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(-) Description

Title :  SOLUTION STRUCTURE OF THE UBIQUITIN-BINDING MOTIF OF HUMAN POLYMERASE IOTA
 
Authors :  M. G. Bomar, S. D'Souza, M. Bienko, I. Dikic, G. Walker
Date :  11 Apr 09  (Deposition) - 23 Feb 10  (Release) - 02 Mar 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (25x)
Keywords :  Ubm, Ubiquitin-Binding Domain, Polymerase Iota, Translesion Synthesis, Tls, Immunoglobulin G-Binding Protein, Ubiquitin-Binding Protein, Transferase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. G. Bomar, S. D'Souza, M. Bienko, I. Dikic, G. C. Walker, P. Zhou
Unconventional Ubiquitin Recognition By The Ubiquitin-Binding Motif Within The Y Family Dna Polymerases Iota And Rev1.
Mol. Cell V. 37 408 2010
PubMed-ID: 20159559  |  Reference-DOI: 10.1016/J.MOLCEL.2009.12.038

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN G-BINDING PROTEIN G, DNA POLYMERASE IOTA
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET30-GB1-FUSION
    FragmentUNP RESIDUES 304-357, 676-715
    GeneSPG, POLI, RAD30B
    Organism ScientificSTREPTOCOCCUS SP., HOMO SAPIENS
    Organism Taxid1320, 9606
    SynonymIGG-BINDING PROTEIN G, RAD30 HOMOLOG B, ETA2

 Structural Features

(-) Chains, Units

  
NMR Structure (25x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2KHU)

(-) Sites  (0, 0)

(no "Site" information available for 2KHU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021245A731TPOLI_HUMANPolymorphism8305AT91T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2KHU)

(-) 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:32
 aligned with POLI_HUMAN | Q9UNA4 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:32
                                   710       720       730  
           POLI_HUMAN   701 KITFPSDIDPQVFYELPEAVQKELLAEWKRAG 732
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------T- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                 2khu A  61 KITFPSDIDPQVFYELPEAVQKELLAEWKRTG  92
                                    70        80        90  

Chain A from PDB  Type:PROTEIN  Length:32
 aligned with SPG2_STRSG | P19909 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:60
                                   359       369       379       389       399       409
           SPG2_STRSG   350 TKTFTVTEKPEVIDASELTPAVTTYKLVINGKTLKGETTTEAVDAATAEKVFKQYANDNG 409
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author ....-----.-----...hhhhh-h..------------hhhhh----hhhhhhhhh-hh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------T- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 2khu A  61 KITF-----P-----SDIDPQVF-YEL------------PEAVQ----KELLAEWKR-TG  92
                               |    65     |  70  | | |  -        77   |    83      | 92
                              64    65    66     73 | |           77  81   82      90 | 
                                                   74 |                              91 
                                                     76                                 

   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 2KHU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2KHU)

(-) Gene Ontology  (22, 22)

NMR Structure(hide GO term definitions)
Chain A   (POLI_HUMAN | Q9UNA4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    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:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    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:0042276    error-prone translesion synthesis    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions and causes an increase in the endogenous mutation level. For example, in E. coli, a low fidelity DNA polymerase, pol V, copies lesions that block replication fork progress. This produces mutations specifically targeted to DNA template damage sites, but it can also produce mutations at undamaged sites.
    GO:0019985    translesion synthesis    The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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.

Chain A   (SPG2_STRSG | P19909)
molecular function
    GO:0019864    IgG binding    Interacting selectively and non-covalently with an immunoglobulin of an IgG isotype.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        POLI_HUMAN | Q9UNA41t3n 1zet 2alz 2dpi 2dpj 2fll 2fln 2flp 2khw 2ktf 2l0f 2l0g 2mbb 3epg 3epi 3g6v 3g6x 3g6y 3gv5 3gv7 3gv8 3h40 3h4b 3h4d 3ngd 3osn 3q8p 3q8q 3q8r 3q8s 4ebc 4ebd 4ebe 4eyh 4eyi 4fs1 4fs2 5kt2 5kt3 5kt4 5kt5 5kt6 5kt7 5ulw 5ulx
        SPG2_STRSG | P199091fcc 1fcl 1fd6 1gb4 1gjs 1gjt 1ibx 1p7e 1p7f 1qkz 1uwx 1zxh 2gi9 2i2y 2i38 2igg 2jsv 2ju6 2khw 2kn4 2kq4 2kwd 2lum 2n9k 2n9l 2oed 2on8 2onq 2plp 2qmt 3fil 3ui3 3v3x 4oza 4ozb 4ozc 4wh4 5bmg 5bmh 5bmi 5hfy 5hg2 5hi1

(-) Related Entries Specified in the PDB File

2khw SOLUTION STRUCTURE OF THE HUMAN POLYMERASE IOTA UBM2- UBIQUITIN COMPLEX