3ihq

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras

Structural highlights

3ihq is a 2 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SPX_BACSU Interferes with activator-stimulated transcription by interaction with the RNA polymerase alpha-CTD. May function to globally reduce transcription of genes involved in growth- and development-promoting processes and to increase transcription of genes involved in thiol homeostasis, during periods of extreme stress. Negatively affects competence and sporulation. Its degradation by the MecA/ClpXP complex is needed for competence development.^[1] ^[2]

Evolutionary Conservation

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

Publication Abstract from PubMed

BACKGROUND: Spx, an ArsC (arsenate reductase) family member, is a global transcriptional regulator of the microbial stress response and is highly conserved amongst Gram-positive bacteria. Bacillus subtilis Spx protein exerts positive and negative control of transcription through its interaction with the C-terminal domain of the RNA polymerase (RNAP) alpha subunit (alphaCTD). Spx activates trxA (thioredoxin) and trxB (thioredoxin reductase) in response to thiol stress, and bears an N-terminal C10XXC13 redox disulfide center that is oxidized in active Spx. METHODOLOGY/PRINCIPAL FINDINGS: The structure of mutant Spx(C10S) showed a change in the conformation of helix alpha4. Amino acid substitutions R60E and K62E within and adjacent to helix alpha4 conferred defects in Spx-activated transcription but not Spx-dependent repression. Electrophoretic mobility-shift assays showed alphaCTD interaction with trxB promoter DNA, but addition of Spx generated a supershifted complex that was disrupted in the presence of reductant (DTT). Interaction of alphaCTD/Spx complex with promoter DNA required the cis-acting elements -45AGCA-42 and -34AGCG-31 of the trxB promoter. The Spx(G52R) mutant, defective in alphaCTD binding, did not interact with the alphaCTD-trxB complex. Spx(R60E) not only failed to complex with alphaCTD-trxB, but also disrupted alphaCTD-trxB DNA interaction. CONCLUSIONS/SIGNIFICANCE: The results show that Spx and alphaCTD form a complex that recognizes the promoter DNA of an Spx-controlled gene. A conformational change during oxidation of Spx to the disulfide form likely alters the structure of Spx alpha helix alpha4, which contains residues that function in transcriptional activation and alphaCTD/Spx-promoter interaction. The results suggest that one of these residues, R60 of the alpha4 region of oxidized Spx, functions in alphaCTD/Spx-promoter contact but not in alphaCTD interaction.

Promoter recognition by a complex of Spx and the C-terminal domain of the RNA polymerase alpha subunit.,Nakano MM, Lin A, Zuber CS, Newberry KJ, Brennan RG, Zuber P PLoS One. 2010 Jan 13;5(1):e8664. PMID:20084284^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Nakano MM, Hajarizadeh F, Zhu Y, Zuber P. Loss-of-function mutations in yjbD result in ClpX- and ClpP-independent competence development of Bacillus subtilis. Mol Microbiol. 2001 Oct;42(2):383-94. PMID:11703662
↑ Nakano S, Nakano MM, Zhang Y, Leelakriangsak M, Zuber P. A regulatory protein that interferes with activator-stimulated transcription in bacteria. Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):4233-8. Epub 2003 Mar 17. PMID:12642660 doi:http://dx.doi.org/10.1073/pnas.0637648100
↑ Nakano MM, Lin A, Zuber CS, Newberry KJ, Brennan RG, Zuber P. Promoter recognition by a complex of Spx and the C-terminal domain of the RNA polymerase alpha subunit. PLoS One. 2010 Jan 13;5(1):e8664. PMID:20084284 doi:10.1371/journal.pone.0008664

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ihq"

Categories: Bacillus subtilis | Large Structures | Brennan RG | Newberry KJ

@@ Line 1: / Line 1: @@
-[[Image:3ihq.png|left|200px]]
-{{STRUCTURE_3ihq|  PDB=3ihq  |  SCENE=  }}
+==Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras==
+<StructureSection load='3ihq' size='340' side='right'caption='[[3ihq]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3ihq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IHQ 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]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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=3ihq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ihq OCA], [https://pdbe.org/3ihq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ihq RCSB], [https://www.ebi.ac.uk/pdbsum/3ihq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ihq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SPX_BACSU SPX_BACSU] Interferes with activator-stimulated transcription by interaction with the RNA polymerase alpha-CTD. May function to globally reduce transcription of genes involved in growth- and development-promoting processes and to increase transcription of genes involved in thiol homeostasis, during periods of extreme stress. Negatively affects competence and sporulation. Its degradation by the MecA/ClpXP complex is needed for competence development.<ref>PMID:11703662</ref> <ref>PMID:12642660</ref>
+== 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/ih/3ihq_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=3ihq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: Spx, an ArsC (arsenate reductase) family member, is a global transcriptional regulator of the microbial stress response and is highly conserved amongst Gram-positive bacteria. Bacillus subtilis Spx protein exerts positive and negative control of transcription through its interaction with the C-terminal domain of the RNA polymerase (RNAP) alpha subunit (alphaCTD). Spx activates trxA (thioredoxin) and trxB (thioredoxin reductase) in response to thiol stress, and bears an N-terminal C10XXC13 redox disulfide center that is oxidized in active Spx. METHODOLOGY/PRINCIPAL FINDINGS: The structure of mutant Spx(C10S) showed a change in the conformation of helix alpha4. Amino acid substitutions R60E and K62E within and adjacent to helix alpha4 conferred defects in Spx-activated transcription but not Spx-dependent repression. Electrophoretic mobility-shift assays showed alphaCTD interaction with trxB promoter DNA, but addition of Spx generated a supershifted complex that was disrupted in the presence of reductant (DTT). Interaction of alphaCTD/Spx complex with promoter DNA required the cis-acting elements -45AGCA-42 and -34AGCG-31 of the trxB promoter. The Spx(G52R) mutant, defective in alphaCTD binding, did not interact with the alphaCTD-trxB complex. Spx(R60E) not only failed to complex with alphaCTD-trxB, but also disrupted alphaCTD-trxB DNA interaction. CONCLUSIONS/SIGNIFICANCE: The results show that Spx and alphaCTD form a complex that recognizes the promoter DNA of an Spx-controlled gene. A conformational change during oxidation of Spx to the disulfide form likely alters the structure of Spx alpha helix alpha4, which contains residues that function in transcriptional activation and alphaCTD/Spx-promoter interaction. The results suggest that one of these residues, R60 of the alpha4 region of oxidized Spx, functions in alphaCTD/Spx-promoter contact but not in alphaCTD interaction.
-===Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras===
+Promoter recognition by a complex of Spx and the C-terminal domain of the RNA polymerase alpha subunit.,Nakano MM, Lin A, Zuber CS, Newberry KJ, Brennan RG, Zuber P PLoS One. 2010 Jan 13;5(1):e8664. PMID:20084284<ref>PMID:20084284</ref>
-{{ABSTRACT_PUBMED_20084284}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3ihq" style="background-color:#fffaf0;"></div>
-[[3ihq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IHQ OCA].
 ==See Also==
-*[[RNA polymerase|RNA polymerase]]
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:020084284</ref><ref group="xtra">PMID:016249335</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Bacillus subtilis]]
-[[Category: DNA-directed RNA polymerase]]
+[[Category: Large Structures]]
-[[Category: Brennan, R G.]]
+[[Category: Brennan RG]]
-[[Category: Newberry, K J.]]
+[[Category: Newberry KJ]]
-[[Category: Disulfide bond]]
-[[Category: Dna-directed rna polymerase]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Oxidative stress]]
-[[Category: Redox-active center]]
-[[Category: Rna polymerase]]
-[[Category: Spx]]
-[[Category: Stress response]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Transcription-transferase complex]]
-[[Category: Transferase]]

3ihq

From Proteopedia

Current revision

Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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