PDBsum entry 1sl8

Luminescent protein

PDB id: 1sl8

Contents

Protein chain

181 a.a.

Metals

_CA ×3

Waters ×154

References listed in PDB file

Key reference

Title

All three ca2+-Binding loops of photoproteins bind calcium ions: the crystal structures of calcium-Loaded apo-Aequorin and apo-Obelin.

Authors

L.Deng, E.S.Vysotski, S.V.Markova, Z.J.Liu, J.Lee, J.Rose, B.C.Wang.

Ref.

Protein Sci, 2005, 14, 663-675. [DOI no: 10.1110/ps.041142905]

PubMed id

15689515

Abstract

The crystal structures of calcium-loaded apo-aequorin and apo-obelin have been determined at resolutions 1.7A and 2.2 A, respectively. A calcium ion is observed in each of the three EF-hand loops that have the canonical calcium-binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration. The calcium-loaded apo-protein retain the same compact scaffold and overall fold as the unreacted photoproteins containing the bound substrate, 2-hyroperoxycoelenterazine, and also the same as the Ca2+-discharged obelin bound with product, coleneteramide. Nevertheless, there are easily discerned shifts in both helix and loop regions, and the shifts are not the same between the two proteins. It is suggested that these photoproteins to sense Ca2+ concentration transients and to produce their bioluminescence response on the millisecond timescale. A mechanism of intrastructural transmission of the calcium signal is proposed.

Figure 6.
Hydrogen-bond interactions between helix A and helix H, and helix A and the C terminus in conformation states II and V. (A) Obelin (PDB code1EL4; state II). (B) Aequorin (PDB code 1EJ3, monomer B; state II). (C) Ca^2+-loaded apo-obelin (state V). (D) Ca^2+-loaded apo-aequorin (state V). The photoprotein conformation states II and V are from Figure 1 [triangle] Figure 1.-. The residues for the Ca^2+-loaded apo-aequorin are numbered according to that used for the aequorin structure (PDB code 1EJ3).

Figure 7.
Stereo view of helix A in conformation states II and V. (A) Obelin (PDB code1EL4; state II). (B) Ca^2+-loaded apo-obelin (state V). (C) Aequorin (PDB code 1EJ3, monomer B; state II). (D) Ca^2+-loaded apo-aequorin (state V). The photoprotein conformation states II and V are from Figure 1 [triangle] Figure 1.-. The residues for the Ca^2+-loaded state of apo-aequorin are numbered according to that used for the aequorin structure (PDB code 1EJ3).

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2005, 14, 663-675) copyright 2005.

Secondary reference #1

Title

Structure of the ca2+-Regulated photoprotein obelin at 1.7 a resolution determined directly from its sulfur substructure.

Authors

Z.J.Liu, E.S.Vysotski, C.J.Chen, J.P.Rose, J.Lee, B.C.Wang.

Ref.

Protein Sci, 2000, 9, 2085-2093. [DOI no: 10.1110/ps.9.11.2085]

PubMed id

11152120

Secondary reference #2

Title

Preparation and preliminary study of crystals of the recombinant calcium-Regulated photoprotein obelin from the bioluminescent hydroid obelia longissima.

Authors

E.S.Vysotski, Z.J.Liu, J.Rose, B.C.Wang, J.Lee.

Ref.

Acta Crystallogr D Biol Crystallogr, 1999, 55, 1965-1966. [DOI no: 10.1107/S0907444999011828]

PubMed id

10531510

Figure 1.
Figure 1 Crystal of the photoprotein obelin, grown from 1.4 M sodium citrate. Approximate dimensions are 0.1 × 0.1 × 1.0 mm.

The above figure is reproduced from the cited reference with permission from the IUCr

Secondary reference #3

Title

Structural basis for the emission of violet bioluminescence from a w92f obelin mutant.

Authors

L.Deng, E.S.Vysotski, Z.J.Liu, S.V.Markova, N.P.Malikova, J.Lee, J.Rose, B.C.Wang.

Ref.

FEBS Lett, 2001, 506, 281-285. [DOI no: 10.1016/S0014-5793(01)02937-4]

PubMed id

11602262

Figure 3.
Fig. 3. Stereoview of the electron density map and substrate structure including residue Y190, within the binding cavity of W92F obelin. There is sufficient electron density around the C2-position of coelenterazine to account for a peroxy substitution. The electron density is weaker here than over the rest of the molecule as also observed in aequorin by Head et al. [5].

Figure 4.
Fig. 4. Two-dimensional picture showing that the W92F mutation produces no significant change in the dimensionality of the 2-peroxycoelenterazine within the photoprotein binding site. Distances are in Å: red, WT-obelin; bold, W92F.

The above figures are reproduced from the cited reference with permission from the Federation of European Biochemical Societies

Secondary reference #4

Title

Violet bioluminescence and fast kinetics from w92f obelin: structure-Based proposals for the bioluminescence triggering and the identification of the emitting species.

Authors

E.S.Vysotski, Z.J.Liu, S.V.Markova, J.R.Blinks, L.Deng, L.A.Frank, M.Herko, N.P.Malikova, J.P.Rose, B.C.Wang, J.Lee.

Ref.

Biochemistry, 2003, 42, 6013-6024. [DOI no: 10.1021/bi027258h]

PubMed id

12755603

Secondary reference #5

Title

Atomic resolution structure of obelin: soaking with calcium enhances electron density of the second oxygen atom substituted at the c2-Position of coelenterazine.

Authors

Z.J.Liu, E.S.Vysotski, L.Deng, J.Lee, J.Rose, B.C.Wang.

Ref.

Biochem Biophys Res Commun, 2003, 311, 433-439. [DOI no: 10.1016/j.bbrc.2003.09.231]

PubMed id

14592432

Secondary reference #6

Title

Preparation and X-Ray crystallographic analysis of the ca2+-Discharged photoprotein obelin.

Authors

L.Deng, S.V.Markova, E.S.Vysotski, Z.J.Liu, J.Lee, J.Rose, B.C.Wang.

Ref.

Acta Crystallogr D Biol Crystallogr, 2004, 60, 512-514. [DOI no: 10.1107/S090744490302852X]

PubMed id

14993677

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a perfect match.

Figure 1.
Figure 1 (a) Crystal of Ca^2+-discharged W92F obelin (0.05 × 0.1 × 0.25 mm); (b) fluorescence of the crystal on excitation by near-UV.

The above figure is reproduced from the cited reference with permission from the IUCr