Firefly Luciferase

Family Ties

Luciferase belongs to a family of AMP-dependent enzymes found in both eukaryotes and prokaryotes, and which are thought to act via ATP-dependent covalent binding of AMP to their substrate. Members of this family with known structures include insect luciferase (EC 1.13.12.7), Bacillus sp. gramicidin S synthetase I and dihydroxybenzoate-AMP ligase (DhbE; EC 2.7.7.58), yeast/bacterial acetyl-CoA synthetase (EC 6.2.1.1), bacterial long chain fatty acid-CoA ligase (EC 6.2.1.3), and bacterial 4-chlorobenzoyl-CoA ligase. In general, these enzymes are multi-domain proteins consisting of two or more domains belonging to different structural classes.

What InterPro Tells Us

P08659 North American Firefly (Photinus pyralis) luciferase

InterPro Domain Architecture

InterPro Entry	Signatures	Graphical Match	Method Name
IPR000873	PF00501		AMP-binding
IPR000873	PR00154		AMPBINDING
IPR000873	PS00455		AMP_BINDING
Structural Features
1lci	1lci
2.30.38.10.2	1lci03
3.30.300.30.2	1lci04
3.40.50.980.3	1lci01
3.40.50.980.4	1lci02
4.10.8.10.1	1ba305
e.23.1.1	d1lci__

From the graphical match above, you can see that the signatures are all grouped into one InterPro entry for firefly luciferase. IPR000873 represents the AMP-binding domain, which contains a Ser/Thr/Gly (STG) rich region that is further characterised by a conserved Pro-Lys-Gly (PKG) triplet. This domain is found in various AMP-dependent enzymes, including various closely related synthases and ligases. IPR000873 is represented by three signatures: PF00501 from the PFAM database (covers almost the entire domain), PR00154 from the PRINTS database (2-motif fingerprint spanning the STG-rich region, where motif 2 contains the PKG triplet), and PS00455 from the PROSITE database.

The remaining seven entries in the table above give information on the structure of this protein, presenting known structural data from the structural database PDB (green stripe) and the structural classification databases CATH (pink stripe) and SCOP (black stripe) (the names such as 1lci03 are derived from the PDB entry upon which they are based, here PDB entry 1lci, fragment 3). The graphical match for the PDB entry 1lci displays the full length of the original PDB entry, here covering the entire protein. The CATH and SCOP entries breakdown the PDB data into its constituent domains based on structure, and provide a structural classification for each domain. SCOP classifies the protein as one functional entity with multiple domains, while CATH divides the protein into five structurally distinct domains: an N-terminal domain {1ba305} with irregular structure; the next two domains {1lci01 and 1lci02} with an aba 3-layer sandwich structure (Rossmann fold); the next domain {1lci03} with a mainly b-roll fold; and the C-terminal domain {1lci04} with an ab 2-layer sandwich fold. In several papers, the first 4 CATH domains are often described together as one large N-terminal region, consisting of a b-barrel and 2 b-sheets flanked by a-helices to form a ababa 5-layer structure; the C-terminal domain (5^th CATH domain) is considered separately, physically divided from the N-terminal region by a wide cleft.

What the Structure Tells Us

Structures associated with firefly luciferase can be viewed using AstexViewer®, which is linked from the Match Table via the logo on the InterPro page (please note, there is no link directly from this page to the AstexViewer®, therefore you need to go to the link on the InterPro page for P08659). The AstexViewer® displays the PDB structure with the specific CATH or SCOP domain highlighted.

There are structures available for various luciferases (firefly and bacterial) in the Protein Data Bank (PDB). A detailed description and visualisation of the structural features of firefly luciferase can be found at the PDB ‘Molecule of the Month’. The crystallographic structures of luciferase enzymes have provided insight into the mechanism of action of this important enzyme.

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