This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3glb

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of the effector binding domain of a CATM variant (R156H)

Structural highlights

3glb is a 4 chain structure with sequence from Acinetobacter baylyi ADP1. This structure supersedes the now removed PDB entry 2h9q. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[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

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.

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^[4]

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

References

↑ Romero-Arroyo CE, Schell MA, Gaines GL 3rd, Neidle EL. catM encodes a LysR-type transcriptional activator regulating catechol degradation in Acinetobacter calcoaceticus. J Bacteriol. 1995 Oct;177(20):5891-8. PMID:7592340
↑ Clark TJ, Momany C, Neidle EL. The benPK operon, proposed to play a role in transport, is part of a regulon for benzoate catabolism in Acinetobacter sp. strain ADP1. Microbiology. 2002 Apr;148(Pt 4):1213-23. PMID:11932465
↑ Brzostowicz PC, Reams AB, Clark TJ, Neidle EL. Transcriptional cross-regulation of the catechol and protocatechuate branches of the beta-ketoadipate pathway contributes to carbon source-dependent expression of the Acinetobacter sp. strain ADP1 pobA gene. Appl Environ Microbiol. 2003 Mar;69(3):1598-606. PMID:12620848
↑ Craven SH, Ezezika OC, Haddad S, Hall RA, Momany C, Neidle EL. Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1. Mol Microbiol. 2009 May;72(4):881-94. Epub 2009 Apr 8. PMID:19400783 doi:10.1111/j.1365-2958.2009.06686.x

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/3glb"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the effector binding domain of a CATM variant (R156H)==
-<StructureSection load='3glb' size='340' side='right' caption='[[3glb]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='3glb' size='340' side='right'caption='[[3glb]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3glb]] is a 4 chain structure with sequence 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GLB FirstGlance]. <br>
+<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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2h9b|2h9b]], [[2h98|2h98]], [[2f7b|2f7b]], [[2h99|2h99]], [[2f7a|2f7a]], [[2f7c|2f7c]]</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>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">catM, catR, ACIAD1445 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=472 Acinetobacter sp.])</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=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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3glb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3glb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3glb RCSB], [http://www.ebi.ac.uk/pdbsum/3glb PDBsum]</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>
+    <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/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=3glb ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 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==
+*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Acinetobacter sp.]]
+[[Category: Acinetobacter baylyi ADP1]]
-[[Category: Craven, S H.]]
+[[Category: Large Structures]]
-[[Category: Ezezika, O C.]]
+[[Category: Craven SH]]
-[[Category: Momany, C.]]
+[[Category: Ezezika OC]]
-[[Category: Neidle, E L.]]
+[[Category: Momany C]]
-[[Category: Activator]]
+[[Category: Neidle EL]]
-[[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]]

3glb

From Proteopedia

Current revision

Crystal structure of the effector binding domain of a CATM variant (R156H)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox