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(-) Description

Title :  YEAST CUL1WHB-DCN1P ACETYLATED UBC12N COMPLEX
 
Authors :  D. C. Scott, J. K. Monda, E. J. Bennett, J. W. Harper, B. A. Schulman
Date :  11 Aug 11  (Deposition) - 12 Oct 11  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,D  (1x)
Biol. Unit 2:  A,B,C  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  E2:E3, Ligase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. C. Scott, J. K. Monda, E. J. Bennett, J. W. Harper, B. A. Schulman
N-Terminal Acetylation Acts As An Avidity Enhancer Within A Interconnected Multiprotein Complex.
Science V. 334 674 2011
PubMed-ID: 21940857  |  Reference-DOI: 10.1126/SCIENCE.1209307

(-) Compounds

Molecule 1 - DEFECTIVE IN CULLIN NEDDYLATION PROTEIN 1
    ChainsB, A
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 70-269
    GeneDCN1, YLR128W, L3111
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
 
Molecule 2 - NEDD8-CONJUGATING ENZYME UBC12
    ChainsC, D
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 2-24
    GeneL2142.3, UBC12, YLR306W
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
    SynonymRUB1-CONJUGATING ENZYME, RUB1-PROTEIN LIGASE, UBIQUITIN CARRIER PROTEIN 12

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB D
Biological Unit 2 (1x)ABC 
Biological Unit 3 (1x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP

(-) Sites  (0, 0)

(no "Site" information available for 3TDI)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DCUN1PS51229 DCUN1 domain profile.DCN1_YEAST70-266
 
  2A:70-266
B:70-266
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DCUN1PS51229 DCUN1 domain profile.DCN1_YEAST70-266
 
  2A:70-266
B:70-266
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DCUN1PS51229 DCUN1 domain profile.DCN1_YEAST70-266
 
  2A:70-266
B:70-266
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DCUN1PS51229 DCUN1 domain profile.DCN1_YEAST70-266
 
  2A:70-266
B:70-266

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR128W1YLR128W.1XII:398531-3985333DCN1_YEAST1-110--
1.2YLR128W2YLR128W.2XII:398628-399434807DCN1_YEAST2-2692682A:68-269
B:69-268
202
200

(-) 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:202
 aligned with DCN1_YEAST | Q12395 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:202
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267  
           DCN1_YEAST    68 PPVYPKELTQVFEHYINNNLFDIDSLVKFIEELGYNLEDLATLCLAHLLGYKKLEEPLKREDFLSTWFMQGCSTISDMQECIKTLDVKLHEDLQYFTQIYNYAFNLILDPNRKDIDTDEGIQYWKLFFQPEYPVRMEPDLLEAWFRFLRDEGKTTISKDTWRMLLLFFKRYPTIQKIISDYDETAAWPFIIDEFYECLQDQQ 269
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.....hhhhhhhhhhhhh.....hhhhhhhhhh.........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh........hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh.hhhhhhhhh......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --DCUN1  PDB: A:70-266 UniProt: 70-266                                                                                                                                                                 --- PROSITE
               Transcript 1 Exon 1.2  PDB: A:68-269 UniProt: 2-269 [INCOMPLETE]                                                                                                                                                        Transcript 1
                 3tdi A  68 GSVYPKELTQVFEHYINNNLFDIDSLVKFIEELGYNLEDLATLCLAHLLGYKKLEEPLKREDFLSTWFMQGCSTISDMQECIKTLDVKLHEDLQYFTQIYNYAFNLILDPNRKDIDTDEGIQYWKLFFQPEYPVRMEPDLLEAWFRFLRDEGKTTISKDTWRMLLLFFKRYPTIQKIISDYDETAAWPFIIDEFYECLQDQQ 269
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267  

Chain B from PDB  Type:PROTEIN  Length:200
 aligned with DCN1_YEAST | Q12395 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:200
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268
           DCN1_YEAST    69 PVYPKELTQVFEHYINNNLFDIDSLVKFIEELGYNLEDLATLCLAHLLGYKKLEEPLKREDFLSTWFMQGCSTISDMQECIKTLDVKLHEDLQYFTQIYNYAFNLILDPNRKDIDTDEGIQYWKLFFQPEYPVRMEPDLLEAWFRFLRDEGKTTISKDTWRMLLLFFKRYPTIQKIISDYDETAAWPFIIDEFYECLQDQ 268
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.....hhhhhhhhhhhhh.....hhhhhhhhhh.........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh........hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh.hhhhhhhhh......hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -DCUN1  PDB: B:70-266 UniProt: 70-266                                                                                                                                                                 -- PROSITE
               Transcript 1 Exon 1.2  PDB: B:69-268 UniProt: 2-269 [INCOMPLETE]                                                                                                                                                      Transcript 1
                 3tdi B  69 SVYPKELTQVFEHYINNNLFDIDSLVKFIEELGYNLEDLATLCLAHLLGYKKLEEPLKREDFLSTWFMQGCSTISDMQECIKTLDVKLHEDLQYFTQIYNYAFNLILDPNRKDIDTDEGIQYWKLFFQPEYPVRMEPDLLEAWFRFLRDEGKTTISKDTWRMLLLFFKRYPTIQKIISDYDETAAWPFIIDEFYECLQDQ 268
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268

Chain C from PDB  Type:PROTEIN  Length:14
 aligned with UBC12_YEAST | P52491 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:14
                             1            
                             |       9    
          UBC12_YEAST     - -MLKLRQLQKKKQK  13
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 3tdi C   1 xMLKLRQLQKKKQK  14
                            |       10    
                            1-ACE         

Chain D from PDB  Type:PROTEIN  Length:13
 aligned with UBC12_YEAST | P52491 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:13
                             1           
                             |       9   
          UBC12_YEAST     - -MLKLRQLQKKKQ  12
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 3tdi D   1 xMLKLRQLQKKKQ  13
                            |       10   
                            1-ACE        

   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 3TDI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DCN1_YEAST | Q12395)
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: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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
    GO:0031624    ubiquitin conjugating enzyme binding    Interacting selectively and non-covalently with a ubiquitin conjugating enzyme, any of the E2 proteins.
    GO:0032182    ubiquitin-like protein binding    Interacting selectively and non-covalently with a small conjugating protein such as ubiquitin or a ubiquitin-like protein.
biological process
    GO:0051443    positive regulation of ubiquitin-protein transferase activity    Any process that activates, maintains or increases the rate of ubiquitin transferase activity.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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.

Chain C,D   (UBC12_YEAST | P52491)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019788    NEDD8 transferase activity    Catalysis of the transfer of NEDD8 from one protein to another via the reaction X-NEDD8 + Y --> Y-NEDD8 + X, where both X-NEDD8 and Y-NEDD8 are covalent linkages.
    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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DCN1_YEAST | Q123952is9 2l4e 2l4f 3bq3 3o2p 3o6b
        UBC12_YEAST | P524913o2u

(-) Related Entries Specified in the PDB File

3tdu 3tdz