5KYT: Luciferin 4-monooxygenase

Structure of Photinus pyralis Luciferase red light emitting variant. Determined by X-ray diffraction at 2.0 Å resolution. Released 21 Dec 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Photinus pyralis
Chains: 2
Atoms: 9,046
Mol. weight: 123.25 kDa
Ligands: SLU
Released: 21 Dec 2016

Explore 5KYT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KYT contains 57 α-helices and 69 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 27 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	1
α-helix	22-34	13
β-strand	40-44	5	2
β-strand	49-52	4	2
α-helix	53-69	17
β-strand	77-81	5	3
α-helix	89-98	10
β-strand	101-104	4	3
α-helix	111-121	11
β-strand	125-128	4	3
α-helix	130-132	3
α-helix	133-140	8
β-strand	148-151	4	3
β-strand	158	1	4
β-strand	161	1	4
β-strand	163	1	3
α-helix	164-169	6
α-helix	178-180	3
α-helix	183-185	3
β-strand	192-197	6	3
α-helix	198	1
β-strand	207-211	5	3
α-helix	212-223	12
β-strand	236-239	4	2
α-helix	246-257	12
β-strand	261-264	4	2
α-helix	270-279	10
β-strand	284-287	4	2
α-helix	289-291	3
α-helix	292-296	5
α-helix	301-303	3
β-strand	311-315	5	2
α-helix	321-330	10
β-strand	337-341	5	2
α-helix	343-345	3
β-strand	348-351	4	2
β-strand	363	1	1
β-strand	364-365	2	2
α-helix	366	1
β-strand	370-374	5	1
α-helix	380	1
β-strand	381	1	1
α-helix	382	1
β-strand	388-393	6	1
β-strand	400-401	2	3
α-helix	405-411	7
β-strand	412	1	1
β-strand	418-426	9	1
β-strand	432-437	6	1
α-helix	438-440	3
β-strand	442-444	3	5
β-strand	447-449	3	5
α-helix	451-459	9
β-strand	466-473	8	6
β-strand	478	1	5
β-strand	479-486	8	6
α-helix	496-503	8
α-helix	508-510	3
β-strand	515-519	5	6
β-strand	524	1	7
β-strand	530	1	7
α-helix	532-542	11

Chain B: 30 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	8
α-helix	10-11	2
α-helix	13	1
α-helix	16-18	3
α-helix	22-34	13
β-strand	40-44	5	9
β-strand	49-52	4	9
α-helix	53-70	18
β-strand	77-81	5	10
α-helix	89-98	10
β-strand	101-104	4	10
α-helix	111-121	11
β-strand	125-128	4	10
α-helix	130-132	3
α-helix	133-140	8
β-strand	148-151	4	10
β-strand	158	1	11
β-strand	161	1	11
β-strand	163	1	10
α-helix	164-171	8
α-helix	173	1
α-helix	178-180	3
β-strand	192-198	7	10
β-strand	206-211	6	10
α-helix	212-222	11
β-strand	236-239	4	9
α-helix	246-257	12
β-strand	261-264	4	9
α-helix	270-279	10
β-strand	284-287	4	9
α-helix	289-295	7
α-helix	301-303	3
β-strand	311-315	5	9
α-helix	318-320	3
α-helix	321-330	10
β-strand	337-341	5	9
α-helix	343-345	3
β-strand	348-351	4	9
β-strand	363	1	8
β-strand	364-365	2	9
α-helix	366	1
β-strand	370-374	5	8
α-helix	380	1
β-strand	381	1	8
α-helix	382	1
β-strand	388-393	6	8
β-strand	400-401	2	10
α-helix	405-411	7
β-strand	412	1	8
β-strand	418-426	9	8
β-strand	432-437	6	8
α-helix	438-440	3
β-strand	442-444	3	12
β-strand	447-449	3	12
α-helix	451-460	10
β-strand	464-474	11	12
β-strand	478-487	10	12
α-helix	488	1
α-helix	495-503	9
α-helix	508-510	3
β-strand	515-518	4	12
β-strand	524	1	13
β-strand	530	1	13
α-helix	532-543	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Luciferin 4-monooxygenase	A, B	protein	550	Photinus pyralis	P08659 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5KYT_1 Luciferin 4-monooxygenase (chains A, B)
MEDAKNIKKGPAPFYPLEDGTAGEQLHKAMKRYALVPGTIAFTDAHIEVNITYAEYFEMS
VRLAEAMKRYGLNTNHRIVVCSENSLQFFMPVLGALFIGVAVAPANDIYNERELLNSMNI
SQPTVVFVSKKGLQKILNVQKKLPIIQKIIIMDSKTDYQGFQSMYTFVTSHLPPGFNEYD
FVPESFDRDKTIALIMNSSGSTGLPKGVALPHRTACVRFSHARDPIFGNQIIPDTAILSV
VPFHHGFGMFTTLGYLICGFRVVLMYRFEEELFLRSLQDYKIQTALLVPTLFSFFAKSTL
IDKYDLSNLHEIASGGAPLSKEVGEAVAKRFHLPGIRQGYGLTETTSAILITPEGDDKPG
AVGKVVPFFEAKVVDLDTGKTLGVNQRGELCVRGPMIMSGYVNNPEATNALIDKDGWLHS
GDIAYWDEDEHFFIVDRLKSLIKYKGYQVAPAELESILLQHPNIFDAGVAGLPDDDAGEL
PAAVVVLEHGKTMTEKEIVDYVASQVTTAKKLRGGVVFVDEVPKGLTGKLDARKIREILI
KAKKGGKSKL

Ligands and cofactors

ID	Name	Formula	Copies
SLU	5'-O-[N-(dehydroluciferyl)-sulfamoyl] adenosine	C21 H18 N8 O8 S3	2

Water and common crystallization additives (EDO) are not listed.

Primary citation

Cloning of the Orange Light-Producing Luciferase from Photinus scintillans-A New Proposal on how Bioluminescence Color is Determined. Branchini, B.R., Southworth, T.L., Fontaine, D.M. et al. Photochem Photobiol (2017) 93:479-485. DOI 10.1111/php.12671 · PubMed

Other PDB entries of the same protein (UniProt P08659 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3RIX 1.7 Å, 1.7A resolution structure of a firefly luciferase-Aspulvinone J inhibitor complex
1LCI 2.0 Å, Firefly luciferase
3IES 2.0 Å, Firefly luciferase inhibitor complex
5GZ2 2.0 Å, luciferase complex with 7-cy-L
3IER 2.05 Å, Firefly luciferase apo structure (P41 form) with PEG 400 bound
3IEP 2.1 Å, Firefly luciferase apo structure (P41 form)
1BA3 2.2 Å, Firefly luciferase in complex with bromoform
4E5D 2.2 Å, 2.2A resolution structure of a firefly luciferase-benzothiazole inhibitor complex
5DWV 2.3 Å, Crystal structure of the Luciferase complexed with substrate analogue
4G37 2.4 Å, Structure of cross-linked firefly luciferase in second catalytic conformation
5DV9 2.4 Å, Crystal structure of the Luciferase
5GYZ 2.4 Å, luciferase AMP/7-cy-L complex

Browse structure collections

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