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(-) Description

Title :  HUMAN UBIQUITIN-CONJUGATING ENZYME E2 J2
 
Authors :  J. R. Walker, G. V. Avvakumov, S. Xue, P. J. Finerty Jr. , E. M. Newman, F. Mackenzie, J. Weigelt, M. Sundstrom, C. Arrowsmith, A. Edwards, A. Bochkarev, S. Dhe-Paganon, Structural Genomics Consortium (S
Date :  24 Nov 05  (Deposition) - 27 Dec 05  (Release) - 28 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Endoplasmic Reticulum, Ligase, Ubl Conjugation Pathway, Structural Genomics Consortium (Sgc) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Sheng, J. H. Hong, R. Doherty, T. Srikumar, J. Shloush, G. V. Avvakumov, J. R. Walker, S. Xue, D. Neculai, J. W. Wan, S. K. Kim, C. H. Arrowsmith, B. Raught, S. Dhe-Paganon
A Human Ubiquitin Conjugating Enzyme (E2)-Hect E3 Ligase Structure-Function Screen.
Mol Cell Proteomics V. 11 329 2012
PubMed-ID: 22496338  |  Reference-DOI: 10.1074/MCP.O111.013706
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2, J2
    ChainsA, B
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET-28LIC
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneUBE2J2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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 2F4W)

(-) Sites  (0, 0)

(no "Site" information available for 2F4W)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F4W)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:71 -Pro A:72
2Phe B:71 -Pro B:72

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F4W)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2J2_HUMAN15-128
 
  2A:15-128
B:15-128
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2J2_HUMAN15-128
 
  1A:15-128
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2J2_HUMAN15-128
 
  1-
B:15-128

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1oENST000003604661oENSE00001479913chr1:1209106-1208879228UB2J2_HUMAN-00--
1.3aENST000003604663aENSE00002201290chr1:1203372-1203242131UB2J2_HUMAN1-44442A:12-44
B:11-44
33
34
1.6bENST000003604666bENSE00001794958chr1:1198766-119872641UB2J2_HUMAN44-58152A:44-58
B:44-58
15
15
1.8cENST000003604668cENSE00001130956chr1:1192690-1192588103UB2J2_HUMAN58-92352A:58-92
B:58-92
35
35
1.9dENST000003604669dENSE00001049677chr1:1192510-1192372139UB2J2_HUMAN92-138472A:92-138 (gaps)
B:92-138 (gaps)
47
47
1.10cENST0000036046610cENSE00001049676chr1:1191505-119142581UB2J2_HUMAN139-165272A:139-165
B:139-165
27
27
1.11fENST0000036046611fENSE00001314685chr1:1190867-1190544324UB2J2_HUMAN166-259942A:166-168
B:166-171
3
6

(-) 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:147
 aligned with UB2J2_HUMAN | Q8N2K1 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:157
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
          UB2J2_HUMAN    12 TATQRLKQDYLRIKKDPVPYICAEPLPSNILEWHYVVRGPEMTPYEGGYYHGKLIFPREFPFKPPSIYMITPNGRFKCNTRLCLSITDFHPDTWNPAWSVSTILTGLLSFMVEKGPTLGSIETSDFTKRQLAVQSLAFNLKDKVFCELFPEVVEEIK 168
               SCOP domains d2f4wa1 A:12-168 Ubiquitin conjugating enzyme, UBC                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh....eeeeee..eeeeeeeeee..........eeeeeee..........eeee..............----------.....hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---UBIQUITIN_CONJUGAT_2  PDB: A:15-128 UniProt: 15-128                                                               ---------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:12-44          -------------Exon 1.8c  PDB: A:58-92            ----------------------------------------------Exon 1.10c  PDB: A:139-165 1.1 Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.6b      ---------------------------------Exon 1.9d  PDB: A:92-138 (gaps) UniProt: 92-138------------------------------ Transcript 1 (2)
                 2f4w A  12 TATQRLKQDYLRIKKDPVPYICAEPLPSNILEWHYVVRGPEMTPYEGGYYHGKLIFPREFPFKPPSIYMITPNGRFKCNTRLC----------WNPAWSVSTILTGLLSFMVEKGPTLGSIETSDFTKRQLAVQSLAFNLKDKVFCELFPEVVEEIK 168
                                    21        31        41        51        61        71        81        91  |      -   |   111       121       131       141       151       161       
                                                                                                             94        105                                                               

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with UB2J2_HUMAN | Q8N2K1 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:161
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 
          UB2J2_HUMAN    11 TTATQRLKQDYLRIKKDPVPYICAEPLPSNILEWHYVVRGPEMTPYEGGYYHGKLIFPREFPFKPPSIYMITPNGRFKCNTRLCLSITDFHPDTWNPAWSVSTILTGLLSFMVEKGPTLGSIETSDFTKRQLAVQSLAFNLKDKVFCELFPEVVEEIKQKQ 171
               SCOP domains d2f4wb_ B: Ubiquitin conjugating enzyme, UBC                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeeeee..eeeeeeeeee..........eeeeeee..........eeee...............---------.....hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----UBIQUITIN_CONJUGAT_2  PDB: B:15-128 UniProt: 15-128                                                               ------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: B:11-44           -------------Exon 1.8c  PDB: B:58-92            ----------------------------------------------Exon 1.10c  PDB: B:139-165 1.11f  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.6b      ---------------------------------Exon 1.9d  PDB: B:92-138 (gaps) UniProt: 92-138--------------------------------- Transcript 1 (2)
                 2f4w B  11 TTATQRLKQDYLRIKKDPVPYICAEPLPSNILEWHYVVRGPEMTPYEGGYYHGKLIFPREFPFKPPSIYMITPNGRFKCNTRLCL---------WNPAWSVSTILTGLLSFMVEKGPTLGSIETSDFTKRQLAVQSLAFNLKDKVFCELFPEVVEEIKQKQ 171
                                    20        30        40        50        60        70        80        90    |    -    |  110       120       130       140       150       160       170 
                                                                                                               95       105                                                                  

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F4W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F4W)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (UB2J2_HUMAN | Q8N2K1)
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: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: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:1903955    positive regulation of protein targeting to mitochondrion    Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
    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:0006986    response to unfolded protein    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an unfolded protein stimulus.
    GO:0030433    ubiquitin-dependent ERAD pathway    The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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