2vlf: Difference between revisions

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-[[Image:2vlf.png|left|200px]]
-<!--
+==Quinonoid intermediate of Citrobacter freundii tyrosine phenol-lyase formed with alanine==
-The line below this paragraph, containing "STRUCTURE_2vlf", creates the "Structure Box" on the page.
+<StructureSection load='2vlf' size='340' side='right'caption='[[2vlf]], [[Resolution|resolution]] 1.89&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'>[[2vlf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VLF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VLF 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]] 1.89&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=P33:3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL'>P33</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLI:(2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}PROPANOIC+ACID'>PLI</scene></td></tr>
-{{STRUCTURE_2vlf|  PDB=2vlf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vlf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vlf OCA], [https://pdbe.org/2vlf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vlf RCSB], [https://www.ebi.ac.uk/pdbsum/2vlf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vlf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TPL_CITFR TPL_CITFR]
+== 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/vl/2vlf_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=2vlf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Amino acid transformations catalyzed by a number of pyridoxal 5'-phosphate (PLP)-dependent enzymes involve abstraction of the Calpha proton from an external aldimine formed between a substrate and the cofactor leading to the formation of a quinonoid intermediate. Despite the key role played by the quinonoid intermediates in the catalysis by PLP-dependent enzymes, limited accurate information is available about their structures. We trapped the quinonoid intermediates of Citrobacter freundii tyrosine phenol-lyase with L-alanine and L-methionine in the crystalline state and determined their structures at 1.9- and 1.95-A resolution, respectively, by cryo-crystallography. The data reveal a network of protein-PLP-substrate interactions that stabilize the planar geometry of the quinonoid intermediate. In both structures the protein subunits are found in two conformations, open and closed, uncovering the mechanism by which binding of the substrate and restructuring of the active site during its closure protect the quinonoid intermediate from the solvent and bring catalytically important residues into positions suitable for the abstraction of phenol during the beta-elimination of L-tyrosine. In addition, the structural data indicate a mechanism for alanine racemization involving two bases, Lys-257 and a water molecule. These two bases are connected by a hydrogen bonding system allowing internal transfer of the Calpha proton.
-===QUINONOID INTERMEDIATE OF CITROBACTER FREUNDII TYROSINE PHENOL-LYASE FORMED WITH ALANINE===
+Insights into the catalytic mechanism of tyrosine phenol-lyase from X-ray structures of quinonoid intermediates.,Milic D, Demidkina TV, Faleev NG, Matkovic-Calogovic D, Antson AA J Biol Chem. 2008 Oct 24;283(43):29206-14. Epub 2008 Aug 20. PMID:18715865<ref>PMID:18715865</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2vlf" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18715865}}, adds the Publication Abstract to the page
+*[[Tyrosinase 3D structures|Tyrosinase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18715865 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18715865}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[2vlf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VLF OCA].
-==Reference==
-<ref group="xtra">PMID:018715865</ref><references group="xtra"/>
 [[Category: Citrobacter freundii]]
-[[Category: Tyrosine phenol-lyase]]
+[[Category: Large Structures]]
-[[Category: Antson, A A.]]
+[[Category: Antson AA]]
-[[Category: Demidkina, T V.]]
+[[Category: Demidkina TV]]
-[[Category: Matkovic-Calogovic, D.]]
+[[Category: Matkovic-Calogovic D]]
-[[Category: Milic, D.]]
+[[Category: Milic D]]
-[[Category: Lyase]]
-[[Category: Plp-dependent enzyme]]
-[[Category: Tyrosine degradation]]