6ogm: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 6ogm is ~~ON HOLD until Paper~~ Publication

==Crystal structure of apo unFused 4-OT==

== Structural highlights ==

<table><tr><td colspan='2'>[[6ogm]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_lata Burkholderia lata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OGM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OGM 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]] 1.865Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6ogm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ogm OCA], [https://pdbe.org/6ogm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ogm RCSB], [https://www.ebi.ac.uk/pdbsum/6ogm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ogm ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/Q392K7_BURL3 Q392K7_BURL3]

== Publication Abstract from PubMed ==

A 4-oxalocrotonate tautomerase (4-OT) trimer has been isolated from Burkholderia lata, and a kinetic, mechanistic, and structural analysis has been performed. The enzyme is the third described oligomer state for 4-OT along with a homo- and heterohexamer. The 4-OT trimer is part of a small subset of sequences (133 sequences) within the 4-OT subgroup of the tautomerase superfamily (TSF). The TSF has two distinct features: members are composed of a single beta-alpha-beta unit (homo- and heterohexamer) or two consecutively joined beta-alpha-beta units (trimer) and generally have a catalytic amino-terminal proline. The enzyme, designated as fused 4-OT, functions as a 4-OT where the active site groups (Pro-1, Arg-39, Arg-76, Phe-115, Arg-127) mirror those in the canonical 4-OT from Pseudomonas putida mt-2. Inactivation by 2-oxo-3-pentynoate suggests that Pro-1 of fused 4-OT has a low p Ka enabling the prolyl nitrogen to function as a general base. A remarkable feature of the fused 4-OT is the absence of P3 rotational symmetry in the structure (1.5 A resolution). The asymmetric arrangement of the trimer is not due to the fusion of the two beta-alpha-beta building blocks because an engineered "unfused" variant that breaks the covalent bond between the two units (to generate a heterohexamer) assumes the same asymmetric oligomerization state. It remains unknown how the different active site configurations contribute to the observed overall activities and whether the asymmetry has a biological purpose or role in the evolution of TSF members.

~~Authors~~:

Structural, Kinetic, and Mechanistic Analysis of an Asymmetric 4-Oxalocrotonate Tautomerase Trimer.,Baas BJ, Medellin BP, LeVieux JA, de Ruijter M, Zhang YJ, Brown SD, Akiva E, Babbitt PC, Whitman CP Biochemistry. 2019 Jun 4;58(22):2617-2627. doi: 10.1021/acs.biochem.9b00303. Epub, 2019 May 23. PMID:31074977<ref>PMID:31074977</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Burkholderia lata]]

[[Category: Large Structures]]

[[Category: Medellin BP]]

[[Category: Whitman CP]]

[[Category: Zhang YJ]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6ogm is ON HOLD  until Paper Publication
+==Crystal structure of apo unFused 4-OT==
+<StructureSection load='6ogm' size='340' side='right'caption='[[6ogm]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6ogm]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_lata Burkholderia lata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OGM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OGM 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]] 1.865&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6ogm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ogm OCA], [https://pdbe.org/6ogm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ogm RCSB], [https://www.ebi.ac.uk/pdbsum/6ogm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ogm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q392K7_BURL3 Q392K7_BURL3]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A 4-oxalocrotonate tautomerase (4-OT) trimer has been isolated from Burkholderia lata, and a kinetic, mechanistic, and structural analysis has been performed. The enzyme is the third described oligomer state for 4-OT along with a homo- and heterohexamer. The 4-OT trimer is part of a small subset of sequences (133 sequences) within the 4-OT subgroup of the tautomerase superfamily (TSF). The TSF has two distinct features: members are composed of a single beta-alpha-beta unit (homo- and heterohexamer) or two consecutively joined beta-alpha-beta units (trimer) and generally have a catalytic amino-terminal proline. The enzyme, designated as fused 4-OT, functions as a 4-OT where the active site groups (Pro-1, Arg-39, Arg-76, Phe-115, Arg-127) mirror those in the canonical 4-OT from Pseudomonas putida mt-2. Inactivation by 2-oxo-3-pentynoate suggests that Pro-1 of fused 4-OT has a low p Ka enabling the prolyl nitrogen to function as a general base. A remarkable feature of the fused 4-OT is the absence of P3 rotational symmetry in the structure (1.5 A resolution). The asymmetric arrangement of the trimer is not due to the fusion of the two beta-alpha-beta building blocks because an engineered "unfused" variant that breaks the covalent bond between the two units (to generate a heterohexamer) assumes the same asymmetric oligomerization state. It remains unknown how the different active site configurations contribute to the observed overall activities and whether the asymmetry has a biological purpose or role in the evolution of TSF members.
-Authors:
+Structural, Kinetic, and Mechanistic Analysis of an Asymmetric 4-Oxalocrotonate Tautomerase Trimer.,Baas BJ, Medellin BP, LeVieux JA, de Ruijter M, Zhang YJ, Brown SD, Akiva E, Babbitt PC, Whitman CP Biochemistry. 2019 Jun 4;58(22):2617-2627. doi: 10.1021/acs.biochem.9b00303. Epub, 2019 May 23. PMID:31074977<ref>PMID:31074977</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6ogm" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Burkholderia lata]]
+[[Category: Large Structures]]
+[[Category: Medellin BP]]
+[[Category: Whitman CP]]
+[[Category: Zhang YJ]]