PDBsum entry 1qv1

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protein ligands metals links
Luminescent protein PDB id
Jmol PyMol
Protein chain
187 a.a. *
_CO ×2
Waters ×282
* Residue conservation analysis
PDB id:
Name: Luminescent protein
Title: Atomic resolution structure of obelin from obelia longissima
Structure: Obelin. Chain: a. Synonym: obl. Engineered: yes
Source: Obelia longissima. Organism_taxid: 32570. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.10Å     R-factor:   0.133     R-free:   0.158
Authors: Z.J.Liu,E.S.Vysotski,L.Deng,J.Lee,J.Rose,B.C.Wang
Key ref: Z.J.Liu et al. (2003). Atomic resolution structure of obelin: soaking with calcium enhances electron density of the second oxygen atom substituted at the C2-position of coelenterazine. Biochem Biophys Res Commun, 311, 433-439. PubMed id: 14592432 DOI: 10.1016/j.bbrc.2003.09.231
26-Aug-03     Release date:   11-Nov-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q27709  (OBL_OBELO) -  Obelin
195 a.a.
187 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Renilla-luciferin 2-monooxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Renilla-luciferin 2-monooxygenase
Watasenia-luciferin 2-monooxygenase
and Oplophorus-luciferin 2-monooxygenase
      Reaction: Renilla luciferin + O2 = oxidized Renilla luciferin + CO2 + light
Renilla luciferin
Bound ligand (Het Group name = CZH)
matches with 91.18% similarity
+ O(2)
= oxidized Renilla luciferin
+ CO(2)
+ light
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     bioluminescence   1 term 
  Biochemical function     metal ion binding     2 terms  


DOI no: 10.1016/j.bbrc.2003.09.231 Biochem Biophys Res Commun 311:433-439 (2003)
PubMed id: 14592432  
Atomic resolution structure of obelin: soaking with calcium enhances electron density of the second oxygen atom substituted at the C2-position of coelenterazine.
Z.J.Liu, E.S.Vysotski, L.Deng, J.Lee, J.Rose, B.C.Wang.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
18264586 M.S.Titushin, S.V.Markova, L.A.Frank, N.P.Malikova, G.A.Stepanyuk, J.Lee, and E.S.Vysotski (2008).
Coelenterazine-binding protein of Renilla muelleri: cDNA cloning, overexpression, and characterization as a substrate of luciferase.
  Photochem Photobiol Sci, 7, 189-196.  
15689515 L.Deng, E.S.Vysotski, S.V.Markova, Z.J.Liu, J.Lee, J.Rose, and B.C.Wang (2005).
All three Ca2+-binding loops of photoproteins bind calcium ions: the crystal structures of calcium-loaded apo-aequorin and apo-obelin.
  Protein Sci, 14, 663-675.
PDB codes: 1sl7 1sl8
15632284 S.Toma, K.T.Chong, A.Nakagawa, K.Teranishi, S.Inouye, and O.Shimomura (2005).
The crystal structures of semi-synthetic aequorins.
  Protein Sci, 14, 409-416.
PDB codes: 1uhh 1uhi 1uhj 1uhk
15155735 L.Deng, S.V.Markova, E.S.Vysotski, Z.J.Liu, J.Lee, J.Rose, and B.C.Wang (2004).
Crystal structure of a Ca2+-discharged photoprotein: implications for mechanisms of the calcium trigger and bioluminescence.
  J Biol Chem, 279, 33647-33652.
PDB code: 1s36
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.