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(-) Description

Title :  APC10/DOC1 SUBUNIT OF S. CEREVISIAE
 
Authors :  S. W. N. Au, X. Leng, J. W. A. D. E. Harper, D. Barford
Date :  28 Nov 01  (Deposition) - 15 Mar 02  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cell Cycle, Apc10/Doc1, Apc/Cyclosome, Ubiquitination, E3 Ubiquitin Ligase, Beta Sandwich, Jelly Roll (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. W. N. Au, X. Leng, J. W. A. D. E. Harper, D. Barford
Implications For The Ubiquitination Reaction Of The Anaphase-Promoting Complex From The Crystal Structure Of Th Doc1/Apc10 Subunit.
J. Mol. Biol. V. 316 955 2002
PubMed-ID: 11884135  |  Reference-DOI: 10.1006/JMBI.2002.5399

(-) Compounds

Molecule 1 - DOC1/APC10
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28M
    Expression System StrainB834
    Expression System Taxid562
    FragmentRESIDUE 63-283
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1BR6Ligand/IonBROMIDE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:243binding site for residue BR A 301
2AC2SOFTWAREGLY A:131 , LYS A:187binding site for residue BR A 302
3AC3SOFTWAREHIS A:192 , GLN A:229binding site for residue BR A 303
4AC4SOFTWAREGLY B:131 , PRO B:133 , LYS B:187 , MET B:202binding site for residue BR B 301
5AC5SOFTWAREASN B:82 , GLN B:89binding site for residue BR B 302
6AC6SOFTWAREGLN B:229binding site for residue BR B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GQP)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:152 -Pro A:153
2Gln B:152 -Pro B:153

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GQP)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DOCPS51284 DOC domain profile.APC10_YEAST60-246
 
  2A:93-257
B:93-257

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGL240W1YGL240W.1VII:48613-49365753APC10_YEAST1-2502502A:63-257 (gaps)
B:63-257 (gaps)
195
195

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:181
 aligned with APC10_YEAST | P53068 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:195
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
          APC10_YEAST    30 SVLVLDDRIVDAATKDLYVNGFQEEIQYQNPTPENLQHMFHQGIEILDSARMINVTHLALWKPSSFKLGNPVDFALDDNYDTFWQSDGGQPHQLDIMFSKRMDICVMAIFFSMIADESYAPSLVKVYAGHSPSDARFYKMLEVRNVNGWVALRFLDNREDDQLLKCQFIRLLFPVNHENGKDTHLRGIRLYVPSN 224
               SCOP domains d1gqpa_ A: APC10/DOC1 s      ubunit of the anaphase-promoting complex                                                                                                                               SCOP domains
               CATH domains 1gqpA00 A:63-256 Galact      ose-binding domain-like                                                                                                                                              - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhh........------..hhhhhhhhhhhhhhhhhh..eee.hhhheeee.......hhhhhh.......ee......eeeeeeeeeeeee.eeeeeeehhhhh...eeeeeeeee......eeeeeeeeee.eeeeee..--------.eeeeeeeeeeeee.......ee..eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------DOC  PDB: A:93-257 UniProt: 60-246                                                                                                                                    PROSITE
               Transcript 1 Exon 1.1  PDB: A:63-257 (gaps) UniProt: 1-250 [INCOMPLETE]                                                                                                                                          Transcript 1
                 1gqp A  63 SVLVLDDRIVDAATKDLYVNGFQ------NPTPENLQHMFHQGIEILDSARMINVTHLALWKPSSFKLGNPVDFALDDNYDTFWQSDGGQPHQLDIMFSKRMDICVMAIFFSMIADESYAPSLVKVYAGHSPSDARFYKMLEVRNVNGWVALRF--------LLKCQFIRLLFPVNHENGKDTHLRGIRLYVPSN 257
                                    72        82  |     92       102       112       122       132       142       152       162       172       182       192       202       212   |     -  |    232       242       252     
                                                 85     92                                                                                                                         216      225                                

Chain B from PDB  Type:PROTEIN  Length:189
 aligned with APC10_YEAST | P53068 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:195
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
          APC10_YEAST    30 SVLVLDDRIVDAATKDLYVNGFQEEIQYQNPTPENLQHMFHQGIEILDSARMINVTHLALWKPSSFKLGNPVDFALDDNYDTFWQSDGGQPHQLDIMFSKRMDICVMAIFFSMIADESYAPSLVKVYAGHSPSDARFYKMLEVRNVNGWVALRFLDNREDDQLLKCQFIRLLFPVNHENGKDTHLRGIRLYVPSN 224
               SCOP domains d1gqpb_      B: APC10/D OC1 subunit of the anaphase-promoting complex                                                                                                                               SCOP domains
               CATH domains 1gqpB00      B:63-256 G alactose-binding domain-like                                                                                                                                              - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..-----..........-.......hhhhhhhhhhhhhhhhhhh..ee.hhhheeee.......hhhhhh.......ee......eeeeeeeeeeeee.eeeeeeehhhhh...eeeeeeeee......eeeeeeeeee.eeeeee...........eeeeeeeeeeeee.......ee..eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------DOC  PDB: B:93-257 UniProt: 60-246                                                                                                                                    PROSITE
               Transcript 1 Exon 1.1  PDB: B:63-257 (gaps) UniProt: 1-250 [INCOMPLETE]                                                                                                                                          Transcript 1
                 1gqp B  63 SVLVLDDR-----TKDLYVNGFQ-EIQYQNPTPENLQHMFHQGIEILDSARMINVTHLALWKPSSFKLGNPVDFALDDNYDTFWQSDGGQPHQLDIMFSKRMDICVMAIFFSMIADESYAPSLVKVYAGHSPSDARFYKMLEVRNVNGWVALRFLDNREDDQLLKCQFIRLLFPVNHENGKDTHLRGIRLYVPSN 257
                                   | -   |    82  | |   92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252     
                                  70    76       85 |                                                                                                                                                                          
                                                   87                                                                                                                                                                          

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GQP)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (APC10_YEAST | P53068)
molecular function
    GO:0030234    enzyme regulator activity    Binds to and modulates the activity of an enzyme.
    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.
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:0031497    chromatin assembly    The assembly of DNA, histone proteins, other associated proteins, and sometimes RNA, into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus.
    GO:1904668    positive regulation of ubiquitin protein ligase activity    Any process that activates or increases the frequency, rate or extent of ubiquitin protein ligase activity.
    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.
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: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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