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from Vibrio harveyi

The purpose of luciferase is to catalyze the reaction

FMNH2 + O2 + RCHO -> 
FMN + RCOOH + H2 + light (490nm)

where RCHO is a long chain aldehyde. The enzyme is a heterodimer consisting of an alpha- (40 kDa) and a beta-subunit (37 kDa). The subunits are homologous (gene duplication), the larger one contains 29 additional amino acids. Of these only a few are visible by x-ray in the protein crystal  , the others are in an unordered loop which is proteolytically sensitive. 32% of the sequences are identical  .

Both subunits display similar tertiary structures featuring the topology of a single (beta/alpha)8 barrel each. Such a structure is formed by the consecutively changing order of alpha helices and beta sheets  . Here the aspect is parallel to the axis of the alpha subunit's barrel and near perpendicular to the beta one. By turning the molecule the twist between the subunits is recognizable.

The contact between the subunits is accomplished by two helices each  . Especially close are Gly64  , which are conserved in both subunits of all luciferases. Also conserved are His45 and Glu88  , which form hydrogen bonds. The same holds for the pair Thr80 and Arg85  . The side chain of Arg85 contacts both oxygen atoms of the threonine across the subunit interface.

Besides polar interactions there are hydrophobic contacts responsible for the sticking of the subunits. Many of the amino acids involved are conserved, too. Hydrophobic forces are found mainly between a loop (stabilized itself by internal hydrogen bonds) in one subunit and a loop as well as part of a helix in the other subunit. The reciprocal pair of contacts is also in effect  .

Beta strand 3 in the alpha subunit ends with a bulge protruding into the barrel  . Here Ala74 and Ala75 form a (in case of non-proline rare) cis-peptide bond. This cis-bond is situated near to the C-terminus of the barrel, where all known proteins with (beta/alpha)8 barrels contain their active center. This constitutes the bottom floor of the barrel  . Both alanines are part of a pocket, in which His44 and Cys106 have an essential part: mutation or chemical modification abolish the function of the enzyme. Cys106 is somewhat involved in binding the flavine; the shape of the pocket caused by the cis-bond is important for the function of the enzyme. Also amino acids of the beta-subunit are involved  .
The helices forming the (beta/alpha)8 barrels may easily be superimposed by symmetry operations along the axis of the enzyme. This doesn't hold for the positions of the more peripheral helices. Especially helix 4a of the alpha subunit is located furter away from the axis than the corresponding helix of the beta subunit  . This implies a more easy access to the pocket of the alpha subunit. The corresponding structure in the beta subunit is not enzymatically active.

The active site of luciferase is found at the carboxy terminus of the beta barrel in the alpha subunit near to the cis-bound alanines  . The cosubstrate FMNH2 is bound by Trp194 and Trp250 (the flavine itself is absent from the crystal)  . A spacefilling view of the vicinity of the active site demonstrates the shape of the substrate binding pocket  . The entry channel is lined at the surface of the enzyme by helix 5 and its loop connecting to strand 5 and helix 7a  . It opens wide enough to accommodate all substrates for the luciferase reaction.

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Literature: AJ Fisher et al, The 1.5-Å resolution structure of bacterial luciferase in low salt conditions, J. Biol. Chem. 271 (1996) 21956-21968

6-97 - Rolf Bergmann