4ytt: Difference between revisions

Line 1:

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

~~The entry~~ 4ytt is ~~ON HOLD until Paper~~ Publication

==Crystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with 6-deoxy L-psicose==

== Structural highlights ==

<table><tr><td colspan='2'>[[4ytt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YTT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YTT FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PUD:6-DEOXY-L-PSICOSE'>PUD</scene>, <scene name='pdbligand=PUF:6-DEOXY-ALPHA-L-PSICOFURANOSE'>PUF</scene></td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ytt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ytt OCA], [http://pdbe.org/4ytt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ytt RCSB], [http://www.ebi.ac.uk/pdbsum/4ytt PDBsum]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Pseudomonas cichoriiid-tagatose 3-epimerase (P. cichoriid-TE) can efficiently catalyze the epimerization of not only d-tagatose to d-sorbose, but also d-fructose to d-psicose, and is used for the production of d-psicose from d-fructose. The crystal structures of P. cichoriid-TE alone and in complexes with d-tagatose and d-fructose were determined at resolutions of 1.79, 2.28, and 2.06 A, respectively. A subunit of P. cichoriid-TE adopts a (beta/alpha)(8) barrel structure, and a metal ion (Mn(2+)) found in the active site is coordinated by Glu152, Asp185, His211, and Glu246 at the end of the beta-barrel. P. cichoriid-TE forms a stable dimer to give a favorable accessible surface for substrate binding on the front side of the dimer. The simulated omit map indicates that O2 and O3 of d-tagatose and/or d-fructose coordinate Mn(2+), and that C3-O3 is located between carboxyl groups of Glu152 and Glu246, supporting the previously proposed mechanism of deprotonation/protonation at C3 by two Glu residues. Although the electron density is poor at the 4-, 5-, and 6-positions of the substrates, substrate-enzyme interactions can be deduced from the significant electron density at O6. The O6 possibly interacts with Cys66 via hydrogen bonding, whereas O4 and O5 in d-tagatose and O4 in d-fructose do not undergo hydrogen bonding to the enzyme and are in a hydrophobic environment created by Phe7, Trp15, Trp113, and Phe248. Due to the lack of specific interactions between the enzyme and its substrates at the 4- and 5-positions, P. cichoriid-TE loosely recognizes substrates in this region, allowing it to efficiently catalyze the epimerization of d-tagatose and d-fructose (C4 epimer of d-tagatose) as well. Furthermore, a C3-O3 proton-exchange mechanism for P. cichoriid-TE is suggested by X-ray structural analysis, providing a clear explanation for the regulation of the ionization state of Glu152 and Glu246.

~~Authors:~~ Yoshida, H., ~~Yoshihara~~, ~~A., Ishii~~, T., Izumori, K., Kamitori, S.

Crystal structures of D-tagatose 3-epimerase from Pseudomonas cichorii and its complexes with D-tagatose and D-fructose.,Yoshida H, Yamada M, Nishitani T, Takada G, Izumori K, Kamitori S J Mol Biol. 2007 Nov 23;374(2):443-53. Epub 2007 Sep 19. PMID:17936787<ref>PMID:17936787</ref>

~~Description: Crystal structure~~ of D-~~tagatose 3~~-~~epimerase C66S from Pseudomonas cichorii in complex with 6-deoxy L-psicose~~

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

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

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Ishii, T]]

[[Category: Izumori, K]]

[[Category: Kamitori, S]]

[[Category: Yoshida, H]]

[[Category: Yoshihara, A]]

[[Category: ~~Yoshida, H~~]]

[[Category: Epimerase]]

[[Category: ~~Kamitori, S]]~~

[[Category: Isomerase]]

~~[[Category: Izumori, K~~]]

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 4ytt is ON HOLD  until Paper Publication
+==Crystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with 6-deoxy L-psicose==
+<StructureSection load='4ytt' size='340' side='right' caption='[[4ytt]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4ytt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YTT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YTT FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PUD:6-DEOXY-L-PSICOSE'>PUD</scene>, <scene name='pdbligand=PUF:6-DEOXY-ALPHA-L-PSICOFURANOSE'>PUF</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xsl|4xsl]], [[4xsm|4xsm]], [[4ytq|4ytq]], [[4ytr|4ytr]], [[4yts|4yts]], [[4ytu|4ytu]], [[4yvl|4yvl]]</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ytt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ytt OCA], [http://pdbe.org/4ytt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ytt RCSB], [http://www.ebi.ac.uk/pdbsum/4ytt PDBsum]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Pseudomonas cichoriiid-tagatose 3-epimerase (P. cichoriid-TE) can efficiently catalyze the epimerization of not only d-tagatose to d-sorbose, but also d-fructose to d-psicose, and is used for the production of d-psicose from d-fructose. The crystal structures of P. cichoriid-TE alone and in complexes with d-tagatose and d-fructose were determined at resolutions of 1.79, 2.28, and 2.06 A, respectively. A subunit of P. cichoriid-TE adopts a (beta/alpha)(8) barrel structure, and a metal ion (Mn(2+)) found in the active site is coordinated by Glu152, Asp185, His211, and Glu246 at the end of the beta-barrel. P. cichoriid-TE forms a stable dimer to give a favorable accessible surface for substrate binding on the front side of the dimer. The simulated omit map indicates that O2 and O3 of d-tagatose and/or d-fructose coordinate Mn(2+), and that C3-O3 is located between carboxyl groups of Glu152 and Glu246, supporting the previously proposed mechanism of deprotonation/protonation at C3 by two Glu residues. Although the electron density is poor at the 4-, 5-, and 6-positions of the substrates, substrate-enzyme interactions can be deduced from the significant electron density at O6. The O6 possibly interacts with Cys66 via hydrogen bonding, whereas O4 and O5 in d-tagatose and O4 in d-fructose do not undergo hydrogen bonding to the enzyme and are in a hydrophobic environment created by Phe7, Trp15, Trp113, and Phe248. Due to the lack of specific interactions between the enzyme and its substrates at the 4- and 5-positions, P. cichoriid-TE loosely recognizes substrates in this region, allowing it to efficiently catalyze the epimerization of d-tagatose and d-fructose (C4 epimer of d-tagatose) as well. Furthermore, a C3-O3 proton-exchange mechanism for P. cichoriid-TE is suggested by X-ray structural analysis, providing a clear explanation for the regulation of the ionization state of Glu152 and Glu246.
-Authors: Yoshida, H., Yoshihara, A., Ishii, T., Izumori, K., Kamitori, S.
+Crystal structures of D-tagatose 3-epimerase from Pseudomonas cichorii and its complexes with D-tagatose and D-fructose.,Yoshida H, Yamada M, Nishitani T, Takada G, Izumori K, Kamitori S J Mol Biol. 2007 Nov 23;374(2):443-53. Epub 2007 Sep 19. PMID:17936787<ref>PMID:17936787</ref>
-Description: Crystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with 6-deoxy L-psicose
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 4ytt" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Ishii, T]]
+[[Category: Izumori, K]]
+[[Category: Kamitori, S]]
+[[Category: Yoshida, H]]
 [[Category: Yoshihara, A]]
-[[Category: Yoshida, H]]
+[[Category: Epimerase]]
-[[Category: Kamitori, S]]
+[[Category: Isomerase]]
-[[Category: Izumori, K]]