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(-) Description

Title :  SOLUTION STRUCTURE OF THE ZF-HIT DOMAIN IN DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 59
 
Authors :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Tarada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 07  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Structure Genomics, Zf-Hit Domain, Dead Box Polypeptide 59 Isoform 2, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Gene Regulation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Tarada, S. Yokoyama
Solution Structure Of The Zf-Hit Domain In Dead (Asp-Glu-Ala-Asp) Box Polypeptide 59
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE ATP-DEPENDENT RNA HELICASE DDX59
    ChainsA
    EC Number3.6.1.-
    EngineeredYES
    Expression System PlasmidP060925-04
    Expression System Vector TypePLASMID
    FragmentZF-HIT DOMAIN
    GeneRP11-92G12.2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymDEAD BOX PROTEIN 59, ZINC FINGER HIT DOMAIN- CONTAINING PROTEIN 5

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:22 , CYS A:25 , CYS A:41 , CYS A:45BINDING SITE FOR RESIDUE ZN A 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_031424I107VDDX59_HUMANPolymorphism3795634AI21V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003313141bENSE00001936522chr1:200639097-200638895203DDX59_HUMAN-00--
1.3bENST000003313143bENSE00002179737chr1:200635879-200635065815DDX59_HUMAN1-2682681A:1-60 (gaps)67
1.4aENST000003313144aENSE00001774634chr1:200633214-200633047168DDX59_HUMAN269-324560--
1.5ENST000003313145ENSE00001710255chr1:200628244-20062815590DDX59_HUMAN325-354300--
1.8bENST000003313148bENSE00001632882chr1:200619804-200619553252DDX59_HUMAN355-438840--
1.9aENST000003313149aENSE00000796421chr1:200618354-200618202153DDX59_HUMAN439-489510--
1.10ENST0000033131410ENSE00000796420chr1:200617695-200617567129DDX59_HUMAN490-532430--
1.11cENST0000033131411cENSE00001909196chr1:200613645-200613167479DDX59_HUMAN533-619870--

(-) 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:60
 aligned with DDX59_HUMAN | Q5T1V6 from UniProtKB/Swiss-Prot  Length:619

    Alignment length:67
                                    89        99       109       119       129       139       
          DDX59_HUMAN    80 GAKDSHPSEEPVKSFSKTQRWAEPGEPICVVCGRYGEYICDKTDEDVCSLECKAKHLLQVKEKEEKS 146
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......-------........................ee......ee..hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------V--------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3b  PDB: A:1-60 (gaps) UniProt: 1-268 [INCOMPLETE]           Transcript 1
                 2yqp A   1 GSSGSS-------GFSKTQRWAEPGEPICVVCGRYGEYICDKTDEDVCSLECKAKHLLQVKEKEEKS  60
                                 |   -   |    13        23        33        43        53       
                                 6       7                                                     

   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 2YQP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YQP)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (DDX59_HUMAN | Q5T1V6)
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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
biological process
    GO:0010501    RNA secondary structure unwinding    The process in which a secondary structure of RNA are broken or 'melted'.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.
    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.

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