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(-) Description

Title :  STRUCTURE OF NAB2P TANDEM ZINC FINGER 34
 
Authors :  S. Martinez-Lumbreras, C. M. Santiveri, Y. Mirassou, S. Zorrilla, J. M. Perez- Canadillas
Date :  16 Jan 13  (Deposition) - 11 Sep 13  (Release) - 09 Jul 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Rna Binding Protein, Ccch-Type Zinc Finger, Mrna Export, Poly(A) Length Control, Polyadenosine Rna Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Martinez-Lumbreras, C. M. Santiveri, Y. Mirassou, S. Zorrilla, J. M. Perez-Canadillas
Two Singular Types Of Ccch Tandem Zinc Finger In Nab2P Contribute To Polyadenosine Rna Recognition.
Structure V. 21 1800 2013
PubMed-ID: 23994011  |  Reference-DOI: 10.1016/J.STR.2013.07.019

(-) Compounds

Molecule 1 - NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN NAB2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    Fragment: ZINC FINGERS 3 AND 4, RESIDUES 333-401
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: NAB2P

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:340 , CYS A:346 , CYS A:351 , HIS A:355BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWARECYS A:371 , CYS A:377 , CYS A:382 , HIS A:386BINDING SITE FOR RESIDUE ZN A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZJ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZJ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZJ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZJ2)

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGL122C1YGL122C.1VII:280529-2789521578NAB2_YEAST1-5255251A:331-40171

(-) 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:71
 aligned with NAB2_YEAST | P32505 from UniProtKB/Swiss-Prot  Length:525

    Alignment length:71
                                   340       350       360       370       380       390       400 
           NAB2_YEAST   331 KPVQTGIVLCKFGALCSNPSCPFGHPTPANEDAKVIDLMWCDKNLTCDNPECRKAHSSLSKIKEVKPISQK 401
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh..........................hhhhh...........hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:331-401 UniProt: 1-525 [INCOMPLETE]                    Transcript 1
                 3zj2 A 331 GSVQTGIVLCKFGALCSNPSCPFGHPTPANEDAKVIDLMWCDKNLTCDNPECRKAHSSLSKIKEVKPISQK 401
                                   340       350       360       370       380       390       400
   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 3ZJ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZJ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZJ2)

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (NAB2_YEAST | P32505)
molecular function
    GO:0008097    5S rRNA binding    Interacting selectively and non-covalently with 5S ribosomal RNA, the smallest RNA constituent of a ribosome.
    GO:0008312    7S RNA binding    Interacting selectively and non-covalently with 7S RNA, the RNA component of the signal recognition particle (SRP).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008143    poly(A) binding    Interacting selectively and non-covalently with a sequence of adenylyl residues in an RNA molecule, such as the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA.
    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).
    GO:0033204    ribonuclease P RNA binding    Interacting selectively and non-covalently with the RNA subunit of ribonuclease P.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
biological process
    GO:0006378    mRNA polyadenylation    The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
    GO:1900364    negative regulation of mRNA polyadenylation    Any process that stops, prevents or reduces the frequency, rate or extent of mRNA polyadenylation.
    GO:1900152    negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay    Any process that stops, prevents or reduces the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay.
    GO:0016973    poly(A)+ mRNA export from nucleus    The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.
    GO:0045945    positive regulation of transcription from RNA polymerase III promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase III promoter.
    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.
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
        NAB2_YEAST | P32505: 2jps 2lhn 2v75 3lcn 3zj1 4jlq 5l2l

(-) Related Entries Specified in the PDB File

3zj1 STRUCTURE OF NAB2P TANDEM ZINC FINGER 12