4ras

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:51, 1 March 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 3: Line 3:
<StructureSection load='4ras' size='340' side='right'caption='[[4ras]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='4ras' size='340' side='right'caption='[[4ras]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4ras]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Aminobacter_sp._pht-3b Aminobacter sp. pht-3b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RAS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RAS FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4ras]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Nitratireductor_pacificus_pht-3B Nitratireductor pacificus pht-3B]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RAS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RAS FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2.3&#8491;</td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NA2_14372 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=391937 Aminobacter sp. Pht-3B])</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=4ras FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ras OCA], [http://pdbe.org/4ras PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ras RCSB], [http://www.ebi.ac.uk/pdbsum/4ras PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ras 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=4ras FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ras OCA], [https://pdbe.org/4ras PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ras RCSB], [https://www.ebi.ac.uk/pdbsum/4ras PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ras ProSAT]</span></td></tr>
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/K2MB66_9HYPH K2MB66_9HYPH]
-
Organohalide chemistry underpins many industrial and agricultural processes, and a large proportion of environmental pollutants are organohalides. Nevertheless, organohalide chemistry is not exclusively of anthropogenic origin, with natural abiotic and biological processes contributing to the global halide cycle. Reductive dehalogenases are responsible for biological dehalogenation in organohalide respiring bacteria, with substrates including polychlorinated biphenyls or dioxins. Reductive dehalogenases form a distinct subfamily of cobalamin (B12)-dependent enzymes that are usually membrane associated and oxygen sensitive, hindering detailed studies. Here we report the characterization of a soluble, oxygen-tolerant reductive dehalogenase and, by combining structure determination with EPR (electron paramagnetic resonance) spectroscopy and simulation, show that a direct interaction between the cobalamin cobalt and the substrate halogen underpins catalysis. In contrast to the carbon-cobalt bond chemistry catalysed by the other cobalamin-dependent subfamilies, we propose that reductive dehalogenases achieve reduction of the organohalide substrate via halogen-cobalt bond formation. This presents a new model in both organohalide and cobalamin (bio)chemistry that will guide future exploitation of these enzymes in bioremediation or biocatalysis.
+
-
 
+
-
Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation.,Payne KA, Quezada CP, Fisher K, Dunstan MS, Collins FA, Sjuts H, Levy C, Hay S, Rigby SE, Leys D Nature. 2014 Oct 19. doi: 10.1038/nature13901. PMID:25327251<ref>PMID:25327251</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4ras" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Aminobacter sp. pht-3b]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Leys, D]]
+
[[Category: Nitratireductor pacificus pht-3B]]
-
[[Category: Payne, K A.P]]
+
[[Category: Leys D]]
-
[[Category: Quezada, C P]]
+
[[Category: Payne KAP]]
-
[[Category: Cobalamin binding]]
+
[[Category: Quezada CP]]
-
[[Category: Ferrodoxin and cobalamin-binding domain]]
+
-
[[Category: Iron sulfur binding]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Reductive dehalogenase]]
+

Current revision

Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation

PDB ID 4ras

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/4ras"
Personal tools