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(-) Description

Title :  SOLUTION STRUCTURE OF CARBOXYL-TERMINAL DOMAIN OF DBP5P
 
Authors :  J. S. Fan, J. Zhang, D. Yang
Date :  28 Nov 08  (Deposition) - 13 Oct 09  (Release) - 13 Oct 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Dbp5P, Atp-Binding, Cytoplasm, Helicase, Hydrolase, Membrane, Mrna Transport, Nuclear Pore Complex, Nucleotide- Binding, Nucleus, Phosphoprotein, Protein Transport, Rna- Binding, Translocation, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. S. Fan, Z. Cheng, J. Zhang, C. Noble, Z. Zhou, H. Song, D. Yang
Solution And Crystal Structures Of Mrna Exporter Dbp5P And Its Interaction With Nucleotides.
J. Mol. Biol. V. 388 1 2009
PubMed-ID: 19281819  |  Reference-DOI: 10.1016/J.JMB.2009.03.004
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE DBP5
    ChainsA
    EC Number3.6.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid562
    Expression System VectorPET-M
    Expression System Vector TypeVECTOR
    FragmentRESIDUES 296-482
    GeneDBP5, RAT8, YOR046C
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymDEAD BOX PROTEIN 5, HELICASE CA5/6, RIBONUCLEIC ACID-TRAFFICKING PROTEIN 8

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2KBF)

(-) Sites  (0, 0)

(no "Site" information available for 2KBF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2KBF)

(-) Sequences/Alignments

NMR Structure
   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:187
 aligned with DBP5_YEAST | P20449 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:187
                                   305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       
           DBP5_YEAST   296 TNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTDDWDEVEKIVKKVLKD 482
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------Helicase_C-2kbfA01 A:348-431                                                        --------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee...hhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhh....eeee....hhhhh......eee...........hhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhh....eee....hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2kbf A 296 TNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTDDWDEVEKIVKKVLKD 482
                                   305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       

   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 2KBF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (25, 25)

NMR Structure(hide GO term definitions)
Chain A   (DBP5_YEAST | P20449)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004004    ATP-dependent RNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003724    RNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix.
    GO:0008186    RNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000822    inositol hexakisphosphate binding    Interacting selectively and non-covalently with inositol hexakisphosphate.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0010501    RNA secondary structure unwinding    The process in which a secondary structure of RNA are broken or 'melted'.
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    GO:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006415    translational termination    The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005934    cellular bud tip    The end of a cellular bud distal to the site of attachment to the mother cell.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005643    nuclear pore    Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
    GO:0044614    nuclear pore cytoplasmic filaments    Filamentous extensions on cytoplasmic face of the nuclear pore complex (NPC). In S. cerevisiae, Nup159p, Nup82p, and Nup42p contribute to the cytoplasmic filaments. In vertebrates, Nup358 is a major component.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005844    polysome    A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DBP5_YEAST | P204492kbe 3gfp 3peu 3pev 3pew 3pey 3rrm 3rrn 5elx

(-) Related Entries Specified in the PDB File

2kbe