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(-) Description

Title :  PROTEASE-ASSOCIATED DOMAIN OF THE E3 LIGASE GRAIL
 
Authors :  J. R. Walker, L. Yermekbayeva, A. Seitova, J. Weigelt, C. Bountra, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Struct Genomics Consortium (Sgc)
Date :  18 Jul 09  (Deposition) - 29 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  E3 Ligase, Energy, Pa Domain, Transmembrane, Protein Turnover, Ubl Conjugation Pathway, Glycoprotein, Structural Genomics Consortium, Sgc, Ligase, Membrane, Metal-Binding, Zinc-Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Walker, L. Yermekbayeva, A. Seitova, J. Weigelt, C. Bountra, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Pa Domain Of The E3 Ligase Grail
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE RNF128
    ChainsA
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System PlasmidPFHMSP-LIC-N
    Expression System StrainSF9
    Expression System Taxid7108
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 38-204
    GeneGRAIL, RNF128
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRING FINGER PROTEIN 128, GENE RELATED TO ENERGY IN LYMPHOCYTES PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:99 , ASN A:101BINDING SITE FOR RESIDUE NAG A 301

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:96 -A:126

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:90 -Gly A:91
2Gly A:200 -Pro A:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ICU)

(-) Sequences/Alignments

Asymmetric Unit
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:171
 aligned with RN128_HUMAN | Q8TEB7 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:192
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202  
          RN128_HUMAN    13 GGCGFSRLLAWCFLLALSPQAPGSRGAEAVWTAYLNVSWRVPHTGVNRTVWELSEEGVYGQDSPLEPVAGVLVPPDGPGALNACNPHTNFTVPTVWGSTVQVSWLALIQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAVDIVAIMIGNLKGTKILQSIQRGIQVTMVIEVGKKHGPWVN 204
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .--------------...-------....eeeeeeeeeee........eeeeeeeeeee........eeeeee..............................eeeeee.....hhhhhhhhhhhh...eeeee....................eeeeehhhhhhhhhhhhhh...eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3icu A  34 G--------------AMD-------GAEAVWTAYLNVSWRVPHTGVNRTVWELSEEGVYGQDSPLEPVAGVLVPPDGPGALNACNPHTNFTVPTVWGSTVQVSWLALIQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAVDIVAIMIGNLKGTKILQSIQRGIQVTMVIEVGKKHGPWVN 204
                            |        -     | | -     |  42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202  
                            |             35 |      38                                                                                                                                                                      
                           34               37                                                                                                                                                                              

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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 3ICU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A   (RN128_HUMAN | Q8TEB7)
molecular function
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0042036    negative regulation of cytokine biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cytokines.
    GO:1904352    positive regulation of protein catabolic process in the vacuole    Any process that activates or increases the frequency, rate or extent of protein catabolic process in the vacuole.
    GO:0061462    protein localization to lysosome    A process in which a protein is transported to, or maintained in, a location within a lysosome.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042787    protein ubiquitination involved in ubiquitin-dependent protein catabolic process    The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
    GO:0031647    regulation of protein stability    Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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