1g3w: Difference between revisions

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<StructureSection load='1g3w' size='340' side='right'caption='[[1g3w]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='1g3w' size='340' side='right'caption='[[1g3w]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1g3w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_diphtheriae"_kruse_in_flugge_1886 "bacillus diphtheriae" kruse in flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G3W FirstGlance]. <br>
<table><tr><td colspan='2'>[[1g3w]] 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=1G3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G3W FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fwz|1fwz]], [[1g3s|1g3s]], [[1g3t|1g3t]], [[1g3y|1g3y]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1g3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g3w OCA], [https://pdbe.org/1g3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g3w RCSB], [https://www.ebi.ac.uk/pdbsum/1g3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g3w ProSAT]</span></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=1g3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g3w OCA], [https://pdbe.org/1g3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g3w RCSB], [https://www.ebi.ac.uk/pdbsum/1g3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g3w ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== 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.  
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=1g3w ConSurf].
</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=1g3w ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:11320302<ref>PMID:11320302</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1g3w" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Diphtheria toxin repressor|Diphtheria toxin repressor]]
*[[Diphtheria toxin repressor|Diphtheria toxin repressor]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus diphtheriae kruse in flugge 1886]]
[[Category: Corynebacterium diphtheriae]]
[[Category: Large Structures]]
[[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: Dna binding protein]]
[[Category: Gene regulation]]
[[Category: Iron binding protein]]
[[Category: Iron dependent regulator]]

Latest revision as of 10:22, 7 February 2024

CD-CYS102SER DTXRCD-CYS102SER DTXR

Structural highlights

1g3w 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 2.4Å
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

1g3w, resolution 2.40Å

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