3glb: Difference between revisions

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-{{Seed}}
-[[Image:3glb.jpg|left|200px]]
-<!--
+==Crystal structure of the effector binding domain of a CATM variant (R156H)==
-The line below this paragraph, containing "STRUCTURE_3glb", creates the "Structure Box" on the page.
+<StructureSection load='3glb' size='340' side='right'caption='[[3glb]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3glb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baylyi_ADP1 Acinetobacter baylyi ADP1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2h9q 2h9q]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GLB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GLB FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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=CCU:(2Z,4Z)-HEXA-2,4-DIENEDIOIC+ACID'>CCU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3glb|  PDB=3glb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3glb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3glb OCA], [https://pdbe.org/3glb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3glb RCSB], [https://www.ebi.ac.uk/pdbsum/3glb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3glb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CATM_ACIAD CATM_ACIAD] Positively regulates the expression of catA, catBCIJFD and benPK in response to cis,cis-muconate. It binds to the catB-catM intercistronic region, to a specific sequence upstream of catA and to the benPK promoter region. Can also repress pca genes.<ref>PMID:7592340</ref> <ref>PMID:11932465</ref> <ref>PMID:12620848</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/gl/3glb_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=3glb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BenM and CatM control transcription of a complex regulon for aromatic compound degradation. These Acinetobacter baylyi paralogues belong to the largest family of prokaryotic transcriptional regulators, the LysR-type proteins. Whereas BenM activates transcription synergistically in response to two effectors, benzoate and cis,cis-muconate, CatM responds only to cis,cis-muconate. Here, site-directed mutagenesis was used to determine the physiological significance of an unexpected benzoate-binding pocket in BenM discovered during structural studies. Residues in BenM were changed to match those of CatM in this hydrophobic pocket. Two BenM residues, R160 and Y293, were found to mediate the response to benzoate. Additionally, alteration of these residues caused benzoate to inhibit activation by cis,cis-muconate, positioned in a separate primary effector-binding site of BenM. The location of the primary site, in an interdomain cleft, is conserved in diverse LysR-type regulators. To improve understanding of this important family, additional regulatory mutants were analysed. The atomic-level structures were characterized of the effector-binding domains of variants that do not require inducers for activation, CatM(R156H) and BenM(R156H,T157S). These structures clearly resemble those of the wild-type proteins in their activated muconate-bound complexes. Amino acid replacements that enable activation without effectors reside at protein interfaces that may impact transcription through effects on oligomerization.
-===Crystal structure of the effector binding domain of a CATM variant (R156H)===
+Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1.,Craven SH, Ezezika OC, Haddad S, Hall RA, Momany C, Neidle EL Mol Microbiol. 2009 May;72(4):881-94. Epub 2009 Apr 8. PMID:19400783<ref>PMID:19400783</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3glb" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19400783}}, adds the Publication Abstract to the page
+*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19400783 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19400783}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Acinetobacter baylyi ADP1]]
-GLB is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Acinetobacter_sp. Acinetobacter sp.]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2h9q 2h9q]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GLB OCA].
+[[Category: Large Structures]]
+[[Category: Craven SH]]
-==Reference==
+[[Category: Ezezika OC]]
-<ref group="xtra">PMID:19400783</ref><references group="xtra"/>
+[[Category: Momany C]]
-[[Category: Acinetobacter sp.]]
+[[Category: Neidle EL]]
-[[Category: Craven, S H.]]
-[[Category: Ezezika, O C.]]
-[[Category: Momany, C.]]
-[[Category: Neidle, E L.]]
-[[Category: Activator]]
-[[Category: Aromatic hydrocarbons catabolism]]
-[[Category: Benm]]
-[[Category: Catm]]
-[[Category: Dna-binding]]
-[[Category: Lttr]]
-[[Category: Lysr-type transcriptional regulator]]
-[[Category: Repressor]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Transcriptional activator]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 20 16:53:04 2009''