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(-) Description

Title :  STRUCTURAL BASIS FOR RECOGNITION OF THE MRNA CLASS II AU-RICH ELEMENT BY THE TANDEM ZINC FINGER DOMAIN OF TIS11D
 
Authors :  B. P. Hudson, M. A. Martinez-Yamout, H. J. Dyson, P. E. Wright
Date :  12 Nov 03  (Deposition) - 02 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,D  (20x)
Keywords :  Tis11 Ttp Tristetraprolin Butyrate Response Factor Erf Nup475 Zfp Zn Zinc Finger Rna Ss Single-Stranded Are Utr Tandem Intercalation Intercalate Specific, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. P. Hudson, M. A. Martinez-Yamout, H. J. Dyson, P. E. Wright
Recognition Of The Mrna Au-Rich Element By The Zinc Finger Domain Of Tis11D.
Nat. Struct. Mol. Biol. V. 11 257 2004
PubMed-ID: 14981510  |  Reference-DOI: 10.1038/NSMB738
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BUTYRATE RESPONSE FACTOR 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ZFP36L2, BRF2, TIS11D, ERF2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TIS11D PROTEIN, EGF-RESPONSE FACTOR 2, ERF-2
 
Molecule 2 - RNA (5'-R(*UP*UP*AP*UP*UP*UP*AP*UP*U)-3')
    Chains: D
    Engineered: YES
    Other Details: SYNTHETIC
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:159 , CYS A:168 , CYS A:174 , HIS A:178BINDING SITE FOR RESIDUE ZN A 221
2AC2SOFTWARECYS A:197 , CYS A:206 , CYS A:212 , HIS A:216BINDING SITE FOR RESIDUE ZN A 222

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_C3H1PS50103 Zinc finger C3H1-type profile.TISD_HUMAN153-181
191-219		  2A:153-181
A:191-219

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002823881ENSE00001069476chr2:43453748-43453404345TISD_HUMAN1-17170--
1.2ENST000002823882ENSE00001005644chr2:43452891-434495413351TISD_HUMAN18-4944771A:151-22070

(-) 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:70
 aligned with TISD_HUMAN | P47974 from UniProtKB/Swiss-Prot  Length:494

    Alignment length:70
                                   160       170       180       190       200       210       220
           TISD_HUMAN   151 STRYKTELCRPFEESGTCKYGEKCQFAHGFHELRSLTRHPKYKTELCRTFHTIGFCPYGPRCHFIHNADE 220
               SCOP domains d1rgoa1 A:151-186                   d1rgoa2 A:187-220                  SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------zf-CCCH-1rgoA01 A:192-218  -- Pfam domains (1)
           Pfam domains (2) -----------------------------------------zf-CCCH-1rgoA02 A:192-218  -- Pfam domains (2)
         Sec.struct. author ........hhhhhhhh...hhhhh....hhhhh.............hhhhhhhh...hhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --ZF_C3H1  PDB: A:153-181      ---------ZF_C3H1  PDB: A:191-219      - PROSITE
               Transcript 1 Exon 1.2  PDB: A:151-220 UniProt: 18-494 [INCOMPLETE]                  Transcript 1
                 1rgo A 151 STRYKTELCRPFEESGTCKYGEKCQFAHGFHELRSLTRHPKYKTELCRTFHTIGFCPYGPRCHFIHNADE 220
                                   160       170       180       190       200       210       220


Chain D from PDB  Type:RNA  Length:9
                                         
                 1rgo D   1 UUAUUUAUU   9
   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, 2)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1RGO)

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: no clan defined [family: zf-CCCH] (2)

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (TISD_HUMAN | P47974)
molecular function
    GO:0017091    AU-rich element binding    Interacting selectively and non-covalently with a region of RNA containing frequent adenine and uridine bases.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0035925    mRNA 3'-UTR AU-rich region binding    Interacting selectively and non-covalently with a region containing frequent adenine and uridine bases within the 3' untranslated region of a mRNA molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0033077    T cell differentiation in thymus    The process in which a precursor cell type acquires the specialized features of a T cell via a differentiation pathway dependent upon transit through the thymus.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0060216    definitive hemopoiesis    A second wave of blood cell production that, in vertebrates, generates long-term hemopoietic stem cells that continously provide erythroid, myeloid and lymphoid lineages throughout adulthood.
    GO:0030097    hemopoiesis    The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
    GO:0006402    mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
    GO:2000737    negative regulation of stem cell differentiation    Any process that stops, prevents or reduces the frequency, rate or extent of stem cell differentiation.
    GO:0000288    nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay    A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.
    GO:1900153    positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay    Any process that activates or increases the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay.
    GO:0043488    regulation of mRNA stability    Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048103    somatic stem cell division    The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line.
    GO:0035019    somatic stem cell population maintenance    Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        TISD_HUMAN | P47974: 1w0v 1w0w

(-) Related Entries Specified in the PDB File

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