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(-) Description

Title :  CRYSTAL STRUCTURE OF UBCH8
 
Authors :  T. Mizushima, M. Suzuki, N. Teshima, T. Yamane, S. Murata, K. Tanaka
Date :  10 Mar 05  (Deposition) - 22 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ubiquitin, Ubiquitin Conjugating Enzyme, E2, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Mizushima, M. Suzuki, N. Teshima, T. Yamane, S. Murata, K. Tanaka
Crystal Structure Of Ubch8
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 L6
    ChainsA, B
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainBL21(RIPL)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-CONJUGATING ENZYME UBCH8, UBIQUITIN- PROTEIN LIGASE L6, UBIQUITIN CARRIER PROTEIN L6, UBCH8, RETINOIC ACID INDUCED GENE B PROTEIN, RIG-B

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1WZV)

(-) Sites  (0, 0)

(no "Site" information available for 1WZV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:43 -Pro A:44
2Tyr A:60 -Pro A:61
3Pro B:43 -Pro B:44
4Tyr B:60 -Pro B:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2L6_HUMAN5-138
 
  2A:4-137
B:4-137
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2L6_HUMAN75-90
 
  2A:74-89
B:74-89
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2L6_HUMAN5-138
 
  1A:4-137
-
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2L6_HUMAN75-90
 
  1A:74-89
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2L6_HUMAN5-138
 
  1-
B:4-137
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2L6_HUMAN75-90
 
  1-
B:74-89

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002871562aENSE00001106587chr11:57335280-57335058223UB2L6_HUMAN1-992A:2-8
B:2-8
7
7
1.4bENST000002871564bENSE00001804366chr11:57327905-5732781096UB2L6_HUMAN10-41322A:9-40
B:9-40
32
32
1.5ENST000002871565ENSE00001685802chr11:57322096-57321910187UB2L6_HUMAN42-104632A:41-103
B:41-103
63
63
1.6eENST000002871566eENSE00002184446chr11:57319982-57319135848UB2L6_HUMAN104-153502A:103-151
B:103-151
49
49

(-) 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:150
 aligned with UB2L6_HUMAN | O14933 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:150
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152
          UB2L6_HUMAN     3 ASMRVVKELEDLQKKPPPYLRNLSSDDANVLVWHALLLPDQPPYHLKAFNLRISFPPEYPFKPPMIKFTTKIYHPNVDENGQICLPIISSENWKPCTKTCQVLEALNVLVNRPNIREPLRMDLADLLTQNPELFRKNAEEFTLRFGVDRP 152
               SCOP domains d1wzva1 A:2-151 Ubiquitin conjugating enzyme, UBC                                                                                                      SCOP domains
               CATH domains 1wzvA00 A:2-151 Ubiquitin Conjugating Enzyme                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....eeeeee......eeeeee.....hhh.eeeeeeee..........eeee................hhhhh........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --UBIQUITIN_CONJUGAT_2  PDB: A:4-137 UniProt: 5-138                                                                                     -------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------UBIQUITIN_CONJUG-------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.2a   Exon 1.4b  PDB: A:9-40          Exon 1.5  PDB: A:41-103 UniProt: 42-104                        ------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------Exon 1.6e  PDB: A:103-151 UniProt: 104-153        Transcript 1 (2)
                 1wzv A   2 ASMRVVKELEDLQKKPPPYLRNLSSDDANVLVWHALLLPDQPPYHLKAFNLRISFPPEYPFKPPMIKFTTKIYHPNVDENGQICLPIISSENWKPCTKTCQVLEALNVLVNRPNIREPLRMDLADLLTQNPELFRKNAEEFTLRFGVDRP 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with UB2L6_HUMAN | O14933 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:150
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152
          UB2L6_HUMAN     3 ASMRVVKELEDLQKKPPPYLRNLSSDDANVLVWHALLLPDQPPYHLKAFNLRISFPPEYPFKPPMIKFTTKIYHPNVDENGQICLPIISSENWKPCTKTCQVLEALNVLVNRPNIREPLRMDLADLLTQNPELFRKNAEEFTLRFGVDRP 152
               SCOP domains d1wzvb_ B: automated matches                                                                                                                           SCOP domains
               CATH domains 1wzvB00 B:2-151 Ubiquitin Conjugating Enzyme                                                                                                           CATH domains
           Pfam domains (1) ---UQ_con-1wzvB01 B:5-143                                                                                                                     -------- Pfam domains (1)
           Pfam domains (2) ---UQ_con-1wzvB02 B:5-143                                                                                                                     -------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhh....eeeeee......eeeeee.....hhhhh.eeeeee..........eeee................hhhhh........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --UBIQUITIN_CONJUGAT_2  PDB: B:4-137 UniProt: 5-138                                                                                     -------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------UBIQUITIN_CONJUG-------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.2a   Exon 1.4b  PDB: B:9-40          Exon 1.5  PDB: B:41-103 UniProt: 42-104                        ------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------Exon 1.6e  PDB: B:103-151 UniProt: 104-153        Transcript 1 (2)
                 1wzv B   2 ASMRVVKELEDLQKKPPPYLRNLSSDDANVLVWHALLLPDQPPYHLKAFNLRISFPPEYPFKPPMIKFTTKIYHPNVDENGQICLPIISSENWKPCTKTCQVLEALNVLVNRPNIREPLRMDLADLLTQNPELFRKNAEEFTLRFGVDRP 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

   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)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: UBC (69)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (UB2L6_HUMAN | O14933)
molecular function
    GO:0042296    ISG15 transferase activity    Catalysis of the transfer of ISG15 from one protein to another via the reaction X-ISG15 + Y --> Y-ISG15 + X, where both X-ISG15 and Y-ISG15 are covalent linkages.
    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: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:0019787    ubiquitin-like protein transferase activity    Catalysis of the transfer of a ubiquitin-like from one protein to another via the reaction X-ULP + Y --> Y-ULP + X, where both X-ULP and Y-ULP are covalent linkages. ULP represents a ubiquitin-like protein.
    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:0032020    ISG15-protein conjugation    The covalent addition to a protein of ISG15, a ubiquitin-like protein.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    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:0019941    modification-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 modification of the target protein.
    GO:0032480    negative regulation of type I interferon production    Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0019985    translesion synthesis    The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.
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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UB2L6_HUMAN | O149331wzw 2kjh

(-) Related Entries Specified in the PDB File

1wzw THE SAME PROTEIN IN A DIFFERENT SPACE GROUP