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(-) Description

Title :  STRUCTURE OF A FLAVIN-BINDING DOMAIN, LOV2, FROM THE CHIMERIC PHYTOCHROME/PHOTOTROPIN PHOTORECEPTOR PHY3
 
Authors :  S. Crosson, K. Moffat
Date :  17 Oct 00  (Deposition) - 21 Mar 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.73
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 :  Phototropin, Lov, Pas Fold, Photoreceptor, Flavoprotein, Fmn-Binding Domain, Alpha-Beta Structure, Signaling Protein, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Crosson, K. Moffat
Structure Of A Flavin-Binding Plant Photoreceptor Domain: Insights Into Light-Mediated Signal Transduction
Proc. Natl. Acad. Sci. Usa V. 98 2995 2001
PubMed-ID: 11248020  |  Reference-DOI: 10.1073/PNAS.051520298
(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
    Expression System Plasmid: PCAL-NEK
    Expression System Strain: BL21
    Expression System Taxid: 511693
    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

 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
1AC1SOFTWAREHOH A:34 , HOH A:46 , THR A:934 , ASN A:941 , ASN A:965 , CYS A:966 , ARG A:967 , LEU A:969 , GLN A:970 , VAL A:979 , ILE A:982 , ARG A:983 , ASN A:998 , ASN A:1008 , PHE A:1010 , PHE A:1025 , GLY A:1027 , GLN A:1029BINDING SITE FOR RESIDUE FMN A 1033
2AC2SOFTWAREHOH B:51 , THR B:934 , ASN B:941 , ASN B:965 , CYS B:966 , ARG B:967 , LEU B:969 , GLN B:970 , VAL B:979 , ILE B:982 , ARG B:983 , ASN B:998 , ASN B:1008 , PHE B:1010 , PHE B:1025 , GLY B:1027 , GLN B:1029BINDING SITE FOR RESIDUE FMN B 2033
3AC3SOFTWAREHOH C:25 , THR C:934 , ASN C:941 , ASN C:965 , CYS C:966 , ARG C:967 , LEU C:969 , GLN C:970 , VAL C:979 , ILE C:982 , ARG C:983 , ASN C:998 , ASN C:1008 , PHE C:1010 , PHE C:1025 , GLY C:1027 , GLN C:1029BINDING SITE FOR RESIDUE FMN C 3033
4AC4SOFTWAREHOH D:3 , HOH D:49 , THR D:934 , ASN D:941 , ASN D:965 , CYS D:966 , ARG D:967 , LEU D:969 , GLN D:970 , VAL D:979 , ILE D:982 , ARG D:983 , ASN D:998 , ASN D:1008 , PHE D:1010 , PHE D:1025 , GLY D:1027 , GLN D:1029BINDING SITE FOR RESIDUE FMN D 4033

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G28)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1G28)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G28)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1G28)

(-) Exons   (0, 0)

(no "Exon" information available for 1G28)

(-) 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 d1g28a_ A: Photoreceptor phy3 flavin-binding domain, lov2                                                SCOP domains
               CATH domains 1g28A00 A:929-1032  [code=3.30.450.20, no name defined]                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........eeeehhhhhhhhh.hhhhhh..hhhhh.....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeee........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                1g28 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 d1g28b_ B: Photoreceptor phy3 flavin-binding domain, lov2                                                SCOP domains
               CATH domains 1g28B00 B:929-1032  [code=3.30.450.20, no name defined]                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........eeeehhhhhhhhh.hhhhhh..hhhhh.....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeee........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                1g28 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 d1g28c_ C: Photoreceptor phy3 flavin-binding domain, lov2                                                SCOP domains
               CATH domains 1g28C00 C:929-1032  [code=3.30.450.20, no name defined]                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........eeeehhhhhhhhh.hhhhhh..hhhhh.....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeee........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                1g28 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 d1g28d_ D: Photoreceptor phy3 flavin-binding domain, lov2                                                SCOP domains
               CATH domains 1g28D00 D:929-1032  [code=3.30.450.20, no name defined]                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........eeeehhhhhhhhh.hhhhhh..hhhhh.....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeee........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                1g28 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  (0, 0)

(no "Pfam Domain" information available for 1G28)

(-) 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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  1g28
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 Related Entries

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        Q9ZWQ6_ADICA | Q9ZWQ6: 1jnu

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