Proteopedia

1bi0: Difference between revisions

← Older edit
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1bi0.gif|left|200px]]
<!--
The line below this paragraph, containing "STRUCTURE_1bi0", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_1bi0|  PDB=1bi0  |  SCENE=  }}
'''STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR'''


==STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR==
<StructureSection load='1bi0' size='340' side='right'caption='[[1bi0]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1bi0]] 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=1BI0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BI0 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]] 2.3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <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=1bi0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bi0 OCA], [https://pdbe.org/1bi0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bi0 RCSB], [https://www.ebi.ac.uk/pdbsum/1bi0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bi0 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/bi/1bi0_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1bi0 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The diphtheria toxin repressor (DtxR) from Corynebacterium diphtheriae is a divalent metal-activated repressor of chromosomal genes that encode proteins responsible for siderophore-mediated iron uptake and also of the gene of certain corynebacteriophages that encodes diphtheria toxin. DtxR consists of two 25.3-kDa three-domain subunits and is a member of a family of related repressor proteins in several Gram-positive bacterial species, some of which are important human pathogens. In this paper, we report on the first high resolution crystal structures of apo-DtxR in two related space groups. In addition, crystal structures of Zn-DtxR were determined in the same two space groups. The resolutions of the structures range from 2.2 to 2.4 A. The four refined models of the apo- and the holo-repressor exhibit quite similar metal binding centers, which do, however, show higher thermal motion in the apo-structures. All four structures reported differ from each other in one important aspect. The N-terminal DNA-binding domain and the last 20 residues of the dimerization domain of each subunit move significantly with respect to the core of the DtxR dimer, which consists of residues 74-120 from both subunits. These results provide the first indication of a conformational change that may occur upon binding of the holo-repressor to DNA.


==Overview==
Motion of the DNA-binding domain with respect to the core of the diphtheria toxin repressor (DtxR) revealed in the crystal structures of apo- and holo-DtxR.,Pohl E, Holmes RK, Hol WG J Biol Chem. 1998 Aug 28;273(35):22420-7. PMID:9712865<ref>PMID:9712865</ref>
The diphtheria toxin repressor (DtxR) from Corynebacterium diphtheriae is a divalent metal-activated repressor of chromosomal genes that encode proteins responsible for siderophore-mediated iron uptake and also of the gene of certain corynebacteriophages that encodes diphtheria toxin. DtxR consists of two 25.3-kDa three-domain subunits and is a member of a family of related repressor proteins in several Gram-positive bacterial species, some of which are important human pathogens. In this paper, we report on the first high resolution crystal structures of apo-DtxR in two related space groups. In addition, crystal structures of Zn-DtxR were determined in the same two space groups. The resolutions of the structures range from 2.2 to 2.4 A. The four refined models of the apo- and the holo-repressor exhibit quite similar metal binding centers, which do, however, show higher thermal motion in the apo-structures. All four structures reported differ from each other in one important aspect. The N-terminal DNA-binding domain and the last 20 residues of the dimerization domain of each subunit move significantly with respect to the core of the DtxR dimer, which consists of residues 74-120 from both subunits. These results provide the first indication of a conformational change that may occur upon binding of the holo-repressor to DNA.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1BI0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BI0 OCA].
</div>
<div class="pdbe-citations 1bi0" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Motion of the DNA-binding domain with respect to the core of the diphtheria toxin repressor (DtxR) revealed in the crystal structures of apo- and holo-DtxR., Pohl E, Holmes RK, Hol WG, J Biol Chem. 1998 Aug 28;273(35):22420-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9712865 9712865]
*[[Diphtheria toxin repressor|Diphtheria toxin repressor]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Corynebacterium diphtheriae]]
[[Category: Corynebacterium diphtheriae]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Hol, W G.]]
[[Category: Hol WG]]
[[Category: Pohl, E.]]
[[Category: Pohl E]]
[[Category: Dna-binding]]
[[Category: Iron]]
[[Category: Repressor]]
[[Category: Transcription regulation]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 11:32:19 2008''

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/w/1bi0"