PDBsum entry 1qv1

Luminescent protein

PDB id: 1qv1

Contents

Protein chain

187 a.a. *

Ligands

CZH

GOL

Metals

_CO ×2

_CA

__K

Waters ×282

* Residue conservation analysis

References listed in PDB file

Key reference

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

Abstract

The spatial structure of the Ca(2+)-regulated photoprotein obelin has been solved to resolution of 1.1A. Two oxygen atoms are revealed substituted at the C2-position of the coelenterazine in contrast to the obelin structure at 1.73A resolution where one oxygen atom only was disclosed. The electron density of the second oxygen atom was very weak but after exposing the crystals to a trace of Ca(2+), the electron densities of both oxygen atoms became equally intense. In addition, one Ca(2+) was found bound in the loop of the first EF-hand motif. Four of the ligands were provided by protein residues Asp30, Asn32, Asn34, and the main chain oxygen of Lys36. The other two were from water molecules. From a comparison of B-factors for the residues constituting the active site, it is suggested that the variable electron densities observed in various photoprotein structures could be attributed to different mobilities of the peroxy oxygen atoms.

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