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(-) Description

Title :  A PHD FINGER MOTIF IN THE C-TERMINUS OF RAG2 MODULATES RECOMBINATION ACTIVITY
 
Authors :  D. Ivanov, S. G. Hyberts, Z. Sun, G. Wagner
Date :  17 Oct 07  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  V(D)J Recombination, Phosphoinositide Signaling, Rag2, Phd Domain, Dna Recombination, Dna-Binding, Endonuclease, Hydrolase, Nuclease, Nucleus (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. K. Elkin, D. Ivanov, M. Ewalt, C. G. Ferguson, S. G. Hyberts, Z. Y. Sun, G. D. Prestwich, J. Yuan, G. Wagner, M. A. Oettinger, O. P. Gozani
A Phd Finger Motif In The C Terminus Of Rag2 Modulates Recombination Activity.
J. Biol. Chem. V. 280 28701 2005
PubMed-ID: 15964836  |  Reference-DOI: 10.1074/JBC.M504731200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - V(D)J RECOMBINATION-ACTIVATING PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-6P-3
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneRAG2, RAG-2
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymRAG-2

 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:419 , CYS A:423 , VAL A:425 , HIS A:455 , CYS A:458BINDING SITE FOR RESIDUE ZN A 488
2AC2SOFTWARECYS A:446 , HIS A:452 , CYS A:478 , HIS A:481BINDING SITE FOR RESIDUE ZN A 489

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENSMUST000000440311aENSMUSE00000230550chr2:101464875-101465027153RAG2_MOUSE-00--
1.2ENSMUST000000440312ENSMUSE00000230542chr2:101468294-10146835663RAG2_MOUSE-00--
1.3bENSMUST000000440313bENSMUSE00000230533chr2:101469479-1014726853207RAG2_MOUSE1-5365361A:406-487 (gaps)115

(-) 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:82
 aligned with RAG2_MOUSE | P21784 from UniProtKB/Swiss-Prot  Length:527

    Alignment length:115
                                   382       392       402       412       422       432       442       452       462       472       482     
           RAG2_MOUSE   373 GDSTPFEDSEEFCFSAEATSFDGDDEFDTYNEDDEDDESVTGYWITCCPTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERTLIHLSEGSNKYYCNEHVQIARA 487
               SCOP domains -----------------------------------------d2jwoa1 A:414-487 V(D)J recombination-activating protein 2, Rag2           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------RAG2_PHD-2jwoA01 A:414-487                                                 Pfam domains
         Sec.struct. author .---..----------------.....--------------..............................ee.......ee.hhhhh.hhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3b  PDB: A:406-487 (gaps) UniProt: 1-536 [INCOMPLETE]                                                        Transcript 1
                 2jwo A 406 G---PL----------------GSPEF--------------GYWITCCPTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERTLIHLSEGSNKYYCNEHVQIARA 487
                            |   ||   -         -  |   |  -         - |     422       432       442       452       462       472       482     
                            | 407|              409 413            414                                                                         
                          406  408                                                                                                             

   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, 1)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (24, 24)

NMR Structure(hide GO term definitions)
Chain A   (RAG2_MOUSE | P21784)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    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:0035091    phosphatidylinositol binding    Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0005547    phosphatidylinositol-3,4,5-trisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,4,5-trisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3', 4' and 5' positions.
    GO:0043325    phosphatidylinositol-3,4-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions.
    GO:0080025    phosphatidylinositol-3,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 5' positions.
    GO:0005546    phosphatidylinositol-4,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
    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:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0002358    B cell homeostatic proliferation    The non-specific expansion of B cell populations within a whole or part of an organism to reach to a total number of B cells which will then remain stable over time in the absence of an external stimulus.
    GO:0002326    B cell lineage commitment    The process in which a lymphoid progenitor cell becomes committed to become any type of B cell.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0030217    T cell differentiation    The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
    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:0002360    T cell lineage commitment    The process in which a lymphoid progenitor cell becomes committed to becoming any type of T cell.
    GO:0033151    V(D)J recombination    The process in which immune receptor V, D, and J, or V and J gene segments, depending on the specific receptor, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS).
    GO:0046622    positive regulation of organ growth    Any process that activates or increases the frequency, rate or extent of growth of an organ of an organism.
    GO:0002331    pre-B cell allelic exclusion    Expression of a single heavy chain allele during pre-B cell differentiation.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
cellular 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAG2_MOUSE | P217842v83 2v85 2v86 2v87 2v88 2v89 4wwx

(-) Related Entries Specified in the PDB File

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