1mjm: Difference between revisions

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-[[Image:1mjm.gif|left|200px]]
- {{Structure
+==METHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO HALF OF THE CONSENSUS OPERATOR SEQUENCE==
-|PDB= 1mjm |SIZE=350|CAPTION= <scene name='initialview01'>1mjm</scene>, resolution 2.20&Aring;
+<StructureSection load='1mjm' size='340' side='right'caption='[[1mjm]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
+<table><tr><td colspan='2'>[[1mjm]] 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=1MJM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MJM FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-|GENE= METJ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mjm OCA], [https://pdbe.org/1mjm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mjm RCSB], [https://www.ebi.ac.uk/pdbsum/1mjm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mjm ProSAT]</span></td></tr>
-|DOMAIN=
+</table>
-|RELATEDENTRY=[[1mj2|1MJ2]], [[1mjo|1MJO]], [[1mjp|1MJP]], [[1mjq|1MJQ]]
+== Function ==
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1mjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mjm OCA], [http://www.ebi.ac.uk/pdbsum/1mjm PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1mjm RCSB]</span>
+[https://www.uniprot.org/uniprot/METJ_ECOLI METJ_ECOLI] This regulatory protein, when combined with SAM (S-adenosylmethionine) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated.[HAMAP-Rule:MF_00744]
-}}
+== 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/mj/1mjm_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=1mjm ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: The methionine repressor, MetJ, represses the transcription of genes involved in methionine biosynthesis by binding to arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. Naturally occurring operators differ from the consensus sequence to a greater extent as the number of metboxes increases. MetJ, while accommodating this sequence variation in natural operators, is very sensitive to particular base changes, even where bases are not directly contacted in the crystal structure of a complex formed between the repressor and consensus operator. RESULTS: Here we report the high-resolution structure of a MetJ mutant, Q44K, bound to the consensus operator sequence (Q44Kwt19) and two related sequences containing mutations at sites believed to be important for indirect readout at non-contacted bases. The overall structure of the Q44Kwt19 complex is very similar to the wild-type complex, but there are small variations in sugar-phosphate backbone conformation and direct contacts to the DNA bases. The mutant complexes show a mixture of direct and indirect readout of sequence variations, with differences in direct contacts and DNA conformation. CONCLUSIONS: Comparison of the wild-type and mutant repressor-operator complexes shows that the repressor makes sufficiently strong interactions with the sugar-phosphate backbone to accommodate some variation in operator sequence with minor changes in direct bases contacts. The reduction in repressor affinity for the two mutant repressor complexes can be partially attributed to a loss in direct contacts to the DNA. In one case, however, the replacement of a flexible TA base-step leads to an unfavourable DNA conformation that reduces the stability of the repressor-operator complex.
-'''METHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO HALF OF THE CONSENSUS OPERATOR SEQUENCE'''
+Direct and indirect readout in mutant Met repressor-operator complexes.,Garvie CW, Phillips SE Structure. 2000 Sep 15;8(9):905-14. PMID:10986458<ref>PMID:10986458</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1mjm" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-BACKGROUND: The methionine repressor, MetJ, represses the transcription of genes involved in methionine biosynthesis by binding to arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. Naturally occurring operators differ from the consensus sequence to a greater extent as the number of metboxes increases. MetJ, while accommodating this sequence variation in natural operators, is very sensitive to particular base changes, even where bases are not directly contacted in the crystal structure of a complex formed between the repressor and consensus operator. RESULTS: Here we report the high-resolution structure of a MetJ mutant, Q44K, bound to the consensus operator sequence (Q44Kwt19) and two related sequences containing mutations at sites believed to be important for indirect readout at non-contacted bases. The overall structure of the Q44Kwt19 complex is very similar to the wild-type complex, but there are small variations in sugar-phosphate backbone conformation and direct contacts to the DNA bases. The mutant complexes show a mixture of direct and indirect readout of sequence variations, with differences in direct contacts and DNA conformation. CONCLUSIONS: Comparison of the wild-type and mutant repressor-operator complexes shows that the repressor makes sufficiently strong interactions with the sugar-phosphate backbone to accommodate some variation in operator sequence with minor changes in direct bases contacts. The reduction in repressor affinity for the two mutant repressor complexes can be partially attributed to a loss in direct contacts to the DNA. In one case, however, the replacement of a flexible TA base-step leads to an unfavourable DNA conformation that reduces the stability of the repressor-operator complex.
+*[[Met repressor|Met repressor]]
+== References ==
-==About this Structure==
+<references/>
-MJM is a [[Single protein]] structure of 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=1MJM OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Direct and indirect readout in mutant Met repressor-operator complexes., Garvie CW, Phillips SE, Structure. 2000 Sep 15;8(9):905-14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10986458 10986458]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Garvie, C W.]]
+[[Category: Garvie CW]]
-[[Category: Phillips, S E.V.]]
+[[Category: Phillips SEV]]
-[[Category: complex (transcription regulation/dna)]]
-[[Category: dna]]
-[[Category: methionine repressor]]
-[[Category: metj]]
-[[Category: s-adenosyl methionine]]
-[[Category: sheet-helix-helix]]
-[[Category: transcription regulation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:16:52 2008''