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(-) Description

Title :  SOLUTION STRUCTURE OF THE UQ_CON DOMAIN FROM HUMAN NEDD8-CONJUGATING ENZYME NCE2
 
Authors :  H. Endo, K. Izumi, M. Yoshida, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 Feb 07  (Deposition) - 14 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Non-Proline Cis Peptide Bond, E2 Conjugating Enzyme, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Endo, K. Izumi, M. Yoshida, F. Hayashi, S. Yokoyama
Solution Structure Of The Uq_con Domain From Human Nedd8-Conjugating Enzyme Nce2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEDD8-CONJUGATING ENZYME UBE2F
    ChainsA
    EC Number6.3.2.-
    EngineeredYES
    Expression System PlasmidP050314-14
    Expression System Vector TypePLASMID
    FragmentUQ_CON
    GeneNCE2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymUBIQUITIN-CONJUGATING ENZYME E2 F, NEDD8 PROTEIN LIGASE UBE2F, NEDD8 CARRIER PROTEIN UBE2F, NEDD8- CONJUGATING ENZYME 2, NEDD8-CONJUGATING ENZYME NCE2

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2EDI)

(-) Sites  (0, 0)

(no "Site" information available for 2EDI)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Tyr A:73 -Asn A:74

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBE2F_HUMAN35-174  1A:17-156
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBE2F_HUMAN105-120  1A:87-102

(-) Exons   (9, 9)

NMR Structure (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000002729301cENSE00001841551chr2:238875597-238875774178UBE2F_HUMAN-00--
1.3ENST000002729303ENSE00000965342chr2:238881734-238881867134UBE2F_HUMAN1-40401A:1-22 (gaps)28
1.6ENST000002729306ENSE00001639741chr2:238896605-23889663430UBE2F_HUMAN40-50111A:22-3211
1.8ENST000002729308ENSE00001685506chr2:238903386-23890345166UBE2F_HUMAN50-72231A:32-5423
1.10cENST0000027293010cENSE00001722321chr2:238925208-23892527568UBE2F_HUMAN72-94231A:54-7623
1.11cENST0000027293011cENSE00001595446chr2:238933983-23893405371UBE2F_HUMAN95-118241A:77-10024
1.12bENST0000027293012bENSE00001722543chr2:238939197-23893925458UBE2F_HUMAN118-137201A:100-11920
1.13aENST0000027293013aENSE00001619260chr2:238940863-23894089533UBE2F_HUMAN138-148111A:120-13011
1.14cENST0000027293014cENSE00001638076chr2:238944519-23894458163UBE2F_HUMAN149-169211A:131-15121
1.15sENST0000027293015sENSE00001638496chr2:238949929-2389512361308UBE2F_HUMAN170-185161A:152-16716

(-) 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:173
 aligned with UBE2F_HUMAN | Q969M7 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:179
                                                                                                                                                                                                      185      
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182  |      
          UBE2F_HUMAN    13 GLKGSRTAATASDSTRRVSVRDKLLVKEVAELEANLPCTCKVHFPDPNKLHCFQLTVTPDEGYYQGGKFQFETEVPDAYNMVPPKVKCLTKIWHPNITETGEICLSLLREHSIDGTGWAPTRTLKDVVWGLNSLFTDLLNFDDPLNIEAAEHHLRDKEDFRNKVDDYIKRYAR------   -
               SCOP domains d2edi      a_ A: automated matches                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....------.......hhhhhhhhhhhhhhhhhh...eeee.........eeeee...........eeeeee..........eeee..................................hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------UBIQUITIN_CONJUGAT_2  PDB: A:17-156 UniProt: 35-174                                                                                         ----------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------UBIQUITIN_CONJUG----------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3  PDB: A:1-22 (gaps)-------------------------------Exon 1.10c  PDB: A:54-7Exon 1.11c  PDB: A:77-10-------------------Exon 1.13a Exon 1.14c           Exon 1.15s      ------ Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.6   -------------------------------------------------------------------Exon 1.12b          ------------------------------------------------------ Transcript 1 (2)
           Transcript 1 (3) -------------------------------------Exon 1.8  PDB: A:32-54 ----------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 2edi A   1 GSSGS------SGSTRRVSVRDKLLVKEVAELEANLPCTCKVHFPDPNKLHCFQLTVTPDEGYYQGGKFQFETEVPDAYNMVPPKVKCLTKIWHPNITETGEICLSLLREHSIDGTGWAPTRTLKDVVWGLNSLFTDLLNFDDPLNIEAAEHHLRDKEDFRNKVDDYIKRYARSGPSSG 173
                                |    - |      14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164         
                                5      6                                                                                                                                                                       

   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, 1)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (UBE2F_HUMAN | Q969M7)
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: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.
    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:0006301    postreplication repair    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication.
    GO:0070534    protein K63-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is added to a protein. K63-linked ubiquitination does not target the substrate protein for degradation, but is involved in several pathways, notably as a signal to promote error-free DNA postreplication repair.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
cellular component
    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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  Cis Peptide Bonds
    Tyr A:73 - Asn A:74   [ RasMol ]  
 

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 Related Entries

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UniProtKB/Swiss-Prot
        UBE2F_HUMAN | Q969M73fn1 4gba

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