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 :  STRUCTURE OF VP14 IN COMPLEX WITH OXYGEN
 
Authors :  S. A. Messing, S. B. Gabelli, L. M. Amzel
Date :  28 Jun 10  (Deposition) - 10 Nov 10  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Dioxygenase, Seven Blade Beta Propeller, Abscisic Acid, Non Heme Iron, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Messing, S. B. Gabelli, I. Echeverria, J. T. Vogel, J. C. Guan, B. C. Tan, H. J. Klee, D. R. Mccarty, L. M. Amzel
Structural Insights Into Maize Viviparous14, A Key Enzyme I The Biosynthesis Of The Phytohormone Abscisic Acid.
Plant Cell V. 22 2970 2010
PubMed-ID: 20884803  |  Reference-DOI: 10.1105/TPC.110.074815

(-) Compounds

Molecule 1 - 9-CIS-EPOXYCAROTENOID DIOXYGENASE 1, CHLOROPLASTIC
    Chains: A
    EC Number: 1.13.11.51
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL C2X HV
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VP14
    Organism Common: MAIZE
    Organism Scientific: ZEA MAYS
    Organism Taxid: 4577
    Synonym: PROTEIN VIVIPAROUS14, VP-14

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1DIO3Ligand/Ion1,4-DIETHYLENE DIOXIDE
2FE21Ligand/IonFE (II) ION
3OH1Ligand/IonHYDROXIDE ION
4OXY1Ligand/IonOXYGEN MOLECULE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREOXY A:1 , OH A:2 , HIS A:298 , HIS A:347 , HIS A:412 , HIS A:590BINDING SITE FOR RESIDUE FE2 A 605
2AC2SOFTWAREOH A:2 , HIS A:347 , HIS A:412 , HIS A:590 , FE2 A:605BINDING SITE FOR RESIDUE OXY A 1
3AC3SOFTWAREOXY A:1 , HIS A:298 , HIS A:347 , HIS A:590 , FE2 A:605BINDING SITE FOR RESIDUE OH A 2
4AC4SOFTWAREPRO A:134 , ARG A:193BINDING SITE FOR RESIDUE DIO A 2946
5AC5SOFTWAREPHE A:162 , ASP A:163BINDING SITE FOR RESIDUE DIO A 2948

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:410 -A:431

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NPE)

(-) 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:522
 aligned with NCED1_MAIZE | O24592 from UniProtKB/Swiss-Prot  Length:604

    Alignment length:522
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602  
          NCED1_MAIZE    83 QLNLFQRAAAAALDAFEEGFVANVLERPHGLPSTADPAVQIAGNFAPVGERPPVHELPVSGRIPPFIDGVYARNGANPCFDPVAGHHLFDGDGMVHALRIRNGAAESYACRFTETARLRQERAIGRPVFPKAIGELHGHSGIARLALFYARAACGLVDPSAGTGVANAGLVYFNGRLLAMSEDDLPYHVRVADDGDLETVGRYDFDGQLGCAMIAHPKLDPATGELHALSYDVIKRPYLKYFYFRPDGTKSDDVEIPLEQPTMIHDFAITENLVVVPDHQVVFKLQEMLRGGSPVVLDKEKTSRFGVLPKHAADASEMAWVDVPDCFCFHLWNAWEDEATGEVVVIGSCMTPADSIFNESDERLESVLTEIRLDARTGRSTRRAVLPPSQQVNLEVGMVNRNLLGRETRYAYLAVAEPWPKVSGFAKVDLSTGELTKFEYGEGRFGGEPCFVPMDPAAAHPRGEDDGYVLTFVHDERAGTSELLVVNAADMRLEATVQLPSRVPFGFHGTFITGQELEAQAA 604
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------------------------------RPE65-3npeA01 A:124-596                                                                                                                                                                                                                                                                                                                                                                                                                                                                  -------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...............hhhhhhhhhhh....eeeee...eee......eeeeee.............hhhhh..eeeeeeee..eeeeeeeee..hhhhhhhhhhh..............hhhhhhhhhhhhhhh...hhhhh.......eeee..eeee.......eeeee.....eeeeee.hhhhh.........ee......eeeee.........eeeee.........ee............ee...eeeeee..eee.hhhhh.....eee......eeeeee....hhhhheeee....eeeeeeeeee......eeeeeeee................eeeeeee......eeeee.........eeeeee.hhhh.....eeeeee........eeeeee.....eeeee..........eeee.............eeeeeeee......eeeeeee....eeeeeeee.........eeeeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3npe A  83 QLNLFQRAAAAALDAFEEGFVANVLERPHGLPSTADPAVQIAGNFAPVGERPPVHELPVSGRIPPFIDGVYARNGANPCFDPVAGHHLFDGDGMVHALRIRNGAAESYACRFTETARLRQERAIGRPVFPKAIGELHGHSGIARLALFYARAACGLVDPSAGTGVANAGLVYFNGRLLAMSEDDLPYHVRVADDGDLETVGRYDFDGQLGCAMIAHPKLDPATGELHALSYDVIKRPYLKYFYFRPDGTKSDDVEIPLEQPTMIHDFAITENLVVVPDHQVVFKLQEMLRGGSPVVLDAAKTSRFGVLPKHAADASEMAWVDVPDCFCFHLWNAWEDEATGEVVVIGSCMTPADSIFNESDERLESVLTEIRLDARTGRSTRRAVLPPSQQVNLEVGMVNRNLLGRETRYAYLAVAEPWPKVSGFAKVDLSTGELTKFEYGEGRFGGEPCFVPMDPAAAHPRGEDDGYVLTFVHDERAGTSELLVVNAADMRLEATVQLPSRVPFGFHGTFITGQELEAQAA 604
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602
   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 3NPE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: RPE65] (2)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NCED1_MAIZE | O24592)
molecular function
    GO:0045549    9-cis-epoxycarotenoid dioxygenase activity    Catalysis of the reactions: a 9-cis-epoxycarotenoid + O2 = 2-cis,4-trans-xanthoxin + a 12'-apo-carotenal; 9-cis-violaxanthin + O2 = 2-cis,4-trans-xanthoxin + (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-dihydro-12'-apo-beta-caroten-12'-al; and 9'-cis-neoxanthin + O2 = 2-cis,4-trans-xanthoxin + (3S,5R,6R)-5,6-dihydroxy-6,7-didehydro-5,6-dihydro-12'-apo-beta-caroten-12'-al.
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0016702    oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is incorporated into a donor.
biological process
    GO:0009688    abscisic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of abscisic acid, 5-(1-hydroxy-2,6,6,trimethyl-4-oxocyclohex-2-en-1-y1)-3-methylpenta-2,4-dienoic acid.
    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.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

 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
    DIO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OXY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3npe)
 

(-) 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
  3npe
    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
  NCED1_MAIZE | O24592
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.13.11.51
    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
  NCED1_MAIZE | O24592
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3NPE)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3NPE)