Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  N- AND C-TERMINAL HELICES OF OAT LOV2 (404-546) ARE INVOLVED IN LIGHT-INDUCED SIGNAL TRANSDUCTION (ROOM TEMPERATURE (293K) LIGHT STRUCTURE OF LOV2 (404-546))
 
Authors :  A. S. Halavaty, K. Moffat
Date :  22 May 07  (Deposition) - 11 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Lov2, Kinase, Transferase, Atp-Binding, Avena Sativa, Serine/Threonine-Protein Kinase, Light-Induced Signal Transduction, Phototropin1, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Halavaty, K. Moffat
N- And C-Terminal Flanking Regions Modulate Light-Induced Signal Transduction In The Lov2 Domain Of The Blue Light Sensor Phototropin 1 From Avena Sativa.
Biochemistry V. 46 14001 2007
PubMed-ID: 18001137  |  Reference-DOI: 10.1021/BI701543E

(-) Compounds

Molecule 1 - NPH1-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS-GB1-PARALLEL1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: LIGHT, OXYGEN, VOLTAGE DOMAIN, RESIDUES 404-546
    Organism Common: OAT
    Organism Scientific: AVENA SATIVA
    Organism Taxid: 4498
    Synonym: LOV2

 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
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:416 , THR A:418 , ASN A:425 , ASN A:449 , CYS A:450 , ARG A:451 , LEU A:453 , GLN A:454 , VAL A:463 , ARG A:467 , ILE A:470 , ASN A:482 , ASN A:492 , PHE A:494 , LEU A:496 , PHE A:509 , ILE A:510 , GLY A:511 , GLN A:513 , HOH A:2137BINDING SITE FOR RESIDUE FMN A1547
2AC2SOFTWAREPHE A:403 , LEU A:404 , GLN A:502 , ARG A:526 , HOH A:2110BINDING SITE FOR RESIDUE GOL A1548

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V1B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V1B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V1B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V1B)

(-) Exons   (0, 0)

(no "Exon" information available for 2V1B)

(-) 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:144
 aligned with O49003_AVESA | O49003 from UniProtKB/TrEMBL  Length:923

    Alignment length:144
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542    
         O49003_AVESA   403 DLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAEREGVMLIKKTAENIDEAAKEL 546
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----------PAS_9-2v1bA01 A:413-518                                                                                   ---------------------------- Pfam domains
         Sec.struct. author ....hhhhh...eeee........eeeehhhhhhhhh.hhhhhh..hhhhhh....hhhhhhhhhhhhhh...eeeeeeee.....eeeeeeeeeeee.....eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2v1b A 403 FLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAEREGVMLIKKTAENIDEAAKEL 546
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542
   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  (0, 0)

(no "SCOP Domain" information available for 2V1B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V1B)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PAS_Fold (84)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O49003_AVESA | O49003)
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: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.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
biological process
    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: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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2v1b)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2v1b
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  O49003_AVESA | O49003
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  O49003_AVESA | O49003
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O49003_AVESA | O49003: 2v0u 2v0w 2v1a 2wkp 2wkq 2wkr 4wf0 5efw 5hzh 5hzi 5hzj 5hzk

(-) Related Entries Specified in the PDB File

2v0u N- AND C-TERMINAL HELICES OF OAT LOV2 ( 404-546) ARE INVOLVED IN LIGHT-INDUCED SIGNAL TRANSDUCTION (CRYO DARK STRUCTURE OF LOV2 (404-546))
2v0w N- AND C-TERMINAL HELICES OF OAT LOV2 ( 404-546) ARE INVOLVED IN LIGHT-INDUCED SIGNAL TRANSDUCTION (CRYO-TRAPPED LIGHT STRUCTURE OF LOV2 (404-546))
2v1a N- AND C-TERMINAL HELICES OF OAT LOV2 ( 404-546) ARE INVOLVED IN LIGHT-INDUCED SIGNAL TRANSDUCTION (ROOM TEMPERATURE (293K) DARK STRUCTURE OF LOV2 (404-546))