2ycp: Difference between revisions
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==F448H mutant of tyrosine phenol-lyase from Citrobacter freundii in complex with quinonoid intermediate formed with 3-fluoro-L-tyrosine== | |||
<StructureSection load='2ycp' size='340' side='right'caption='[[2ycp]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2ycp]] is a 4 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=2YCP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YCP FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <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=P61:(2E)-3-(3-FLUORO-4-HYDROXYPHENYL)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}PROPANOIC+ACID'>P61</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=2ycp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ycp OCA], [https://pdbe.org/2ycp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ycp RCSB], [https://www.ebi.ac.uk/pdbsum/2ycp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ycp ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/TPL_CITFR TPL_CITFR] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The key step in the enzymatic reaction catalyzed by tyrosine phenol-lyase (TPL) is reversible cleavage of the Cbeta-Cgamma bond of l-tyrosine. Here, we present X-ray structures for two enzymatic states that form just before and after the cleavage of the carbon-carbon bond. As for most other pyridoxal 5'-phosphate-dependent enzymes, the first state, a quinonoid intermediate, is central for the catalysis. We captured this relatively unstable intermediate in the crystalline state by introducing substitutions Y71F or F448H in Citrobacter freundii TPL and briefly soaking crystals of the mutant enzymes with a substrate 3-fluoro-l-tyrosine followed by flash-cooling. The X-ray structures, determined at approximately 2.0 A resolution, reveal two quinonoid geometries: "relaxed" in the open and "tense" in the closed state of the active site. The "tense" state is characterized by changes in enzyme contacts made with the substrate's phenolic moiety, which result in significantly strained conformation at Cbeta and Cgamma positions. We also captured, at 2.25 A resolution, the X-ray structure for the state just after the substrate's Cbeta-Cgamma bond cleavage by preparing the ternary complex between TPL, alanine quinonoid and pyridine N-oxide, which mimics the alpha-aminoacrylate intermediate with bound phenol. In this state, the enzyme-ligand contacts remain almost exactly the same as in the "tense" quinonoid, indicating that the strain induced by the closure of the active site facilitates elimination of phenol. Taken together, structural observations demonstrate that the enzyme serves not only to stabilize the transition state but also to destabilize the ground state. | |||
Crystallographic Snapshots of Tyrosine Phenol-lyase Show That Substrate Strain Plays a Role in C-C Bond Cleavage.,Milic D, Demidkina TV, Faleev NG, Phillips RS, Matkovic-Calogovic D, Antson AA J Am Chem Soc. 2011 Oct 19;133(41):16468-76. Epub 2011 Sep 27. PMID:21899319<ref>PMID:21899319</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2ycp" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Tyrosinase 3D structures|Tyrosinase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Citrobacter freundii]] | |||
[[Category: Large Structures]] | |||
[[Category: Antson AA]] | |||
[[Category: Demidkina TV]] | |||
[[Category: Faleev NG]] | |||
[[Category: Matkovic-Calogovic D]] | |||
[[Category: Milic D]] | |||
[[Category: Phillips RS]] | |||
Latest revision as of 11:12, 23 August 2023
F448H mutant of tyrosine phenol-lyase from Citrobacter freundii in complex with quinonoid intermediate formed with 3-fluoro-L-tyrosineF448H mutant of tyrosine phenol-lyase from Citrobacter freundii in complex with quinonoid intermediate formed with 3-fluoro-L-tyrosine
Structural highlights
FunctionPublication Abstract from PubMedThe key step in the enzymatic reaction catalyzed by tyrosine phenol-lyase (TPL) is reversible cleavage of the Cbeta-Cgamma bond of l-tyrosine. Here, we present X-ray structures for two enzymatic states that form just before and after the cleavage of the carbon-carbon bond. As for most other pyridoxal 5'-phosphate-dependent enzymes, the first state, a quinonoid intermediate, is central for the catalysis. We captured this relatively unstable intermediate in the crystalline state by introducing substitutions Y71F or F448H in Citrobacter freundii TPL and briefly soaking crystals of the mutant enzymes with a substrate 3-fluoro-l-tyrosine followed by flash-cooling. The X-ray structures, determined at approximately 2.0 A resolution, reveal two quinonoid geometries: "relaxed" in the open and "tense" in the closed state of the active site. The "tense" state is characterized by changes in enzyme contacts made with the substrate's phenolic moiety, which result in significantly strained conformation at Cbeta and Cgamma positions. We also captured, at 2.25 A resolution, the X-ray structure for the state just after the substrate's Cbeta-Cgamma bond cleavage by preparing the ternary complex between TPL, alanine quinonoid and pyridine N-oxide, which mimics the alpha-aminoacrylate intermediate with bound phenol. In this state, the enzyme-ligand contacts remain almost exactly the same as in the "tense" quinonoid, indicating that the strain induced by the closure of the active site facilitates elimination of phenol. Taken together, structural observations demonstrate that the enzyme serves not only to stabilize the transition state but also to destabilize the ground state. Crystallographic Snapshots of Tyrosine Phenol-lyase Show That Substrate Strain Plays a Role in C-C Bond Cleavage.,Milic D, Demidkina TV, Faleev NG, Phillips RS, Matkovic-Calogovic D, Antson AA J Am Chem Soc. 2011 Oct 19;133(41):16468-76. Epub 2011 Sep 27. PMID:21899319[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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