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(-) Description

Title :  ISOLATED RING DOMAIN
 
Authors :  N. G. Brown, E. R. Watson, F. Weissman, G. Royappa, B. Schulman, M. Jarvi R. Vanderlinden, J. J. Frye, R. Qiao, G. Petzold, J. Peters, H. Stark
Date :  13 Aug 14  (Deposition) - 29 Oct 14  (Release) - 19 Nov 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Ring Domain, Zinc Binding Domain, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. G. Brown, E. R. Watson, F. Weissmann, M. A. Jarvis, R. Vanderlinden, C. R. Grace, J. J. Frye, R. Qiao, P. Dube, G. Petzold, S. E. Cho, O. Alsharif, J. Bao, I. F. Davidson, J. J. Zheng, A. Nourse, I. Kurinov, J. M. Peters, H. Stark, B. A. Schulman
Mechanism Of Polyubiquitination By Human Anaphase-Promoting Complex: Ring Repurposing For Ubiquitin Chain Assembly.
Mol. Cell V. 56 246 2014
PubMed-ID: 25306923  |  Reference-DOI: 10.1016/J.MOLCEL.2014.09.009

(-) Compounds

Molecule 1 - ANAPHASE-PROMOTING COMPLEX SUBUNIT 11
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorGST-FUSION WITH C-TERMINAL CYS-HIS6TAG
    FragmentUNP RESIDUES 17-84
    GeneANAPC11, HSPC214
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPC11, CYCLOSOME SUBUNIT 11, HEPATOCELLULAR CARCINOMA- ASSOCIATED RING FINGER PROTEIN

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

NMR Structure (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

NMR Structure (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:9 , ILE A:11 , CYS A:12 , HIS A:42 , CYS A:45BINDING SITE FOR RESIDUE ZN A 101
2AC2SOFTWARECYS A:20 , CYS A:23 , CYS A:30 , HIS A:44BINDING SITE FOR RESIDUE ZN A 102
3AC3SOFTWARECYS A:37 , HIS A:39 , CYS A:59 , CYS A:62BINDING SITE FOR RESIDUE ZN A 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2MT5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2MT5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2MT5)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_RING_2PS50089 Zinc finger RING-type profile.APC11_HUMAN34-77  1A:20-63
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_RING_2PS50089 Zinc finger RING-type profile.APC11_HUMAN34-77  1A:20-63

(-) Exons   (0, 0)

(no "Exon" information available for 2MT5)

(-) 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:70
 aligned with APC11_HUMAN | Q9NYG5 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:75
                                    19        29        39        49        59        69        79     
           APC11_HUMAN   10 GVATWLWVANDENCGICRMAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLHAQQVQQHCPMCRQEWKFKE 84
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----..............................ee.....eehhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------ZF_RING_2  PDB: A:20-63 UniProt: 34-77      ------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                  2mt5 A  1 GS-----VANDENCGICRMAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLHAQQVQQHCPMCRQEWKFKE 70
                             |     | 5        15        25        35        45        55        65     
                             2     3                                                                   

   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 2MT5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2MT5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2MT5)

(-) Gene Ontology  (22, 22)

NMR Structure(hide GO term definitions)
Chain A   (APC11_HUMAN | Q9NYG5)
molecular function
    GO:0097602    cullin family protein binding    Interacting selectively and non-covalently with any member of the cullin family, hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0034450    ubiquitin-ubiquitin ligase activity    Isoenergetic transfer of ubiquitin from one protein to an existing ubiquitin chain via the reaction X-ubiquitin + Y-ubiquitin -> Y-ubiquitin-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0031145    anaphase-promoting complex-dependent catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, with ubiquitin-protein ligation catalyzed by the anaphase-promoting complex, and mediated by the proteasome.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0051436    negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle    Any process that stops, prevents, or reduces the frequency, rate or extent of ubiquitin ligase activity that contributes to the mitotic cell cycle.
    GO:0045842    positive regulation of mitotic metaphase/anaphase transition    Any process that activates or increases the frequency, rate or extent of the cell cycle process in which a cell progresses from metaphase to anaphase during mitosis, triggered by the activation of the anaphase promoting complex by Cdc20/Sleepy homolog which results in the degradation of Securin.
    GO:0051437    positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition    Any process that activates, maintains or increases the rate of ubiquitin ligase activity that contributes to the regulation of the mitotic cell cycle phase transition.
    GO:0043161    proteasome-mediated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0070979    protein K11-linked ubiquitination    A protein ubiquitination process in which ubiquitin monomers are attached to a protein, and then ubiquitin polymers are formed by linkages between lysine residues at position 11 of the ubiquitin monomers. K11-linked polyubiquitination targets the substrate protein for degradation. The anaphase-promoting complex promotes the degradation of mitotic regulators by assembling K11-linked polyubiquitin chains.
    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:0051439    regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle    A cell cycle process that modulates the frequency, rate or extent of ubiquitin ligase activity that contributes to the mitotic cell cycle.
cellular component
    GO:0005680    anaphase-promoting complex    A ubiquitin ligase complex that degrades mitotic cyclins and anaphase inhibitory protein, thereby triggering sister chromatid separation and exit from mitosis. Substrate recognition by APC occurs through degradation signals, the most common of which is termed the Dbox degradation motif, originally discovered in cyclin B.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        APC11_HUMAN | Q9NYG54r2y 4ui9 5a31 5g04 5g05 5jg6 5khr 5khu 5l9t 5l9u 5lcw

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