Crystal structure of human persulfide dioxygenase: structural basis of ethylmalonic encephalopathy.
Bottom Line: A channel leading to the active site is sufficiently large to accommodate a GSSH substrate.Some of the observed hETHE1 clinical mutations cluster in the active site region.The structure will serve as a basis for detailed functional and mechanistic studies on ETHE1 and will be useful in the development of selective MBL inhibitors.
Affiliation: Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.Show MeSH
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Mentions: The hETHE1 structure reveals an αββα MBL-type fold with two central mixed β-sheets, each containing six strands, surrounded on both sides by helices (Fig. 2A and Supplementary Material, Fig. S2). In β-sheet I, β-strands 1–3 are aligned anti-parallel, with β-strands 3–6 being parallel. In β-sheet II, β-strands 7, 8, 9 and 10 are anti-parallel; β-strands 10 and 13 are parallel and β-strands 13 and 14 are anti-parallel (Supplementary Material, Fig. S2A). Secondary structural elements include: 2 β-sheets, 2 βαβα units, 8 β-hairpins, 6 β-bulges, 14 β-strands, 6 helices, 2 helix–helix interactions and 26 β-turns. Superimposition of the hETHE1 and A. thaliana ETHE1-like (PDB ID: 2GCU) structures reveals high overall fold similarity [root-mean-square deviation (RMSD) 1.43 Å over 230 Cα atoms] between the two proteins (Fig. 2B). Structure-based topology diagrams show conserved structural organization with the exception of the addition of the β11–β12 hairpin in the region linking β10 and β13 of the core fold of hETHE1 compared with the A. thaliana ETHE1 (Supplementary Material, Figs S2A and B). Topology comparisons of hETHE1 with human glyoxalase II (HAGH) and a ‘classical’ metallo-β-lactamase II (BcII) from B. cereus (Supplementary Material, Fig. S2C and D) reveal much more substantial differences in the organization of secondary structure elements. hETHE1 has been assigned as a member of the glyoxalase II family on the basis of sequence alignments (31); however, consistent with the differences in their overall folds (19), hETHE1 does not display glyoxalase II activity, when assayed using the most common glyoxalase II substrate, S-(D)-lactoylglutathione, under standard conditions (11). Enzyme-dependent oxygen consumption activity in the presence of GSSH was observed using the oxygen consumption assay as previously reported (11) (Fig. 3A). Moreover, ETHE1 does not display β-lactamase activity either using a chromogenic cephalosporin (nitrocefin), a penicillin (penicillin G) or a carbapenem (meropenem) as substrates under our standard β-lactamase assay conditions (32).Figure 2.
Affiliation: Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.