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.


3s0m

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:46, 1 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='3s0m' size='340' side='right'caption='[[3s0m]], [[Resolution|resolution]] 2.31&Aring;' scene=''>
<StructureSection load='3s0m' size='340' side='right'caption='[[3s0m]], [[Resolution|resolution]] 2.31&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3s0m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S0M FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3s0m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S0M FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.31&#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;'>[[1j58|1j58]]</div></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU33240, oxalate decarboxylase, oxdC, yvrK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
+
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Oxalate_decarboxylase Oxalate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.2 4.1.1.2] </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=3s0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s0m OCA], [https://pdbe.org/3s0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s0m RCSB], [https://www.ebi.ac.uk/pdbsum/3s0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s0m 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=3s0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s0m OCA], [https://pdbe.org/3s0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s0m RCSB], [https://www.ebi.ac.uk/pdbsum/3s0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s0m ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[https://www.uniprot.org/uniprot/OXDC_BACSU OXDC_BACSU]] Converts oxalate to formate and CO(2) in an O(2)-dependent reaction. Can also catalyze minor side reactions: oxalate oxidation to produce H(2)O(2), and oxalate-dependent, H(2)O(2)-independent dye oxidations.
+
[https://www.uniprot.org/uniprot/OXDC_BACSU OXDC_BACSU] Converts oxalate to formate and CO(2) in an O(2)-dependent reaction. Can also catalyze minor side reactions: oxalate oxidation to produce H(2)O(2), and oxalate-dependent, H(2)O(2)-independent dye oxidations.
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
The conformational properties of an active-site loop segment, defined by residues Ser(161)-Glu(162)-Asn(163)-Ser(164), have been shown to be important for modulating the intrinsic reactivity of Mn(II) in the active site of Bacillus subtilis oxalate decarboxylase. We now detail the functional and structural consequences of removing a conserved Arg/Thr hydrogen-bonding interaction by site-specific mutagenesis. Hence, substitution of Thr-165 by a valine residue gives an OxDC variant (T165V) that exhibits impaired catalytic activity. Heavy-atom isotope effect measurements, in combination with the X-ray crystal structure of the T165V OxDC variant, demonstrate that the conserved Arg/Thr hydrogen bond is important for correctly locating the side chain of Glu-162, which mediates a proton-coupled electron transfer (PCET) step prior to decarboxylation in the catalytically competent form of OxDC. In addition, we show that the T165V OxDC variant exhibits a lower level of oxalate consumption per dioxygen molecule, consistent with the predictions of recent spin-trapping experiments [Imaram et al. (2011) Free Radicals Biol. Med. 50, 1009-1015]. This finding implies that dioxygen might participate as a reversible electron sink in two putative PCET steps and is not merely used to generate a protein-based radical or oxidized metal center.
+
-
 
+
-
A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase.,Saylor BT, Reinhardt LA, Lu Z, Shukla MS, Nguyen L, Cleland WW, Angerhofer A, Allen KN, Richards NG Biochemistry. 2012 Apr 3;51(13):2911-20. Epub 2012 Mar 19. PMID:22404040<ref>PMID:22404040</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3s0m" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Vibrio subtilis ehrenberg 1835]]
+
[[Category: Bacillus subtilis]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Oxalate decarboxylase]]
+
[[Category: Allen KN]]
-
[[Category: Allen, K N]]
+
[[Category: Cleland WW]]
-
[[Category: Cleland, W W]]
+
[[Category: Lu Z]]
-
[[Category: Lu, Z]]
+
[[Category: Reinhardt LA]]
-
[[Category: Reinhardt, L A]]
+
[[Category: Richards NGJ]]
-
[[Category: Richards, N G.J]]
+
[[Category: Saylor BT]]
-
[[Category: Saylor, B T]]
+
[[Category: Shukla MS]]
-
[[Category: Shukla, M S]]
+
-
[[Category: Bicupin]]
+
-
[[Category: Lyase]]
+

Current revision

A Structural Element that Modulates Proton-Coupled Electron Transfer in Oxalate Decarboxylase

PDB ID 3s0m

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/3s0m"
Personal tools