3bhf: Difference between revisions

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-{{Seed}}
-[[Image:3bhf.png|left|200px]]
-<!--
+==Crystal structure of R49K mutant of Monomeric Sarcosine Oxidase crystallized in PEG as precipitant==
-The line below this paragraph, containing "STRUCTURE_3bhf", creates the "Structure Box" on the page.
+<StructureSection load='3bhf' size='340' side='right'caption='[[3bhf]], [[Resolution|resolution]] 2.10&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'>[[3bhf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._(in:_Bacteria) Bacillus sp. (in: Bacteria)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BHF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BHF 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]] 2.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-{{STRUCTURE_3bhf|  PDB=3bhf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bhf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bhf OCA], [https://pdbe.org/3bhf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bhf RCSB], [https://www.ebi.ac.uk/pdbsum/3bhf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bhf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MSOX_BACB0 MSOX_BACB0] Catalyzes the oxidative demethylation of sarcosine. Can also oxidize other secondary amino acids such as N-methyl-L-alanine.[HAMAP-Rule:MF_00516]
+== 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/bh/3bhf_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3bhf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Monomeric sarcosine oxidase (MSOX) contains covalently bound FAD and catalyzes the oxidative demethylation of sarcosine ( N-methylglycine). The side chain of Arg49 is in van der Waals contact with the si face of the flavin ring; sarcosine binds just above the re face. Covalent flavin attachment requires a basic residue (Arg or Lys) at position 49. Although flavinylation is scarcely affected, mutation of Arg49 to Lys causes a 40-fold decrease in k cat and a 150-fold decrease in k cat/ K m sarcosine. The overall structure of the Arg49Lys mutant is very similar to wild-type MSOX; the side chain of Lys49 in the mutant is nearly congruent to that of Arg49 in the wild-type enzyme. The Arg49Lys mutant exhibits several features consistent with a less electropositive active site: (1) Charge transfer bands observed for mutant enzyme complexes with competitive inhibitors absorb at higher energy than the corresponding wild-type complexes. (2) The p K a for ionization at N(3)H of FAD is more than two pH units higher in the mutant than in wild-type MSOX. (3) The reduction potential of the oxidized/radical couple in the mutant is 100 mV lower than in the wild-type enzyme. The lower reduction potential is likely to be a major cause of the reduced catalytic activity of the mutant. Electrostatic interactions with Arg49 play an important role in catalysis and covalent flavinylation. A context-sensitive model for the electrostatic impact of an arginine to lysine mutation can account for the dramatically different consequences of the Arg49Lys mutation on MSOX catalysis and holoenzyme biosysnthesis.
-===Crystal structure of R49K mutant of Monomeric Sarcosine Oxidase crystallized in PEG as precipitant===
+Arginine 49 Is a Bifunctional Residue Important in Catalysis and Biosynthesis of Monomeric Sarcosine Oxidase: A Context-Sensitive Model for the Electrostatic Impact of Arginine to Lysine Mutations(,).,Hassan-Abdallah A, Zhao G, Chen ZW, Mathews FS, Schuman Jorns M Biochemistry. 2008 Feb 6;. PMID:18251505<ref>PMID:18251505</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3bhf" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18251505}}, adds the Publication Abstract to the page
+*[[Sarcosine oxidase|Sarcosine oxidase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18251505 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18251505}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-BHF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BHF OCA].
+[[Category: Chen Z]]
+[[Category: Hassan-Abdallah A]]
-==Reference==
+[[Category: Jorns MS]]
-Arginine 49 Is a Bifunctional Residue Important in Catalysis and Biosynthesis of Monomeric Sarcosine Oxidase: A Context-Sensitive Model for the Electrostatic Impact of Arginine to Lysine Mutations(,)., Hassan-Abdallah A, Zhao G, Chen ZW, Mathews FS, Schuman Jorns M, Biochemistry. 2008 Feb 6;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18251505 18251505]
+[[Category: Mathews FS]]
+[[Category: Zhao G]]
-Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme., Trickey P, Wagner MA, Jorns MS, Mathews FS, Structure. 1999 Mar 15;7(3):331-45. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10368302 10368302]
-[[Category: Bacillus sp.]]
-[[Category: Sarcosine oxidase]]
-[[Category: Single protein]]
-[[Category: Chen, Z.]]
-[[Category: Hassan-Abdallah, A.]]
-[[Category: Jorns, M S.]]
-[[Category: Mathews, F S.]]
-[[Category: Zhao, G.]]
-[[Category: Cytoplasm]]
-[[Category: Fad]]
-[[Category: Flavoprotein oxidase]]
-[[Category: Oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 05:02:31 2008''