PDBsum entry 2d1r

Oxidoreductase

PDB id: 2d1r

Contents

Protein chain

539 a.a. *

Ligands

AMP

OLU

Waters ×626

* Residue conservation analysis

PDB id:

2d1r

Name:

Oxidoreductase

Title:

Crystal structure of the thermostable japanese firefly luciferase complexed with oxyluciferin and amp

Structure:

Luciferin 4-monooxygenase. Chain: a. Synonym: luciferase. Engineered: yes. Mutation: yes

Source:

Luciola cruciata. Japanese firefly. Organism_taxid: 7051. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.60Å R-factor: 0.185 R-free: 0.210

Authors:

T.Nakatsu,S.Ichiyama,J.Hiratake,A.Saldanha,N.Kobashi,K.Sakata,H.Kato, Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

T.Nakatsu et al. (2006). Structural basis for the spectral difference in luciferase bioluminescence. Nature, 440, 372-376. PubMed id: 16541080 DOI: 10.1038/nature04542

Date:

31-Aug-05 Release date: 21-Mar-06

Protein chain

P13129  (LUCI_NIPCR) -  Luciferin 4-monooxygenase from Nipponoluciola cruciata

Seq: 548 a.a.

Struc: 539 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.13.12.7 - firefly luciferase.
• Pathway: Photinus-luciferin 4-monooxygenase (ATP-hydrolysing)
• Reaction: firefly D-luciferin + ATP + O2 = firefly oxyluciferin + hnu + AMP + CO2 + diphosphate

firefly D-luciferin + ATP + O2 = firefly oxyluciferin (Bound ligand (Het Group name = AMP) corresponds exactly) + hnu + AMP + CO2 + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nature04542

Nature 440:372-376 (2006)

PubMed id: 16541080

Structural basis for the spectral difference in luciferase bioluminescence.

T.Nakatsu, S.Ichiyama, J.Hiratake, A.Saldanha, N.Kobashi, K.Sakata, H.Kato.

ABSTRACT

Fireflies communicate with each other by emitting yellow-green to yellow-orange brilliant light. The bioluminescence reaction, which uses luciferin, Mg-ATP and molecular oxygen to yield an electronically excited oxyluciferin species, is carried out by the enzyme luciferase. Visible light is emitted during relaxation of excited oxyluciferin to its ground state. The high quantum yield of the luciferin/luciferase reaction and the change in bioluminescence colour caused by subtle structural differences in luciferase have attracted much research interest. In fact, a single amino acid substitution in luciferase changes the emission colour from yellow-green to red. Although the crystal structure of luciferase from the North American firefly (Photinus pyralis) has been described, the detailed mechanism for the bioluminescence colour change is still unclear. Here we report the crystal structures of wild-type and red mutant (S286N) luciferases from the Japanese Genji-botaru (Luciola cruciata) in complex with a high-energy intermediate analogue, 5'-O-[N-(dehydroluciferyl)-sulfamoyl]adenosine (DLSA). Comparing these structures to those of the wild-type luciferase complexed with AMP plus oxyluciferin (products) reveals a significant conformational change in the wild-type enzyme but not in the red mutant. This conformational change involves movement of the hydrophobic side chain of Ile 288 towards the benzothiazole ring of DLSA. Our results indicate that the degree of molecular rigidity of the excited state of oxyluciferin, which is controlled by a transient movement of Ile 288, determines the colour of bioluminescence during the emission reaction.

Selected figure(s)

Figure 1.
Figure 1: The bioluminescence reaction catalysed by luciferase.
Figure 1 : The bioluminescence reaction catalysed by luciferase. Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg@nature.com-
a, A two-step reaction mechanism via the luciferyl AMP intermediate. b, Structure of DLSA, a luciferyl AMP intermediate analogue.

Figure 4.
Figure 4: Bioluminescence colour of wild-type and three mutant forms (I288V, I288A and S286N) of Lcr luciferases. a, Photographs of bioluminescence by a luciferase-catalysed reaction. The reaction condition was 0.1 mM luciferin, 2 mM ATP, 6 mM MgSO[4], 25 mM HEPES (pH 7.8) and 0.1 mg ml^-1 luciferase in 0.5 ml solution. b, Emission spectra of the four types of Luciola cruciata luciferases.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2006, 440, 372-376) copyright 2006.

Figures were selected by an automated process.