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==Structure of Dimethylformamidase, tetramer, Y440A mutant== | ==Structure of Dimethylformamidase, tetramer, Y440A mutant== | ||
<StructureSection load='6lvd' size='340' side='right'caption='[[6lvd]]' scene=''> | <StructureSection load='6lvd' size='340' side='right'caption='[[6lvd]], [[Resolution|resolution]] 3.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LVD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LVD FirstGlance]. <br> | <table><tr><td colspan='2'>[[6lvd]] is a 8 chain structure with sequence from [http://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=6LVD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LVD FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6lvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lvd OCA], [http://pdbe.org/6lvd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lvd RCSB], [http://www.ebi.ac.uk/pdbsum/6lvd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lvd ProSAT]</span></td></tr> | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dmfase2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1130061 Paracoccus sp. SSG05]), dmfase1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1130061 Paracoccus sp. SSG05])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N,N-dimethylformamidase N,N-dimethylformamidase], with EC number [http://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'>[http://proteopedia.org/fgij/fg.htm?mol=6lvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lvd OCA], [http://pdbe.org/6lvd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lvd RCSB], [http://www.ebi.ac.uk/pdbsum/6lvd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lvd ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6lvd" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Arya, | [[Category: N,N-dimethylformamidase]] | ||
[[Category: Paracoccus sp. ssg05]] | |||
[[Category: Arya, C A]] | |||
[[Category: Casanal, A]] | |||
[[Category: Chopra, G]] | |||
[[Category: Fine, J]] | |||
[[Category: Ramanathan, G]] | |||
[[Category: Subramanian, R]] | |||
[[Category: Vinothkumar, K R]] | |||
[[Category: Yadav, S]] | |||
[[Category: Ab polypeptide]] | |||
[[Category: Amidohydrolase]] | |||
[[Category: Hydrolase]] | |||
[[Category: Mononuclear iron]] | |||
[[Category: Tetramer]] | |||
Revision as of 11:53, 20 July 2020
Structure of Dimethylformamidase, tetramer, Y440A mutantStructure of Dimethylformamidase, tetramer, Y440A mutant
Structural highlights
Publication Abstract from PubMedN,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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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