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(-) Description

Title :  ATOMIC RESOLUTION STRUCTURE OF OBELIN FROM OBELIA LONGISSIMA
 
Authors :  Z. J. Liu, E. S. Vysotski, L. Deng, J. Lee, J. Rose, B. C. Wang
Date :  26 Aug 03  (Deposition) - 11 Nov 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Photoprotein, Obelin, Bioluminescence, Atomic Resolution, Calcium Binding, Ef-Hand, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. J. Liu, E. S. Vysotski, L. Deng, J. Lee, J. Rose, B. C. Wang
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. V. 311 433 2003
PubMed-ID: 14592432  |  Reference-DOI: 10.1016/J.BBRC.2003.09.231
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OBELIN
    Chains: A
    EC Number: 1.13.12.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET19-OL8
    Expression System Strain: BL21-GOLD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: OBELIA LONGISSIMA
    Organism Taxid: 32570
    Synonym: OBL

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CO2Ligand/IonCOBALT (II) ION
3CZH1Ligand/IonC2-HYDROPEROXY-COELENTERAZINE
4GOL1Ligand/IonGLYCEROL
5K1Ligand/IonPOTASSIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:30 , ASN A:32 , ASN A:34 , LYS A:36 , HOH A:3173 , HOH A:3237BINDING SITE FOR RESIDUE CA A 403
2AC2SOFTWAREPHE A:155 , ARG A:156 , CYS A:158 , HOH A:3073 , HOH A:3150 , HOH A:3159BINDING SITE FOR RESIDUE K A 404
3AC3SOFTWAREHIS A:22 , MET A:25 , ILE A:42 , ILE A:50 , PHE A:88 , TRP A:92 , TRP A:114 , GLY A:115 , PHE A:119 , TYR A:138 , ILE A:144 , MET A:171 , HIS A:175 , TRP A:179 , TYR A:190 , HOH A:3042BINDING SITE FOR RESIDUE CZH A 201
4AC4SOFTWAREHIS A:24 , GLY A:143 , ILE A:144 , PRO A:146 , GLY A:193 , VAL A:194 , HOH A:3115BINDING SITE FOR RESIDUE GOL A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QV1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QV1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QV1)

(-) PROSITE Motifs  (2, 6)

Asymmetric/Biological Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.OBL_OBELO17-52
110-145
146-181		  3A:17-52
A:110-145
A:146-181
2EF_HAND_1PS00018 EF-hand calcium-binding domain.OBL_OBELO30-42
123-135
159-171		  3A:30-42
A:123-135
A:159-171

(-) Exons   (0, 0)

(no "Exon" information available for 1QV1)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:187
 aligned with OBL_OBELO | Q27709 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:191
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194 
            OBL_OBELO     5 YAVKLKTDFDNPRWIKRHKHMFDFLDINGNGKITLDEIVSKASDDICAKLEATPEQTKRHQVCVEAFFRGCGMEYGKEIAFPQFLDGWKQLATSELKKWARNEPTLIREWGDAVFDIFDKDGSGTITLDEWKAYGKISGISPSQEDCEATFRHCDLDNSGDLDVDEMTRQHLGFWYTLDPEADGLYGNGVP 195
               SCOP domains d1qv1a_ A: Calcium-regulated photoprotein                                                                                                                                                       SCOP domains
               CATH domains 1qv1A00 A:5-195 EF-hand                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.----.eehhhhhhhhhhhhh...hhhhhhhhhhhh.......eehhhhhhhhhhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------EF_HAND_2  PDB: A:17-52             ---------------------------------------------------------EF_HAND_2  PDB: A:110-145           EF_HAND_2  PDB: A:146-181           -------------- PROSITE (1)
                PROSITE (2) -------------------------EF_HAND_1    --------------------------------------------------------------------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qv1 A   5 YAVKLKTDFDNPRWIKRHKHMFDFLDINGNGKITLDEIVSKASDDICAKLEATPEQTKRHQVCVEAFFRGCGMEYGKEIAFPQFLDGWKQLATSELKKWARNEPTLIREWGDAVFDIFD----GTITLDEWKAYGKISGISPSQEDCEATFRHCDLDNAGDLDVDEMTRQHLGFWYTLDPEADGLYGNGVP 195
                                    14        24        34        44        54        64        74        84        94       104       114        |-   |   134       144       154       164       174       184       194 
                                                                                                                                                123  128
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1QV1)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (OBL_OBELO | Q27709)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.

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  1qv1
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        OBL_OBELO | Q27709: 1el4 1jf0 1jf2 1qv0 1s36 1sl7 1sl9 2f8p 4mrx 4mry 4n1f 4n1g

(-) Related Entries Specified in the PDB File

1ej3 CONTAINS CALCIUM-REGULATED PHOTOPROTEIN AEQUORIN
1el4 CONTAINS CALCIUM-REGULATED PHOTOPROTEIN OBELIN
1jf0 CONTAINS CALCIUM-REGULATED PHOTOPROTEIN OBELIN
1jf2 CONTAINS CALCIUM-REGULATED PHOTOPROTEIN OBELIN W92F MUTANT
1qv0 CONTAINS CALCIUM-REGULATED PHOTOPROTEIN OBELIN