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(-) Description

Title :  STRUCTURE OF THE UBR-BOX OF THE UBR1 UBIQUITIN LIGASE
 
Authors :  E. Matta-Camacho, G. Kozlov, F. Li, K. Gehring
Date :  14 Jul 10  (Deposition) - 11 Aug 10  (Release) - 20 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Zinc Finger-Like, Ubiquitin Ligase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Matta-Camacho, G. Kozlov, F. F. Li, K. Gehring
Structural Basis Of Substrate Recognition And Specificity I The N-End Rule Pathway.
Nat. Struct. Mol. Biol. V. 17 1182 2010
PubMed-ID: 20835242  |  Reference-DOI: 10.1038/NSMB.1894

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE UBR1
    ChainsA, B
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentUBR-BOX, UNP RESIDUES 98-168
    GeneUBR1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymN-RECOGNIN-1, UBIQUITIN-PROTEIN LIGASE E3-ALPHA-1, UBIQUITIN-PROTEIN LIGASE E3-ALPHA-I

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1ZN6Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:99 , CYS A:124 , CYS A:127 , CYS A:149BINDING SITE FOR RESIDUE ZN A 4
2AC2SOFTWARECYS A:127 , CYS A:151 , CYS A:163 , HIS A:166BINDING SITE FOR RESIDUE ZN A 5
3AC3SOFTWARECYS A:112 , CYS A:115 , HIS A:133 , HIS A:136BINDING SITE FOR RESIDUE ZN A 6
4AC4SOFTWARECYS B:99 , CYS B:124 , CYS B:127 , CYS B:149BINDING SITE FOR RESIDUE ZN B 1
5AC5SOFTWARECYS B:127 , CYS B:151 , CYS B:163 , HIS B:166BINDING SITE FOR RESIDUE ZN B 2
6AC6SOFTWARECYS B:112 , CYS B:115 , HIS B:133 , HIS B:136BINDING SITE FOR RESIDUE ZN B 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NY1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NY1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_075179V122LUBR1_HUMANDisease (JBS)  ---A/BV122L
2UniProtVAR_075180C127FUBR1_HUMANDisease (JBS)  ---A/BC127F
3UniProtVAR_024741H136RUBR1_HUMANDisease (JBS)119477054A/BH136R
4UniProtVAR_075181H166RUBR1_HUMANDisease (JBS)  ---A/BH166R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_075179V122LUBR1_HUMANDisease (JBS)  ---AV122L
2UniProtVAR_075180C127FUBR1_HUMANDisease (JBS)  ---AC127F
3UniProtVAR_024741H136RUBR1_HUMANDisease (JBS)119477054AH136R
4UniProtVAR_075181H166RUBR1_HUMANDisease (JBS)  ---AH166R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_075179V122LUBR1_HUMANDisease (JBS)  ---BV122L
2UniProtVAR_075180C127FUBR1_HUMANDisease (JBS)  ---BC127F
3UniProtVAR_024741H136RUBR1_HUMANDisease (JBS)119477054BH136R
4UniProtVAR_075181H166RUBR1_HUMANDisease (JBS)  ---BH166R

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_UBRPS51157 Zinc finger UBR-type profile.UBR1_HUMAN97-168  1A:97-167
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_UBRPS51157 Zinc finger UBR-type profile.UBR1_HUMAN97-168  1A:97-167
Biological Unit 2 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_UBRPS51157 Zinc finger UBR-type profile.UBR1_HUMAN97-168  0-

(-) Exons   (0, 0)

(no "Exon" information available for 3NY1)

(-) Sequences/Alignments

Asymmetric 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:73
 aligned with UBR1_HUMAN | Q8IWV7 from UniProtKB/Swiss-Prot  Length:1749

    Alignment length:88
                                    89        99       109       119       129       139       149       159        
           UBR1_HUMAN    80 GEDPDICLEKLKHSGAFQLCGRVFKSGETTYSCRDCAIDPTCVLCMDCFQDSVHKNHRYKMHTSTGGGFCDCGDTEAWKTGPFCVNHE 167
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .------------.---...........eeeee...........hhhhhhhhhhhhh.eeeee......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------L----F--------R-----------------------------R- SAPs(SNPs)
                    PROSITE -----------------ZF_UBR  PDB: A:97-167 UniProt: 97-168                                   PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 3ny1 A  95 G------------S---QLCGRVFKSGETTYSCRDCAIDPTCVLCMDCFQDSVHKNHRYKMHTSTGGGFCDCGDTEAWKTGPFCVNHE 167
                            |        -   |   |99       109       119       129       139       149       159        
                            |           96  97                                                                      
                           95                                                                                       

Chain B from PDB  Type:PROTEIN  Length:70
 aligned with UBR1_HUMAN | Q8IWV7 from UniProtKB/Swiss-Prot  Length:1749

    Alignment length:70
                                   107       117       127       137       147       157       167
           UBR1_HUMAN    98 LCGRVFKSGETTYSCRDCAIDPTCVLCMDCFQDSVHKNHRYKMHTSTGGGFCDCGDTEAWKTGPFCVNHE 167
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
           Pfam domains (1) zf-UBR-3ny1B01 B:98-167                                                Pfam domains (1)
           Pfam domains (2) zf-UBR-3ny1B02 B:98-167                                                Pfam domains (2)
         Sec.struct. author ..........eeeee..........eehhhhhhhhhhhh.eeeee......................... Sec.struct. author
                 SAPs(SNPs) ------------------------L----F--------R-----------------------------R- SAPs(SNPs)
                    PROSITE ZF_UBR  PDB: - UniProt: 97-168                                         PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 3ny1 B  98 LCGRVFKSGETTYSCRDCAIDPTCVLCMDCFQDSVHKNHRYKMHTSTGGGFCDCGDTEAWKTGPFCVNHE 167
                                   107       117       127       137       147       157       167

   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 3NY1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NY1)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (UBR1_HUMAN | Q8IWV7)
molecular function
    GO:0070728    leucine binding    Interacting selectively and non-covalently with 2-amino-4-methylpentanoic acid.
    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: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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0071233    cellular response to leucine    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 leucine stimulus.
    GO:0032007    negative regulation of TOR signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of TOR signaling.
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0006511    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 a ubiquitin group, or multiple ubiquitin groups, to the protein.
    GO:0071596    ubiquitin-dependent protein catabolic process via the N-end rule pathway    The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the N-end rule pathway. In the N-end rule pathway, destabilizing N-terminal residues (N-degrons) in substrates are recognized by E3 ligases (N-recognins), whereupon the substrates are linked to ubiquitin and then delivered to the proteasome for degradation.
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:0000502    proteasome complex    A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.
    GO:0000151    ubiquitin ligase complex    A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UBR1_HUMAN | Q8IWV75tdc

(-) Related Entries Specified in the PDB File

3ny2 STRUCTURE OF THE UBR-BOX OF UBR2 UBIQUITIN LIGASE
3ny3 STRUCTURE OF THE UBR-BOX OF UBR2 IN COMPLEX WITH N-RECOGNIN