5DQP image
Deposition Date 2015-09-15
Release Date 2016-03-16
Last Version Date 2023-09-27
Entry Detail
PDB ID:
5DQP
Keywords:
Title:
EDTA monooxygenase (EmoA) from Chelativorans sp. BNC1
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.15 Å
R-Value Free:
0.23
R-Value Work:
0.18
R-Value Observed:
0.19
Space Group:
P 43 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:EDTA monooxygenase
Gene (Uniprot):emoA
Chain IDs:A, B
Chain Length:430
Number of Molecules:2
Biological Source:EDTA-degrading bacterium BNC1
Primary Citation
Structural and biochemical characterization of EDTA monooxygenase and its physical interaction with a partner flavin reductase.
Mol.Microbiol. 100 989 1003 (2016)
PMID: 26928990 DOI: 10.1111/mmi.13363

Abstact

Ethylenediaminetetraacetate (EDTA) is currently the most abundant organic pollutant due to its recalcitrance and extensive use. Only a few bacteria can degrade it, using EDTA monooxygenase (EmoA) to initiate the degradation. EmoA is an FMNH2 -dependent monooxygenase that requires an NADH:FMN oxidoreductase (EmoB) to provide FMNH2 as a cosubstrate. Although EmoA has been identified from Chelativorans (ex. Mesorhizobium) sp. BNC1, its catalytic mechanism is unknown. Crystal structures of EmoA revealed a domain-like insertion into a TIM-barrel, which might serve as a flexible lid for the active site. Docking of MgEDTA(2-) into EmoA identified an intricate hydrogen bond network connected to Tyr(71) , which should potentially lower its pKa. Tyr(71) , along with nearby Glu(70) and a peroxy flavin, facilitates a keto-enol transition of the leaving acetyl group of EDTA. Further, for the first time, the physical interaction between EmoA and EmoB was observed by ITC, molecular docking and enzyme kinetic assay, which enhanced both EmoA and EmoB activities probably through coupled channelling of FMNH2 .

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