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(-) Description

Title :  FIRST PBZ DOMAIN OF HUMAN APLF PROTEIN IN COMPLEX WITH RIBOFURANOSYLADENOSINE
 
Authors :  D. Neuhaus, S. Eustermann, C. Brockmann, J. Yang
Date :  04 Nov 09  (Deposition) - 19 Jan 10  (Release) - 16 Feb 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Adp-Ribosylation, Dna Damage, Dna Repair, Metal-Binding, Nucleotide-Binding, Nucleus, Zinc, Zinc-Finger, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Eustermann, C. Brockmann, P. V. Mehrotra, J. C. Yang, D. Loakes, S. C. West, I. Ahel, D. Neuhaus
Solution Structures Of The Two Pbz Domains From Human Aplf And Their Interaction With Poly(Adp-Ribose).
Nat. Struct. Mol. Biol. V. 17 241 2010
PubMed-ID: 20098424  |  Reference-DOI: 10.1038/NSMB.1747

(-) Compounds

Molecule 1 - APRATAXIN AND PNK-LIKE FACTOR
    ChainsA
    EC Number4.2.99.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPGEX-6P-1
    FragmentSEQUENCE DATABASE RESIDUES 363-451, PBZ-TYPE 1 DOMAIN
    GeneAPLF, C2ORF13, PALF, XIP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPURINIC-APYRIMIDINIC ENDONUCLEASE APLF, PNK AND APTX-LIKE FHA DOMAIN-CONTAINING PROTEIN, XRCC1-INTERACTING PROTEIN 1

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

NMR Structure (3, 3)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE
2RIB1Ligand/IonRIBOSE
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

NMR Structure (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:379 , CYS A:385 , HIS A:392 , HIS A:398BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWARETYR A:381 , ASN A:384 , CYS A:385 , TYR A:386 , RIB A:1003BINDING SITE FOR RESIDUE ADN A 1002
3AC3SOFTWAREMET A:380 , TYR A:386 , ARG A:387 , ADN A:1002BINDING SITE FOR RESIDUE RIB A 1003

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2KQD)

(-) 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:55
 aligned with APLF_HUMAN | Q8IW19 from UniProtKB/Swiss-Prot  Length:511

    Alignment length:85
                                   342       352       362       372       382       392       402       412     
           APLF_HUMAN   333 GDSLQDESQGSHSESSSNPSNPETLHAKATDSVLQGSEGNKVKRTSCMYGANCYRKNPVHFQHFSHPGDSDYGGVQIVGQDETDD 417
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------zf-CCHH-2kqdA01 A:377-402 --------------- Pfam domains
         Sec.struct. author .------....------------------------.......................hhhhh...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 2kqd A 363 G------PLGS------------------------GSEGNKVKRTSCMYGANCYRKNPVHFQHFSHPGDSDYGGVQIVGQDETDD 417
                            |      366|        -         -     | 372       382       392       402       412     
                            |    364  |                      368                                                 
                          363       367                                                                          

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2KQD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (APLF_HUMAN | Q8IW19)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003906    DNA-(apurinic or apyrimidinic site) lyase activity    Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
    GO:0004520    endodeoxyribonuclease activity    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    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).
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006302    double-strand break repair    The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0051106    positive regulation of DNA ligation    Any process that activates or increases the frequency, rate or extent of DNA ligation, the re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.
    GO:0045191    regulation of isotype switching    Any process that modulates the frequency, rate or extent of isotype switching.
    GO:0000012    single strand break repair    The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.
    GO:0035861    site of double-strand break    A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix.

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 Related Entries

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

UniProtKB/Swiss-Prot
        APLF_HUMAN | Q8IW192kqb 2kqc 2kqe 2kuo 5e50

(-) Related Entries Specified in the PDB File

2kqb FIRST PBZ DOMAIN OF HUMAN APLF PROTEIN
2kqc SECOND PBZ DOMAIN OF HUMAN APLF PROTEIN
2kqe SECOND PBZ DOMAIN OF HUMAN APLF PROTEIN IN COMPLEX WITH RIBOFURANOSYLADENOSINE