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(-) Description

Title :  SOLUTION STRUCTURE OF PHD DOMAIN IN NUCLEIC ACID BINDING PROTEIN-LIKE NP_197993
 
Authors :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  24 May 04  (Deposition) - 24 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Structural Genomics, Phd Domain, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of Phd Domain In Nucleic Acid Binding Protein-Like Np_197993
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHD FINGER FAMILY PROTEIN
    Chains: A
    Engineered: YES
    Expression System Plasmid: L030422-C06
    Expression System Vector Type: PLASMID
    Fragment: PHD DOMAIN
    Gene: RAFL05-17-I01
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: CELL FREE PROTEIN SYNTHESIS

 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:9 , ALA A:11 , CYS A:12 , HIS A:33 , CYS A:36BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:25 , CYS A:28 , CYS A:52 , CYS A:55BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WE9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WE9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WE9)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.ALFL4_ARATH199-251  1A:8-58
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.ALFL4_ARATH202-248  1A:9-55

(-) Exons   (0, 0)

(no "Exon" information available for 1WE9)

(-) 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:64
 aligned with ALFL4_ARATH | O81488 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:97
                                                                                                                        255  
                                   170       180       190       200       210       220       230       240       250    |  
          ALFL4_ARATH   161 SSSKRGSESRAKFSKPEPKDDEEEEEEGVEEEDEDEQGETQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKRARS--   -
               SCOP domains d1w  e9                             a_   A: PHD finger protein At5g26210                          SCOP domains
               CATH domains 1we  9A                             00   A:1-64 Zinc/RING finger domain, C3HC4 (zinc finger)      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...--..-----------------------------..--..............eee......eeehhhh.....hhhh......hhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------ZF_PHD_2  PDB: A:8-58 UniProt: 199-251               ------ PROSITE (1)
                PROSITE (2) -----------------------------------------ZF_PHD_1  PDB: A:9-55 UniProt: 202-248         --------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 1we9 A   1 GSS--GS-----------------------------SG--QCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKSGPSSG  64
                              |  ||  -         -         -      || -|       17        27        37        47        57       
                              3  4|                             6|  8                                                        
                                  5                              7
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WE9)

(-) Gene Ontology  (8, 8)

NMR Structure(hide GO term definitions)
Chain A   (ALFL4_ARATH | O81488)
molecular function
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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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