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(-) Description

Title :  CRYSTAL STRUCTURE OF A CA2+-DISCHARGED PHOTOPROTEIN: IMPLICATIONS FOR THE MECHANISMS OF THE CALCIUM TRIGGER AND THE BIOLUMINESCENCE
 
Authors :  L. Deng, S. V. Markova, E. S. Vysotski, Z. -J. Liu, J. Lee, J. Rose, B. -C. W Southeast Collaboratory For Structural Genomics (Secsg)
Date :  12 Jan 04  (Deposition) - 05 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A
Keywords :  Photoprotein, Obelin, Bioluminescence, Calcium Binding, Ef-Hand, Aequorin, Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Deng, S. V. Markova, E. S. Vysotski, Z. -J. Liu, J. Lee, J. Rose, B. -C. Wang
Crystal Structure Of A Ca2+-Discharged Photoprotein: Implications For Mechanisms Of The Calcium Trigger And Bioluminescence
J. Biol. Chem. V. 279 33647 2004
PubMed-ID: 15155735  |  Reference-DOI: 10.1074/JBC.M402427200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OBELIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET19B+
    Expression System Strain: BL21-GOLD(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    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  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1CEI1Ligand/IonN-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE
2CL1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4NA1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:30 , ASN A:32 , ASN A:34 , LYS A:36 , CL A:402BINDING SITE FOR RESIDUE NA A 401
2AC2SOFTWAREASN A:32 , LYS A:36 , GLU A:41 , NA A:401BINDING SITE FOR RESIDUE CL A 402
3AC3SOFTWAREHIS A:22 , MET A:25 , PHE A:88 , PHE A:92 , ILE A:111 , TRP A:114 , GLY A:115 , TYR A:138 , MET A:171 , HIS A:175 , TRP A:179 , HOH A:403 , HOH A:404 , HOH A:405BINDING SITE FOR RESIDUE CEI A 201
4AC4SOFTWAREPRO A:86 , ASP A:90 , LYS A:93 , TRP A:103 , ASN A:106 , HOH A:417 , HOH A:500BINDING SITE FOR RESIDUE GOL A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S36)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S36)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S36)

(-) 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 1S36)

(-) 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:185
 aligned with OBL_OBELO | Q27709 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:189
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186         
            OBL_OBELO     7 VKLKTDFDNPRWIKRHKHMFDFLDINGNGKITLDEIVSKASDDICAKLEATPEQTKRHQVCVEAFFRGCGMEYGKEIAFPQFLDGWKQLATSELKKWARNEPTLIREWGDAVFDIFDKDGSGTITLDEWKAYGKISGISPSQEDCEATFRHCDLDNSGDLDVDEMTRQHLGFWYTLDPEADGLYGNGVP 195
               SCOP domains d1s36a_ A: Calcium-regulated photoprotein                                                                                                                                                     SCOP domains
               CATH domains 1s36A00 A:7-195 EF-hand                                                                                                                                                                       CATH domains
               Pfam domains ----------------EF_hand_3-1s36A01      -----------------------------------------------EF_hand_5-1s36A02 A:93-173                                                       ---------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......eeehhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh----.eehhhhhhhhhhhhh...hhhhhhhhhhhh.......eehhhhhhhhhhhhh............... 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
                 1s36 A   7 VKLKTDFDNPRWIKRHKHMFDFLDINGNGKITLDEIVSKASDDICAKLEATPEQTKRHQVCVEAFFRGCGMEYGKEIAFPQFLDGFKQLATSELKKWARNEPTLIREWGDAVFDIFD----GTITLDEWKAYGKISGISPSQEDCEATFRHCDLDNSGDLDVDEMTRQHLGFWYTLDPEADGLYGNGVP 195
                                    16        26        36        46        56        66        76        86        96       106       116      |  - |     136       146       156       166       176       186         
                                                                                                                                              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  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: EF_hand (270)

(-) 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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  1s36
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  OBL_OBELO | Q27709
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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 1qv1 1sl7 1sl9 2f8p 4mrx 4mry 4n1f 4n1g

(-) Related Entries Specified in the PDB File

1ej3 CRYSTAL STRUCTURE OF AEQUORIN
1el4 STRUCTURE OF THE CALCIUM-REGULATED PHOTOPROTEIN OBELIN DETERMINED BY SULFUR SAS
1jf0 THE CRYSTAL STRUCTURE OF OBELIN FROM OBELIA GENICULATA AT 1.82 A RESOLUTION
1jf2 CRYSTAL STRUCTURE OF W92F OBELIN MUTANT FROM OBELIA LONGISSIMA AT 1.72 ANGSTROM RESOLUTION
1qv0 ATOMIC RESOLUTION STRUCTURE OF OBELIN FROM OBELIA LONGISSIMA
1qv1 ATOMIC RESOLUTION STRUCTURE OF OBELIN FROM OBELIA LONGISSIMA RELATED ID: OOB-CA_W92F_OBELIN RELATED DB: TARGETDB