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(-) Description

Title :  NMR BASED STRUCTURAL MODEL OF THE UBCH5B-CNOT4 COMPLEX
 
Authors :  C. Dominguez, A. M. J. J. Bonvin, G. S. Winkler, F. M. A. Van Schaik, H. Th. M. Timmers, R. Boelens
Date :  27 Oct 03  (Deposition) - 07 May 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR; THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B  (5x)
Keywords :  Ligase, Ubiquitin Conjugating Enzyme, Ubiquitin Ligase, Ring Finger Protein, Ccr4-Not Complex, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Dominguez, A. M. J. J. Bonvin, G. S. Winkler, F. M. A. Van Schaik, H. Th. M. Timmers, R. Boelens
Structural Model Of The Ubch5B/Cnot4 Complex Revealed By Combining Nmr, Mutagenesis, And Docking Approaches
Structure V. 12 633 2004
PubMed-ID: 15062086  |  Reference-DOI: 10.1016/J.STR.2004.03.004

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2
    Chains: A
    EC Number: 6.3.2.19
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: UBCH5B, UBIQUITIN CARRIER PROTEIN, E2(17)KB 2
 
Molecule 2 - POTENTIAL TRANSCRIPTIONAL REPRESSOR NOT4HP
    Chains: B
    Fragment: RING FINGER, RESIDUES 12-63
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CNOT4, NOT4H

 Structural Features

(-) Chains, Units

  
Theoretical Model (5x): 

Summary Information (see also Sequences/Alignments below)

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

Theoretical Model (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Theoretical Model (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:14 , CYS B:17 , CYS B:38 , CYS B:41BINDING SITE FOR RESIDUE ZN B 79
2AC2SOFTWARECYS B:31 , CYS B:33 , CYS B:53 , CYS B:56BINDING SITE FOR RESIDUE ZN B 80

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UR6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UR6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UR6)

(-) PROSITE Motifs  (3, 3)

Theoretical Model (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2D2_RAT4-136  1A:4-136
UB2D2_XENLA4-136  1A:4-136
UB2D2_HUMAN4-136  1A:4-136
UB2D2_MOUSE4-136  1A:4-136
2ZF_RING_2PS50089 Zinc finger RING-type profile.CNOT4_HUMAN14-57  1B:14-57
3UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2D2_RAT74-89  1A:74-89
UB2D2_XENLA74-89  1A:74-89
UB2D2_HUMAN74-89  1A:74-89
UB2D2_MOUSE74-89  1A:74-89

(-) Exons   (2, 2)

Theoretical Model (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1eENST000003155441eENSE00001353227chr7:135194824-135194637188CNOT4_HUMAN-00--
1.4aENST000003155444aENSE00002198197chr7:135123171-135122906266CNOT4_HUMAN1-58581B:12-5847
1.5dENST000003155445dENSE00000977793chr7:135107102-135106905198CNOT4_HUMAN59-124661B:59-635
1.6ENST000003155446ENSE00001353213chr7:135100011-13509992587CNOT4_HUMAN125-153290--
1.7ENST000003155447ENSE00001353209chr7:135099181-135099080102CNOT4_HUMAN154-187340--
1.8ENST000003155448ENSE00001215573chr7:135098362-135098237126CNOT4_HUMAN188-229420--
1.9bENST000003155449bENSE00001199278chr7:135095398-135095265134CNOT4_HUMAN230-274450--
1.10ENST0000031554410ENSE00001353200chr7:135082978-13508292158CNOT4_HUMAN274-293200--
1.11ENST0000031554411ENSE00001140991chr7:135080635-135080386250CNOT4_HUMAN294-377840--
1.12bENST0000031554412bENSE00001334775chr7:135079167-135078670498CNOT4_HUMAN377-5431670--
1.13aENST0000031554413aENSE00001215504chr7:135073646-1350709232724CNOT4_HUMAN543-575330--

(-) Sequences/Alignments

Theoretical Model
   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:147
 aligned with UB2D2_HUMAN | P62837 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
          UB2D2_HUMAN     1 MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
               SCOP domains d1ur6a_ A: Ubiquitin conjugating enzyme, UBC                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----UQ_con-1ur6A01 A:5-142                                                                                                                    ----- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...............eeeeee............eeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---UBIQUITIN_CONJUGAT_2  PDB: A:4-136 UniProt: 4-136                                                                                    ----------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (6)
                PROSITE (7) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (7)
                PROSITE (8) -------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (8)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ur6 A   1 MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       


Chain A from PDB  Type:PROTEIN  Length:147
 aligned with UB2D2_MOUSE | P62838 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
          UB2D2_MOUSE     1 MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
               SCOP domains d1ur6a_ A: Ubiquitin conjugating enzyme, UBC                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----UQ_con-1ur6A01 A:5-142                                                                                                                    ----- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...............eeeeee............eeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---UBIQUITIN_CONJUGAT_2  PDB: A:4-136 UniProt: 4-136                                                                                    ----------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (6)
                PROSITE (7) -------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (7)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ur6 A   1 MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       


Chain A from PDB  Type:PROTEIN  Length:147
 aligned with UB2D2_RAT | P62839 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
            UB2D2_RAT     1 MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
               SCOP domains d1ur6a_ A: Ubiquitin conjugating enzyme, UBC                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----UQ_con-1ur6A01 A:5-142                                                                                                                    ----- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...............eeeeee............eeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---UBIQUITIN_CONJUGAT_2  PDB: A:4-136 UniProt: 4-136                                                                                    ----------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) -------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (6)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ur6 A   1 MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       


Chain A from PDB  Type:PROTEIN  Length:147
 aligned with UB2D2_XENLA | P62840 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
          UB2D2_XENLA     1 MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
               SCOP domains d1ur6a_ A: Ubiquitin conjugating enzyme, UBC                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----UQ_con-1ur6A01 A:5-142                                                                                                                    ----- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...............eeeeee............eeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---UBIQUITIN_CONJUGAT_2  PDB: A:4-136 UniProt: 4-136                                                                                    ----------- PROSITE (4)
                PROSITE (5) -------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (5)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ur6 A   1 MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       


Chain B from PDB  Type:PROTEIN  Length:52
 aligned with CNOT4_HUMAN | O95628 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:52
                                    21        31        41        51        61  
          CNOT4_HUMAN    12 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED  63
               SCOP domains d1ur6b_ B: Not-4 N-terminal RING finger domain       SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh...........hhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------------------- PROSITE (4)
                PROSITE (5) --ZF_RING_2  PDB: B:14-57 UniProt: 14-57      ------ PROSITE (5)
               Transcript 1 Exon 1.4a  PDB: B:12-58 UniProt: 1-58          1.5d  Transcript 1
                 1ur6 B  12 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED  63
                                    21        31        41        51        61
   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  (2, 2)

Theoretical Model
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1UR6)

(-) Pfam Domains  (1, 1)

Theoretical Model
(-)
Clan: UBC (69)

(-) Gene Ontology  (32, 61)

Theoretical Model(hide GO term definitions)
Chain A   (UB2D2_MOUSE | P62838)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0061631    ubiquitin conjugating enzyme activity    Isoenergetic transfer of ubiquitin from one protein to another via the reaction X-ubiquitin + Y -> Y-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue.
    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.
biological process
    GO:0070936    protein K48-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is added to a protein. K48-linked ubiquitination targets the substrate protein for degradation.
    GO:0051865    protein autoubiquitination    The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    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 A   (UB2D2_HUMAN | P62837)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0061631    ubiquitin conjugating enzyme activity    Isoenergetic transfer of ubiquitin from one protein to another via the reaction X-ubiquitin + Y -> Y-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue.
    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.
biological process
    GO:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0035666    TRIF-dependent toll-like receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the TRIF adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0070936    protein K48-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is added to a protein. K48-linked ubiquitination targets the substrate protein for degradation.
    GO:0051865    protein autoubiquitination    The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0061418    regulation of transcription from RNA polymerase II promoter in response to hypoxia    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
    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.
cellular component
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    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 A   (UB2D2_XENLA | P62840)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.

Chain A   (UB2D2_RAT | P62839)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    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.
biological process
    GO:0070936    protein K48-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is added to a protein. K48-linked ubiquitination targets the substrate protein for degradation.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.

Chain B   (CNOT4_HUMAN | O95628)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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: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: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:0006977    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
    GO:0000289    nuclear-transcribed mRNA poly(A) tail shortening    Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
    GO:0051865    protein autoubiquitination    The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
cellular component
    GO:0030014    CCR4-NOT complex    The evolutionarily conserved CCR4-NOT complex is involved in several aspects of mRNA metabolism, including repression and activation of mRNA initiation, control of mRNA elongation, and the deadenylation and subsequent degradation of mRNA. In Saccharomyces the CCR4-NOT complex comprises a core complex of 9 proteins (Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p), Caf4p, Caf16p, and several less well characterized proteins.
    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: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
        CNOT4_HUMAN | O95628: 1e4u
        UB2D2_HUMAN | P62837: 1w4u 2clw 2esk 2eso 2esp 2esq 3a33 3jvz 3jw0 3l1y 3tgd 3zni 4a49 4a4b 4a4c 4auq 4ddg 4ddi 4ldt 4v3k 4v3l 4wz3 5d0k 5d0m 5d1k 5d1l 5d1m 5edv 5mnj 5ulf 5ulh 5ulk
        UB2D2_MOUSE | P62838: 1w4u
        UB2D2_RAT | P62839: 1w4u
        UB2D2_XENLA | P62840: 1w4u 3eb6

(-) Related Entries Specified in the PDB File

1e4u N-TERMINAL RING FINGER DOMAIN OF HUMAN NOT-4