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(-) Description

Title :  PHOTOEXCITED STRUCTURE OF THE PLANT PHOTORECEPTOR DOMAIN, PHY3 LOV2
 
Authors :  S. Crosson, K. Moffat
Date :  25 Jul 01  (Deposition) - 14 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Cysteinyl-Flavin Adduct, Photoexcited, Pas, Lov, Plant Photoreceptor, Phototropin, Photochemistry, Light-Driven Bond, Phy3, Signaling Protein, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Crosson, K. Moffat
Photoexcited Structure Of A Plant Photoreceptor Domain Reveals A Light-Driven Molecular Switch.
Plant Cell V. 14 1067 2002
PubMed-ID: 12034897  |  Reference-DOI: 10.1105/TPC.010475
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHY3 PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PCAL-N-EK
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: FMN-BINDING DOMAIN OF CHIMERIC PHYTOCHROME/PHOTOTROPIN PHOTORECEPTOR, LOV3
    Gene: PHY3
    Organism Scientific: ADIANTUM CAPILLUS-VENERIS
    Organism Taxid: 13818
    Other Details: CONTAINS A CYSTEINYL-FLAVIN C(4A) COVALENT ADDUCT
    Synonym: PHY3 LOV2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:965 , CYS A:966 , ARG A:967 , LEU A:969 , GLN A:970 , ILE A:982 , ARG A:983 , ASN A:998 , ASN A:1008 , PHE A:1010 , GLY A:1027 , GLN A:1029BINDING SITE FOR RESIDUE FMN A 1033
2AC2SOFTWAREHOH B:32 , ASN B:965 , CYS B:966 , ARG B:967 , LEU B:969 , GLN B:970 , ILE B:982 , ARG B:983 , ASN B:998 , ASN B:1008 , PHE B:1010 , GLY B:1027 , GLN B:1029BINDING SITE FOR RESIDUE FMN B 1033
3AC3SOFTWAREHOH C:4 , ASN C:965 , CYS C:966 , ARG C:967 , LEU C:969 , GLN C:970 , ILE C:982 , ARG C:983 , ASN C:998 , ASN C:1008 , PHE C:1010 , GLY C:1027 , GLN C:1029BINDING SITE FOR RESIDUE FMN C 1033
4AC4SOFTWAREASN D:965 , CYS D:966 , ARG D:967 , LEU D:969 , GLN D:970 , ILE D:982 , ARG D:983 , ASN D:998 , ASN D:1008 , PHE D:1010 , GLY D:1027 , GLN D:1029BINDING SITE FOR RESIDUE FMN D 1033

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JNU)

(-) Exons   (0, 0)

(no "Exon" information available for 1JNU)

(-) Sequences/Alignments

Asymmetric 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:104
 aligned with Q9ZWQ6_ADICA | Q9ZWQ6 from UniProtKB/TrEMBL  Length:1465

    Alignment length:104
                                   938       948       958       968       978       988       998      1008      1018      1028    
        Q9ZWQ6_ADICA    929 KSFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKEQRDVTVQVLNYTKGGRAFWNLFHLQVMRDENGDVQYFIGVQQEM 1032
               SCOP domains d1jnua_ A: Photoreceptor phy3 flavin-binding domain, lov2                                                SCOP domains
               CATH domains 1jnuA00 A:929-1032  [code=3.30.450.20, no name defined]                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........eeeehhhhhhhhh.hhhhhh..hhhhhh....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeee........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                1jnu A  929 KSFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKEQRDVTVQVLNYTKGGRAFWNLFHLQVMRDENGDVQYFIGVQQEM 1032
                                   938       948       958       968       978       988       998      1008      1018      1028    


Chain B from PDB  Type:PROTEIN  Length:104
 aligned with Q9ZWQ6_ADICA | Q9ZWQ6 from UniProtKB/TrEMBL  Length:1465

    Alignment length:104
                                   938       948       958       968       978       988       998      1008      1018      1028    
        Q9ZWQ6_ADICA    929 KSFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKEQRDVTVQVLNYTKGGRAFWNLFHLQVMRDENGDVQYFIGVQQEM 1032
               SCOP domains d1jnub_ B: Photoreceptor phy3 flavin-binding domain, lov2                                                SCOP domains
               CATH domains 1jnuB00 B:929-1032  [code=3.30.450.20, no name defined]                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........eeeehhhhhhhhh.hhhhhh..hhhhhh....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeee........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                1jnu B  929 KSFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKEQRDVTVQVLNYTKGGRAFWNLFHLQVMRDENGDVQYFIGVQQEM 1032
                                   938       948       958       968       978       988       998      1008      1018      1028    


Chain C from PDB  Type:PROTEIN  Length:104
 aligned with Q9ZWQ6_ADICA | Q9ZWQ6 from UniProtKB/TrEMBL  Length:1465

    Alignment length:104
                                   938       948       958       968       978       988       998      1008      1018      1028    
        Q9ZWQ6_ADICA    929 KSFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKEQRDVTVQVLNYTKGGRAFWNLFHLQVMRDENGDVQYFIGVQQEM 1032
               SCOP domains d1jnuc_ C: Photoreceptor phy3 flavin-binding domain, lov2                                                SCOP domains
               CATH domains 1jnuC00 C:929-1032  [code=3.30.450.20, no name defined]                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........eeeehhhhhhhhh.hhhhhh..hhhhhh....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeee........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                1jnu C  929 KSFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKEQRDVTVQVLNYTKGGRAFWNLFHLQVMRDENGDVQYFIGVQQEM 1032
                                   938       948       958       968       978       988       998      1008      1018      1028    


Chain D from PDB  Type:PROTEIN  Length:104
 aligned with Q9ZWQ6_ADICA | Q9ZWQ6 from UniProtKB/TrEMBL  Length:1465

    Alignment length:104
                                   938       948       958       968       978       988       998      1008      1018      1028    
        Q9ZWQ6_ADICA    929 KSFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKEQRDVTVQVLNYTKGGRAFWNLFHLQVMRDENGDVQYFIGVQQEM 1032
               SCOP domains d1jnud_ D: Photoreceptor phy3 flavin-binding domain, lov2                                                SCOP domains
               CATH domains 1jnuD00 D:929-1032  [code=3.30.450.20, no name defined]                                                  CATH domains
           Pfam domains (1) PAS_9-1jnuD01 D:929-1032                                                                                 Pfam domains (1)
           Pfam domains (2) PAS_9-1jnuD02 D:929-1032                                                                                 Pfam domains (2)
           Pfam domains (3) PAS_9-1jnuD03 D:929-1032                                                                                 Pfam domains (3)
           Pfam domains (4) PAS_9-1jnuD04 D:929-1032                                                                                 Pfam domains (4)
         Sec.struct. author .eeeee........eeeehhhhhhhhh.hhhhhh..hhhhhh....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeee........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                1jnu D  929 KSFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKEQRDVTVQVLNYTKGGRAFWNLFHLQVMRDENGDVQYFIGVQQEM 1032
                                   938       948       958       968       978       988       998      1008      1018      1028
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PAS_Fold (84)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9ZWQ6_ADICA | Q9ZWQ6)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0000155    phosphorelay sensor kinase activity    Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
    GO:0009881    photoreceptor activity    The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
biological process
    GO:0009584    detection of visible light    The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm.
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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  1jnu
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 Related Entries

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

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        Q9ZWQ6_ADICA | Q9ZWQ6: 1g28

(-) Related Entries Specified in the PDB File

1byw N-TERMINAL PAS DOMAIN OF HERG
1drm FIXL HEME-BINDING PAS DOMAIN
1g28 DARK-STATE STRUCTURE OF PHY3 LOV2, A FMN-BINDING PAS DOMAIN
2phy PHOTOACTIVE YELLOW PROTEIN, A COUMARIC ACID-BINDING PAS DOMAIN