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| | <StructureSection load='4wkm' size='340' side='right'caption='[[4wkm]], [[Resolution|resolution]] 2.15Å' scene=''> | | <StructureSection load='4wkm' size='340' side='right'caption='[[4wkm]], [[Resolution|resolution]] 2.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4wkm]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Citrobacter_freundii_atcc_8090 Citrobacter freundii atcc 8090]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WKM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4wkm]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrobacter_freundii_ATCC_8090_=_MTCC_1658_=_NBRC_12681 Citrobacter freundii ATCC 8090 = MTCC 1658 = NBRC 12681]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WKM FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MUB:N-ACETYLMURAMIC+ACID'>MUB</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MUB:N-ACETYLMURAMIC+ACID'>MUB</scene></td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</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=4wkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wkm OCA], [https://pdbe.org/4wkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wkm RCSB], [https://www.ebi.ac.uk/pdbsum/4wkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wkm ProSAT]</span></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kos|3kos]], [[3kot|3kot]]</td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">D186_13659 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1006003 Citrobacter freundii ATCC 8090])</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=4wkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wkm OCA], [http://pdbe.org/4wkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wkm RCSB], [http://www.ebi.ac.uk/pdbsum/4wkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wkm ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | ==See Also== | | ==See Also== |
| - | *[[Transcriptional activator|Transcriptional activator]] | + | *[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Citrobacter freundii atcc 8090]] | + | [[Category: Citrobacter freundii ATCC 8090 = MTCC 1658 = NBRC 12681]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Mark, B L]] | + | [[Category: Mark BL]] |
| - | [[Category: Reeve, T M]] | + | [[Category: Reeve TM]] |
| - | [[Category: Vadlamani, G]] | + | [[Category: Vadlamani G]] |
| - | [[Category: Lttr]]
| + | |
| - | [[Category: Lysr-type transcriptional regulator]]
| + | |
| - | [[Category: Transcription]]
| + | |
| - | [[Category: Udp-murnac-pentapeptide]]
| + | |
| Structural highlights
Publication Abstract from PubMed
Inducible expression of chromosomal AmpC beta-lactamase is a major cause of beta-lactam antibiotic resistance in the Gram negative bacteria Pseudomonas aeruginosa and Enterobacteriaceae. AmpC expression is induced by the LysR-type transcriptional regulator (LTTR) AmpR, which activates ampC expression in response to changes in peptidoglycan (PG) metabolite levels that occur during exposure to beta-lactams. Under normal conditions, AmpR represses ampC transcription by binding the PG precursor UDP-MurNAc-pentapeptide. When exposed to beta-lactams however, PG catabolites (1,6-anhydroMurNAc-peptides) accumulate in the cytosol, which have been proposed to competitively displace UDP-MurNAcpentapeptide from AmpR and convert it into an activator of ampC transcription. Here we describe the molecular interactions between AmpR (from Citrobacter freundii), its DNA operator, and repressor UDP-MurNAcpentapeptide. Non-denaturing mass spectrometry revealed AmpR to be a homotetramer that is stabilized by DNA containing the T-N11-A LTTR binding motif, and that it can bind four repressor molecules in an apparently stepwise manner. A crystal structure of the AmpR effector-binding domain bound to UDP-MurNAc-pentapeptide revealed that the terminal D-Ala-D-Ala motif of the repressor forms the primary contacts with the protein. This observation supports previous claims that 1,6-anhydro-MurNAc-pentapeptide converts AmpR into an activator of ampC transcription more effectively than 1,6-anhydro-MurNAc-tripeptide (which lacks the D-Ala-D-Ala motif). Finally, small angle X-ray scattering demonstrates that the AmpR-DNA complex adopts a flat conformation similar to the LTTR protein AphB and undergoes only a slight conformational change when binding UDP-MurNAc-pentapeptide. Modeling the AmpR:DNA tetramer bound to UDP-MurNAcpentapeptide predicts that the UDP-MurNAc moiety of the repressor participates in modulating AmpR function.
The beta-lactamase Gene Regulator AmpR is a Tetramer that Recognizes and Binds the D-Ala-D-Ala Motif of its Repressor UDP-MurNAc-pentapeptide.,Vadlamani G, Thomas MD, Patel TR, Donald LJ, Reeve TM, Stetefeld J, Standing KG, Vocadlo DJ, Mark BL J Biol Chem. 2014 Dec 5. pii: jbc.M114.618199. PMID:25480792[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Vadlamani G, Thomas MD, Patel TR, Donald LJ, Reeve TM, Stetefeld J, Standing KG, Vocadlo DJ, Mark BL. The beta-lactamase Gene Regulator AmpR is a Tetramer that Recognizes and Binds the D-Ala-D-Ala Motif of its Repressor UDP-MurNAc-pentapeptide. J Biol Chem. 2014 Dec 5. pii: jbc.M114.618199. PMID:25480792 doi:http://dx.doi.org/10.1074/jbc.M114.618199
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