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(-) Description

Title :  HUMAN UBIQUITIN-CONJUGATING ENZYME E2 H
 
Authors :  A. Bochkarev, H. Cui, J. R. Walker, E. M. Newman, F. Mackenzie, K. P. Batt M. Sundstrom, C. Arrowsmith, A. Edwards, S. Dhe-Paganon, Structural Consortium (Sgc)
Date :  06 Jul 07  (Deposition) - 09 Oct 07  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ubiquitin, Ubiquitin-Conjugating Enzyme, Ube2H, Sgc, Ligase, Structural Genomics, Structural Genomics Consortium (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

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 H
    ChainsA, B
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A-LIC
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-179
    GeneUBE2H
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-PROTEIN LIGASE H, UBIQUITIN CARRIER PROTEIN H, UBCH2, E2-20K

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU B:37 , ILE B:38 , SER B:40 , HIS B:42 , HOH B:214 , HOH B:216BINDING SITE FOR RESIDUE NA B 180

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z5D)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:80 -Pro A:81
2Tyr B:80 -Pro B:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z5D)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBE2H_HUMAN31-139
 
  2A:50-158
B:50-158
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBE2H_HUMAN75-91
 
  2A:94-110
B:94-110

(-) Exons   (7, 14)

Asymmetric/Biological Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003556211aENSE00001414343chr7:129592789-129592343447UBE2H_HUMAN1-18182A:23-37
B:25-37
15
13
1.4bENST000003556214bENSE00001331008chr7:129520811-12952073577UBE2H_HUMAN18-44272A:37-63
B:37-63
27
27
1.5ENST000003556215ENSE00001331006chr7:129519482-12951940875UBE2H_HUMAN44-69262A:63-88
B:63-88
26
26
1.7bENST000003556217bENSE00001340849chr7:129498781-12949874240UBE2H_HUMAN69-82142A:88-101
B:88-101
14
14
1.8bENST000003556218bENSE00001340845chr7:129497403-12949735153UBE2H_HUMAN82-100192A:101-119
B:101-119
19
19
1.9cENST000003556219cENSE00001340844chr7:129479175-129479047129UBE2H_HUMAN100-143442A:119-162
B:119-162
44
44
1.10dENST0000035562110dENSE00001408604chr7:129474901-1294705724330UBE2H_HUMAN143-183412A:162-174
B:162-175
13
14

(-) Sequences/Alignments

Asymmetric/Biological 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:152
 aligned with UBE2H_HUMAN | P62256 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:152
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153  
          UBE2H_HUMAN     4 PSPGKRRMDTDVVKLIESKHEVTILGGLNEFVVKFYGPQGTPYEGGVWKVRVDLPDKYPFKSPSIGFMNKIFHPNIDEASGTVCLDVINQTWTALYDLTNIFESFLPQLLAYPNPIDPLNGDAAAMYLHRPEEYKQKIKEYIQKYATEEALK 155
               SCOP domains d2z5da1 A:23-174 Ubiquitin conjugating enzyme, UBC                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeeeee..eeeeeee..........eeeeeee..........eeee................hhhhhhhhh......hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------UBIQUITIN_CONJUGAT_2  PDB: A:50-158 UniProt: 31-139                                                          ---------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------UBIQUITIN_CONJUGA---------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a      -------------------------Exon 1.5  PDB: A:63-88    ------------Exon 1.8b          ------------------------------------------Exon 1.10d    Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.4b  PDB: A:37-63    ------------------------Exon 1.7b     -----------------Exon 1.9c  PDB: A:119-162 UniProt: 100-143  ------------ Transcript 1 (2)
                 2z5d A  23 PSPGKRRMDTDVIKLIESKHEVTILGGLNEFVVKFYGPQGTPYEGGVWKVRVDLPDKYPFKSPSIGFMNKIFHPNIDEASGTVCLDVINQTWTALYDLTNIFESFLPQLLAYPNPIDPLNGDAAAMYLHRPEEYKQKIKEYIQKYATEEALK 174
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with UBE2H_HUMAN | P62256 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:151
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155 
          UBE2H_HUMAN     6 PGKRRMDTDVVKLIESKHEVTILGGLNEFVVKFYGPQGTPYEGGVWKVRVDLPDKYPFKSPSIGFMNKIFHPNIDEASGTVCLDVINQTWTALYDLTNIFESFLPQLLAYPNPIDPLNGDAAAMYLHRPEEYKQKIKEYIQKYATEEALKE 156
               SCOP domains d2z5db_ B: Ubiquitin conjugating enzyme, UBC                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---UQ_con-2z5dB01 B:28-164                                                                                                                  ----------- Pfam domains (1)
           Pfam domains (2) ---UQ_con-2z5dB02 B:28-164                                                                                                                  ----------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhh...eeeeee..eeeeeee..........eeeeeee..........eeee................hhhhhhhhh....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------UBIQUITIN_CONJUGAT_2  PDB: B:50-158 UniProt: 31-139                                                          ----------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------UBIQUITIN_CONJUGA----------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a    -------------------------Exon 1.5  PDB: B:63-88    ------------Exon 1.8b          ------------------------------------------Exon 1.10d     Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.4b  PDB: B:37-63    ------------------------Exon 1.7b     -----------------Exon 1.9c  PDB: B:119-162 UniProt: 100-143  ------------- Transcript 1 (2)
                 2z5d B  25 PGKRRMDTDVIKLIESKHEVTILGGLNEFVVKFYGPQGTPYEGGVWKVRVDLPDKYPFKSPSIGFMNKIFHPNIDEASGTVCLDVINQTWTALYDLTNIFESFLPQLLAYPNPIDPLNGDAAAMYLHRPEEYKQKIKEYIQKYATEEALKE 175
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174 

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z5D)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: UBC (69)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (UBE2H_HUMAN | P62256)
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: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.
    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:0043161    proteasome-mediated 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 ubiquitin, and mediated by the proteasome.
    GO:0070979    protein K11-linked ubiquitination    A protein ubiquitination process in which ubiquitin monomers are attached to a protein, and then ubiquitin polymers are formed by linkages between lysine residues at position 11 of the ubiquitin monomers. K11-linked polyubiquitination targets the substrate protein for degradation. The anaphase-promoting complex promotes the degradation of mitotic regulators by assembling K11-linked polyubiquitin chains.
    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.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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