This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3rft

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:54, 21 February 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='3rft' size='340' side='right'caption='[[3rft]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='3rft' size='340' side='right'caption='[[3rft]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3rft]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrfc Agrfc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RFT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RFT FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3rft]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RFT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RFT FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3rfv|3rfv]], [[3rfx|3rfx]]</div></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">udh, AGR_L_3333, Atu3143 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRFC])</td></tr>
+
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uronate_dehydrogenase Uronate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.203 1.1.1.203] </span></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=3rft FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rft OCA], [https://pdbe.org/3rft PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rft RCSB], [https://www.ebi.ac.uk/pdbsum/3rft PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rft ProSAT]</span></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=3rft FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rft OCA], [https://pdbe.org/3rft PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rft RCSB], [https://www.ebi.ac.uk/pdbsum/3rft PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rft ProSAT]</span></td></tr>
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/URODH_AGRFC URODH_AGRFC] Catalyzes the oxidation of D-galacturonate and D-glucuronate to galactarate and D-glucarate, respectively. In fact, in water solution the substrate D-galacturonate is predominantly in pyranosic form whose beta anomer is converted by the enzyme to D-galactaro-1,5-lactone; in solution, this reaction product rearranges to the more stable D-galactaro-1,4-lactone. Makes part of the oxidative degradation pathway of D-galacturonate, which allows A.tumefaciens to utilize D-galacturonate as a sole carbon source. Cannot use NADP(+) instead of NAD(+) as cosubstrate. Is not active on D-galactose, D-glucose, D-galactonate and D-gluconate.<ref>PMID:19060141</ref> <ref>PMID:19921179</ref> <ref>PMID:21676870</ref>
-
Uronate dehydrogenase from Agrobacterium tumefaciens (AtUdh) belongs to the short-chain dehydrogenase/reductase (SDR) superfamily and catalyzes the oxidation of D-galacturonic and D-glucuronic acid with NAD+ as a cofactor. We have determined the crystal structures of an apo form of AtUdh, a ternary form in complex with NADH and product (substrate soaked structure) and an inactive Tyr136Ala mutant in complex with NAD+. The crystal structures suggested AtUdh to be a homo-hexamer, which has also been observed to be the major form in solution. The monomer contains a Rossmann fold, essential for nucleotide binding and a common feature of the sort-chain dehydrogenase (SDR) -family enzymes. The ternary complex structure revealed a product, D-galactaro-1,5-lactone, which is bound above the nicotinamide ring. This product rearranges in solution to D-galactaro-1,4-lactone as verified by mass spectrometry analysis, which agrees with our previous NMR study. The crystal structure of the catalytic residue Tyr136 mutant to alanine showed changes in the position of the residues Ile74 and Ser75. This probably altered the binding of the nicotinamide end of NAD+, which was not visible in the electron density map. The structures presented provide novel insights into the cofactor and substrate binding and the reaction mechanism of AtUdh. This information can be applied in the for design of efficient microbial conversion of D-galacturonic acid-based waste materials.
+
-
 
+
-
Crystal structure of uronate dehydrogenase from Agrobacterium tumefaciens.,Parkkinen T, Boer H, Janis J, Andberg M, Penttila M, Koivula A, Rouvinen J J Biol Chem. 2011 Jun 15. PMID:21676870<ref>PMID:21676870</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3rft" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Agrfc]]
+
[[Category: Agrobacterium fabrum str. C58]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Uronate dehydrogenase]]
+
[[Category: Parkkinen T]]
-
[[Category: Parkkinen, T]]
+
[[Category: Rouvinen J]]
-
[[Category: Rouvinen, J]]
+
-
[[Category: Apoenzyme]]
+
-
[[Category: Nad binding]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Rossmann fold]]
+

Current revision

Crystal structure of uronate dehydrogenase from Agrobacterium tumefaciens

PDB ID 3rft

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3rft"
Personal tools