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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF PHOTOPROTEIN CLYTIN
 
Authors :  M. S. Titushin, Y. Li, G. A. Stepanyuk, B. -C. Wang, J. Lee, E. S. Vysotski
Date :  17 Nov 09  (Deposition) - 06 Oct 10  (Release) - 29 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Photoprotein Clytin, Fluorescent Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Titushin, Y. Feng, G. A. Stepanyuk, Y. Li, S. V. Markova, S. Golz, B. -C. Wang, J. Lee, J. Wang, E. S. Vysotski, Z. -J. Liu
Nmr Derived Topology Of A Gfp-Photoprotein Energy Transfer Complex
J. Biol. Chem. V. 285 40891 2010
PubMed-ID: 20926380  |  Reference-DOI: 10.1074/JBC.M110.133843

(-) Compounds

Molecule 1 - APOPHOTOPROTEIN CLYTIN-3
    Chains: A
    EC Number: 1.13.12.5
    Engineered: YES
    Organism Common: PHIALIDIUM GREGARIUM
    Organism Scientific: CLYTIA GREGARIA
    Organism Taxid: 27801
    Synonym: CLYTIN, APOPHOTOPROTEIN CLYTIN-5, APOPHOTOPROTEIN CLYTIN-6

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CZH1Ligand/IonC2-HYDROPEROXY-COELENTERAZINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:25 , MET A:28 , LEU A:32 , ILE A:45 , ILE A:53 , PHE A:91 , TRP A:95 , ILE A:114 , TRP A:117 , GLY A:118 , PHE A:122 , TRP A:138 , TYR A:141 , ILE A:147 , MET A:174 , HIS A:178 , TRP A:182 , TYR A:193 , HOH A:213 , HOH A:314BINDING SITE FOR RESIDUE CZH A 201
2AC2SOFTWAREASP A:33 , ASN A:35 , ASN A:37 , LYS A:39 , HOH A:223BINDING SITE FOR RESIDUE CA A 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KPX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KPX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KPX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KPX)

(-) Exons   (0, 0)

(no "Exon" information available for 3KPX)

(-) 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    
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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:189
 aligned with D7PM14_CLYGR | D7PM14 from UniProtKB/TrEMBL  Length:198

    Alignment length:189
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189         
         D7PM14_CLYGR    10 VKLKTNFEDPKWVNRHKFMFNFLDINGNGKITLDEIVSKASDDICAKLGATPAQTQRHQEAVEAFFKKIGLDYGKEVEFPAFVNGWKELAKHDLKLWSQNKKSLIRNWGEAVFDIFDKDGSGSISLDEWKTYGGISGICPSDEDAEKTFKHCDLDNSGKLDVDEMTRQHLGFWYTLDPNADGLYGNFVP 198
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------EF_hand_4-3kpxA02 A:24-52    -----------------------------------------------------------------------------------------------------EF_hand_3-3kpxA01         ------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------EF_hand_5-3kpxA03 A:111-177                                        --------------------- Pfam domains (2)
         Sec.struct. author ........hhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhh...hhhhhhhhhhhh.......eehhhhhhhhhhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kpx A  10 VKLKTNFEDPKWVNRHKFMFNFLDINGNGKITLDEIVSKASDDICAKLGATPAQTQRHQEAVEAFFKKIGLDYGKEVEFPAFVNGWKELAKHDLKLWSQNKKSLIRNWGEAVFDIFDKDGSGSISLDEWKTYGGISGICPSDEDAEKTFKHCDLDNSGKLDVDEMTRQHLGFWYTLDPNADGLYGNFVP 198
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189
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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  (0, 0)

(no "SCOP Domain" information available for 3KPX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KPX)

(-) Pfam Domains  (3, 3)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (D7PM14_CLYGR | D7PM14)
molecular function
    GO:0050248    Renilla-luciferin 2-monooxygenase activity    Catalysis of the reaction: Renilla luciferin + O2 = oxidized Renilla luciferin + CO2 + light.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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