain forms a salt bridge to Arg80, which in turn interacts with the anion. Replacing either of the, salt-bridge partners with an alanine reduces repressor activity, substantially and it has been inferred that the salt bridge could possibly, control the wedge angle between the DNA-binding domain and the, dimerization domain, thereby modulating repressor activity. Cys102 is a, key residue of metal site 2 and its substitution into a serine abolishes, repressor activity. The crystal structures of Zn-Glu20Ala-DtxR, Zn-Arg80Ala-DtxR, Cd-Cys102Ser-DtxR and apo-Cys102Ser-DtxR in two related, space groups reveal that none of these substitutions leads to dramatic, rearrangements of the DtxR fold. However, the five crystal structures, presented here show significant local changes and a considerable degree of, flexibility of the DNA-binding domain with respect to the dimerization, domain. Furthermore, all five structures deviate significantly from the, structure in the DtxR-DNA complex with respect to overall domain, orientation. These results confirm the importance of the hinge motion for, repressor activity. Since the third domain has often been invisible in, previous crystal structures of DtxR, it is also noteworthy that the, SH3-like domain could be traced in four of the five crystal structures.
<StructureSection load='1g3y' size='340' side='right'caption='[[1g3y]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1g3y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G3Y FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1g3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g3y OCA], [https://pdbe.org/1g3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g3y RCSB], [https://www.ebi.ac.uk/pdbsum/1g3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g3y ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DTXR_CORDI DTXR_CORDI] Iron-binding repressor of the dipheteria toxin gene expression. May serve as a global regulator of gene expression. Represses ripA under iron excess.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g3/1g3y_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1g3y ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1G3Y is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1G3Y OCA].
*[[Diphtheria toxin repressor|Diphtheria toxin repressor]]
 
__TOC__
==Reference==
</StructureSection>
Structures of three diphtheria toxin repressor (DtxR) variants with decreased repressor activity., Pohl E, Goranson-Siekierke J, Choi MK, Roosild T, Holmes RK, Hol WG, Acta Crystallogr D Biol Crystallogr. 2001 May;57(Pt 5):619-27. Epub 2001, Apr 24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11320302 11320302]
[[Category: Corynebacterium diphtheriae]]
[[Category: Corynebacterium diphtheriae]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Goranson-Siekierke, J.]]
[[Category: Goranson-Siekierke J]]
[[Category: Hol, W.G.J.]]
[[Category: Hol WGJ]]
[[Category: Holmes, R.K.]]
[[Category: Holmes RK]]
[[Category: Pohl, E.]]
[[Category: Pohl E]]
[[Category: ZN]]
[[Category: dna-binding protein]]
[[Category: dtxr]]
[[Category: iron-dependent regulator]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:40:58 2007''

Latest revision as of 10:22, 7 February 2024

ARG80ALA DTXRARG80ALA DTXR

Structural highlights

1g3y is a 1 chain structure with sequence from Corynebacterium diphtheriae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DTXR_CORDI Iron-binding repressor of the dipheteria toxin gene expression. May serve as a global regulator of gene expression. Represses ripA under iron excess.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1g3y, resolution 2.80Å

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