6lvc: Difference between revisions

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<StructureSection load='6lvc' size='340' side='right'caption='[[6lvc]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
<StructureSection load='6lvc' size='340' side='right'caption='[[6lvc]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6lvc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_sp._ssg05 Paracoccus sp. ssg05]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LVC FirstGlance]. <br>
<table><tr><td colspan='2'>[[6lvc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_sp._SSG05 Paracoccus sp. SSG05]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LVC FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dmfase2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1130061 Paracoccus sp. SSG05]), dmfase1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1130061 Paracoccus sp. SSG05])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/N,N-dimethylformamidase N,N-dimethylformamidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.56 3.5.1.56] </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=6lvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lvc OCA], [https://pdbe.org/6lvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lvc RCSB], [https://www.ebi.ac.uk/pdbsum/6lvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lvc 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=6lvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lvc OCA], [https://pdbe.org/6lvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lvc RCSB], [https://www.ebi.ac.uk/pdbsum/6lvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lvc ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/I6NT79_9RHOB I6NT79_9RHOB]
N,N-dimethyl formamide (DMF) is an extensively used organic solvent but is also a potent pollutant. Certain bacterial species from genera such as Paracoccus, Pseudomonas, and Alcaligenes have evolved to use DMF as a sole carbon and nitrogen source for growth via degradation by a dimethylformamidase (DMFase). We show that DMFase from Paracoccus sp. strain DMF is a halophilic and thermostable enzyme comprising a multimeric complex of the alpha2 beta2 or (alpha2 beta2 )2 type. One of the three domains of the large subunit and the small subunit are hitherto undescribed protein folds of unknown evolutionary origin. The active site consists of a mononuclear iron coordinated by two Tyr side-chain phenolates and one carboxylate from Glu. The Fe(3+) ion in the active site catalyzes the hydrolytic cleavage of the amide bond in DMF. Kinetic characterization reveals that the enzyme shows cooperativity between subunits, and mutagenesis and structural data provide clues to the catalytic mechanism.
 
A 2-Tyr-1-carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase.,Arya CK, Yadav S, Fine J, Casanal A, Chopra G, Ramanathan G, Vinothkumar KR, Subramanian R Angew Chem Int Ed Engl. 2020 May 25. doi: 10.1002/anie.202005332. PMID:32452120<ref>PMID:32452120</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6lvc" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: N,N-dimethylformamidase]]
[[Category: Paracoccus sp. SSG05]]
[[Category: Paracoccus sp. ssg05]]
[[Category: Arya CA]]
[[Category: Arya, C A]]
[[Category: Casanal A]]
[[Category: Casanal, A]]
[[Category: Chopra G]]
[[Category: Chopra, G]]
[[Category: Fine J]]
[[Category: Fine, J]]
[[Category: Ramanathan G]]
[[Category: Ramanathan, G]]
[[Category: Subramanian R]]
[[Category: Subramanian, R]]
[[Category: Vinothkumar KR]]
[[Category: Vinothkumar, K R]]
[[Category: Yadav S]]
[[Category: Yadav, S]]
[[Category: Ab polypeptide]]
[[Category: Amidohydrolase]]
[[Category: Hydrolase]]
[[Category: Mononuclear iron]]
[[Category: Tetramer]]

Latest revision as of 13:47, 27 March 2024

Structure of Dimethylformamidase, dimerStructure of Dimethylformamidase, dimer

Structural highlights

6lvc is a 4 chain structure with sequence from Paracoccus sp. SSG05. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Electron Microscopy, Resolution 3Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

I6NT79_9RHOB

6lvc, resolution 3.00Å

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OCA
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