|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal structure of the effector binding domain of a CATM variant (R156H)== | | ==Crystal structure of the effector binding domain of a CATM variant (R156H)== |
| - | <StructureSection load='3glb' size='340' side='right' caption='[[3glb]], [[Resolution|resolution]] 2.80Å' scene=''> | + | <StructureSection load='3glb' size='340' side='right'caption='[[3glb]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3glb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aciad Aciad]. 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]] 2.8Å</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=62977 ACIAD])</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://pdbe.org/3glb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3glb RCSB], [http://www.ebi.ac.uk/pdbsum/3glb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3glb ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <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> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| Line 30: |
Line 29: |
| | </div> | | </div> |
| | <div class="pdbe-citations 3glb" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 3glb" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aciad]] | + | [[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]]
| + | |
| Structural highlights
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.
See Also
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
|
