1tf1

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of the E. coli Glyoxylate Regulatory Protein Ligand Binding Domain

Structural highlights

1tf1 is a 4 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

ALLR_ECOLI Negative regulator of allantoin and glyoxylate utilization operons. Binds to the gcl promoter and to the allS-allA intergenic region. Binding to DNA is abolished by glyoxylate.^[1] ^[2] ^[3]

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

The interaction of Escherichia coli AllR regulator with operator DNA is disrupted by the effector molecule glyoxylate. This is a general, yet uncharacterized regulatory mechanism for the large IclR family of transcriptional regulators to which AllR belongs. The crystal structures of the C-terminal effector-binding domain of AllR regulator and its complex with glyoxylate were determined at 1.7 and 1.8 A, respectively. Residues involved in glyoxylate binding were explored in vitro and in vivo. Altering the residues Cys217, Ser234 and Ser236 resulted in glyoxylate-independent repression by AllR. Sequence analysis revealed low conservation of amino acid residues participating in effector binding among IclR regulators, which reflects potential chemical diversity of effector molecules, recognized by members of this family. Comparing the AllR structure to that of Thermotoga maritima TM0065, the other representative of the IclR family that has been structurally characterized, indicates that both proteins assume similar quaternary structures as a dimer of dimers. Mutations in the tetramerization region, which in AllR involve the Cys135-Cys142 region, resulted in dissociation of AllR tetramer to dimers in vitro and were functionally inactive in vivo. Glyoxylate does not appear to function through the inhibition of tetramerization. Using sedimentation velocity, glyoxylate was shown to conformationally change the AllR tetramer as well as monomer and dimer resulting in altered outline of AllR molecules.

Structural and biochemical study of effector molecule recognition by the E.coli glyoxylate and allantoin utilization regulatory protein AllR.,Walker JR, Altamentova S, Ezersky A, Lorca G, Skarina T, Kudritska M, Ball LJ, Bochkarev A, Savchenko A J Mol Biol. 2006 May 5;358(3):810-28. Epub 2006 Mar 3. PMID:16546208^[4]

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

References

↑ Cusa E, Obradors N, Baldoma L, Badia J, Aguilar J. Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli. J Bacteriol. 1999 Dec;181(24):7479-84. PMID:10601204
↑ Rintoul MR, Cusa E, Baldoma L, Badia J, Reitzer L, Aguilar J. Regulation of the Escherichia coli allantoin regulon: coordinated function of the repressor AllR and the activator AllS. J Mol Biol. 2002 Dec 6;324(4):599-610. PMID:12460564 doi:http://dx.doi.org/10.1016/S0022283602011348
↑ Walker JR, Altamentova S, Ezersky A, Lorca G, Skarina T, Kudritska M, Ball LJ, Bochkarev A, Savchenko A. Structural and biochemical study of effector molecule recognition by the E.coli glyoxylate and allantoin utilization regulatory protein AllR. J Mol Biol. 2006 May 5;358(3):810-28. Epub 2006 Mar 3. PMID:16546208 doi:10.1016/j.jmb.2006.02.034
↑ Walker JR, Altamentova S, Ezersky A, Lorca G, Skarina T, Kudritska M, Ball LJ, Bochkarev A, Savchenko A. Structural and biochemical study of effector molecule recognition by the E.coli glyoxylate and allantoin utilization regulatory protein AllR. J Mol Biol. 2006 May 5;358(3):810-28. Epub 2006 Mar 3. PMID:16546208 doi:10.1016/j.jmb.2006.02.034

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1tf1"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of the E. coli Glyoxylate Regulatory Protein Ligand Binding Domain==
-<StructureSection load='1tf1' size='340' side='right' caption='[[1tf1]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='1tf1' size='340' side='right'caption='[[1tf1]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1tf1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TF1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TF1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1tf1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TF1 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1t9l|1t9l]], [[1td5|1td5]], [[1mkm|1mkm]]</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]] 1.8&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">glxa3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=1tf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tf1 OCA], [https://pdbe.org/1tf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tf1 RCSB], [https://www.ebi.ac.uk/pdbsum/1tf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tf1 ProSAT], [https://www.topsan.org/Proteins/MCSG/1tf1 TOPSAN]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tf1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tf1 RCSB], [http://www.ebi.ac.uk/pdbsum/1tf1 PDBsum], [http://www.topsan.org/Proteins/MCSG/1tf1 TOPSAN]</span></td></tr>
+</table>
-<table>
+== Function ==
+[https://www.uniprot.org/uniprot/ALLR_ECOLI ALLR_ECOLI] Negative regulator of allantoin and glyoxylate utilization operons. Binds to the gcl promoter and to the allS-allA intergenic region. Binding to DNA is abolished by glyoxylate.<ref>PMID:10601204</ref> <ref>PMID:12460564</ref> <ref>PMID:16546208</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/tf/1tf1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tf/1tf1_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/chain_selection.php?pdb_ID=2ata 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=1tf1 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1tf1" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 30: / Line 33: @@
 </StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Arrowsmith, C.]]
+[[Category: Large Structures]]
-[[Category: Edwards, A.]]
+[[Category: Arrowsmith C]]
-[[Category: Joachimiak, A.]]
+[[Category: Edwards A]]
-[[Category: Kudrytska, M.]]
+[[Category: Joachimiak A]]
-[[Category: MCSG, Midwest Center for Structural Genomics.]]
+[[Category: Kudrytska M]]
-[[Category: Savchenko, A.]]
+[[Category: Savchenko A]]
-[[Category: Skarina, T.]]
+[[Category: Skarina T]]
-[[Category: Walker, J R.]]
+[[Category: Walker JR]]
-[[Category: Glcr]]
-[[Category: Ligand binding domain]]
-[[Category: Mcsg]]
-[[Category: Midwest center for structural genomic]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]
-[[Category: Transcription]]
-[[Category: Transcriptional regulator]]

1tf1

From Proteopedia

Current revision

Crystal Structure of the E. coli Glyoxylate Regulatory Protein Ligand Binding Domain

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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