PDBsum entry 1vpr

Luminescent protein

PDB id: 1vpr

Contents

Protein chain

351 a.a. *

Waters ×252

* Residue conservation analysis

PDB id:

1vpr

Name:

Luminescent protein

Title:

Crystal structure of a luciferase domain from the dinoflagellate lingulodinium polyedrum

Structure:

Luciferase. Chain: a. Fragment: sequence database residues 866-1241. Engineered: yes

Source:

Lingulodinium polyedrum. Organism_taxid: 160621. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.199 R-free: 0.230

Authors:

L.W.Schultz,L.Liu,M.Cegielski,J.W.Hastings

Key ref:

L.W.Schultz et al. (2005). Crystal structure of a pH-regulated luciferase catalyzing the bioluminescent oxidation of an open tetrapyrrole. Proc Natl Acad Sci U S A, 102, 1378-1383. PubMed id: 15665092 DOI: 10.1073/pnas.0409335102

Date:

15-Nov-04 Release date: 08-Feb-05

Protein chain

O77206  (LUCIF_LINPO) -  Dinoflagellate luciferase from Lingulodinium polyedra

Seq: 1241 a.a.

Struc: 351 a.a.

Enzyme reactions

• Enzyme class: E.C.1.13.12.18 - dinoflagellate luciferase.
• Reaction: dinoflagellate luciferin + O2 = oxidized dinoflagellate luciferin + hnu + H2O + H⁺

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

Key reference

DOI no: 10.1073/pnas.0409335102

Proc Natl Acad Sci U S A 102:1378-1383 (2005)

PubMed id: 15665092

Crystal structure of a pH-regulated luciferase catalyzing the bioluminescent oxidation of an open tetrapyrrole.

L.W.Schultz, L.Liu, M.Cegielski, J.W.Hastings.

ABSTRACT

The luciferase of Lingulodinium polyedrum, a marine bioluminescent dinoflagellate, consists of three similar but not identical domains in a single polypeptide. Each encodes an active luciferase that catalyzes the oxidation of a chlorophyll-derived open tetrapyrrole (dinoflagellate luciferin) to produce blue light. These domains share no sequence similarity with any other in the GenBank database and no structural or motif similarity with any other luciferase. We report here the 1.8-A crystal structure of the third domain, D3, at pH 8, and a mechanism for its activity regulation by pH. D3 consists of two major structural elements: a beta-barrel pocket putatively for substrate binding and catalysis and a regulatory three-helix bundle. N-terminal histidine residues previously shown to regulate activity by pH are at the interface of the helices in the bundle. Molecular dynamics calculations indicate that, in response to changes in pH, these histidines could trigger a large molecular motion of the bundle, thereby exposing the active site to the substrate.

Selected figure(s)

Figure 1.
Fig. 1. Biochemistry of the reaction and the amino acid sequence and three-dimensional structure of LCF D3. (A) Bioluminescent reaction of dinoflagellate luciferin, a chlorophyll-like open tetrapyrrole. The arrow shows the position of enzymatic oxidation. (B) The sequence of LCF D3 with regions of -helix ( ) and -strand ( ) annotated. The Gly-rich sequence (italicized and underlined) connects the N-terminal subdomain to the -barrel comprising strands 5to 14. The four N-terminal histidines (899, 909, 924, and 930) are shown in red and italicized. Two underlined six-residue sequences show the beginning and end of the highly conserved region (991-1136) found in LCFs of all seven species examined (23). (C) A ribbon diagram of the crystal structure of D3 with helices and -strands numbered and color coded as in B. The two N-terminal helices (light blue) and the helix-loop-helix motif (green) are at the top, and the -barrel (dark blue) is below. Ribbon diagrams were produced by using MOLSCRIPT (42) and RASTER3D (43).

Figure 2.
Fig. 2. Structural similarity of D3 to FABP. (A) A ribbon diagram of M-FABP with a bound stearate (14). (B) Superposition of LCF D3 (blue) and M-FABP (red). The D3 and FABP helix-loop-helices differ, whereas the -barrels are closely aligned. An arrow shows the location of residue 1142. (C) Alignment of primary and secondary sequences of D3 and M-FABP within the -barrel region. Red and purple residues are identical or similar, respectively, in the two sequences. Two Gly-Gly sequences (boxes) are present in D3 but absent in M-FABP. -Strands 5-14 in D3 correspond to strands A-J in M-FABP.

Figures were selected by the author.