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(-) Description

Title :  CRYSTAL STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME E2-25KDA (HUNTINGTON INTERACTING PROTEIN 2) M172A MUTANT CRYSTALLIZED AT PH 8.5
 
Authors :  R. C. Wilson, R. C. Hughes, J. W. Flatt, E. J. Meehan, J. D. Ng, P. D. Twigg
Date :  13 Nov 08  (Deposition) - 25 Nov 08  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym./Biol. Unit :  A
Keywords :  Ubiquitin-Conjugating, Huntington Interacting, E2-25K, Ligase, Ubiquitin-Conjugating Enzyme E2 K, E2(25K), Ubiquitin-Protein Ligase, Ubiquitin Carrier Protein, Huntington-Interacting Protein 2, Hip-2, Alternative Splicing, Cytoplasm, Ubl Conjugation, Ubl Conjugation Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. C. Wilson, R. C. Hughes, J. W. Flatt, E. J. Meehan, J. D. Ng, P. D. Twigg
Structure Of Full-Length Ubiquitin-Conjugating Enzyme E2-25 (Huntingtin-Interacting Protein 2).
Acta Crystallogr. , Sect. F V. 65 440 2009
PubMed-ID: 19407372  |  Reference-DOI: 10.1107/S1744309109011117

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 K
    ChainsA
    EC Number2.3.2.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneUBE2K, HIP2, LIG
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymE2 UBIQUITIN-CONJUGATING ENZYME K,HUNTINGTIN-INTERACTING PROTEIN 2,HIP-2,UBIQUITIN CARRIER PROTEIN,UBIQUITIN-CONJUGATING ENZYME E2-25 KDA,UBIQUITIN-CONJUGATING ENZYME E2-25K,UBIQUITIN- PROTEIN LIGASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CA1Ligand/IonCALCIUM ION
3PG42Ligand/IonTETRAETHYLENE GLYCOL
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:185 , LYS A:186 , THR A:192BINDING SITE FOR RESIDUE PG4 A 201
2AC2SOFTWAREVAL A:151 , ARG A:176BINDING SITE FOR RESIDUE PG4 A 202
3AC3SOFTWARECYS A:92 , LYS A:97 , ASP A:124 , PRO A:125BINDING SITE FOR RESIDUE BME A 203
4AC4SOFTWAREASP A:30 , LEU A:31 , GLY A:173BINDING SITE FOR RESIDUE TRS A 204
5AC5SOFTWAREASP A:0 , GLU A:20 , GLN A:99 , HOH A:216 , HOH A:265BINDING SITE FOR RESIDUE CA A 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F92)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:-1 -Asp A:0
2Tyr A:66 -Pro A:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F92)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBE2K_HUMAN7-143  1A:7-143
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBE2K_HUMAN80-96  1A:80-96
3UBAPS50030 Ubiquitin-associated domain (UBA) profile.UBE2K_HUMAN160-200  1A:160-200

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002614271aENSE00001368901chr4:39699664-39700010347UBE2K_HUMAN1-21211A:1-2121
1.2ENST000002614272ENSE00001504557chr4:39739040-3973913394UBE2K_HUMAN22-53321A:22-5332
1.3ENST000002614273ENSE00001504556chr4:39747372-3974743059UBE2K_HUMAN53-72201A:53-7220
1.4ENST000002614274ENSE00001077329chr4:39757277-3975735983UBE2K_HUMAN73-100281A:73-10028
1.5ENST000002614275ENSE00001077323chr4:39776454-39776553100UBE2K_HUMAN100-133341A:100-13334
1.6ENST000002614276ENSE00001077322chr4:39779302-39779430129UBE2K_HUMAN134-176431A:134-17643
1.7hENST000002614277hENSE00001077328chr4:39779980-397844124433UBE2K_HUMAN177-200241A:177-20024

(-) 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:202
 aligned with UBE2K_HUMAN | P61086 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:202
                              1                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198  
          UBE2K_HUMAN     - --MANIAVQRIKREFKEVLKSEETSKNQIKVDLVDENFTELRGEIAGPPDTPYEGGRYQLEIKIPETYPFNPPKVRFITKIWHPNISSVTGAICLDILKDQWAAAMTLRTVLLSLQALLAAAEPDDPQDAVVANQYKQNPEMFKQTARLWAHVYAGAPVSSPEYTKKIENLCAMGFDRNAVIVALSSKSWDVETATELLLSN 200
               SCOP domains d3f92a1 A:-1-156 Ubiquitin-conjugating enzyme E2-25 kDa, E2 domain                                                                                            d3f92a2 A:157-200                            SCOP domains
               CATH domains 3f92A01 A:-1-157 Ubiquitin Conjugating Enzyme                                                                                                                  ------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh..eeeee......eeeeeee..........eeeeeee..........eeee.................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------UBIQUITIN_CONJUGAT_2  PDB: A:7-143 UniProt: 7-143                                                                                        ----------------UBA  PDB: A:160-200 UniProt: 160-200      PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------UBIQUITIN_CONJUGA-------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) --Exon 1.1a  PDB: A:1-2Exon 1.2  PDB: A:22-53          -------------------Exon 1.4  PDB: A:73-100     ---------------------------------Exon 1.6  PDB: A:134-176 UniProt: 134-176  Exon 1.7h  PDB: A:177-20 Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.3            ---------------------------Exon 1.5  PDB: A:100-133          ------------------------------------------------------------------- Transcript 1 (2)
                 3f92 A  -1 FDMANIAVQRIKREFKEVLKSEETSKNQIKVDLVDENFTELRGEIAGPPDTPYEGGRYQLEIKIPETYPFNPPKVRFITKIWHPNISSVTGAICLDILKDQWAAAMTLRTVLLSLQALLAAAEPDDPQDAVVANQYKQNPEMFKQTARLWAHVYAGAPVSSPEYTKKIENLCAAGFDRNAVIVALSSKSWDVETATELLLSN 200
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198  

   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/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F92)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UBE2K_HUMAN | P61086)
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: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.
    GO:0034450    ubiquitin-ubiquitin ligase activity    Isoenergetic transfer of ubiquitin from one protein to an existing ubiquitin chain via the reaction X-ubiquitin + Y-ubiquitin -> Y-ubiquitin-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue.
biological process
    GO:0035458    cellular response to interferon-beta    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-beta stimulus. Interferon-beta is a type I interferon.
    GO:0010994    free ubiquitin chain polymerization    The process of creating free ubiquitin chains, compounds composed of a large number of ubiquitin monomers. These chains are not conjugated to a protein.
    GO:0070059    intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to a stimulus indicating endoplasmic reticulum (ER) stress, and ends when the execution phase of apoptosis is triggered. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
    GO:0010800    positive regulation of peptidyl-threonine phosphorylation    Any process that increases the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    GO:0060340    positive regulation of type I interferon-mediated signaling pathway    Any process that increases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
    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: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:0032434    regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that modulates the frequency, rate or extent of 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: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.
    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:0032433    filopodium tip    The end of a filopodium distal to the body of the cell.
    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
        UBE2K_HUMAN | P610861yla 2o25 3e46 3k9o 3k9p 5dfl

(-) Related Entries Specified in the PDB File

1jbb UBIQUITIN-CONJUGATING ENZYME, UBC13
1yla UBIQUITIN-CONJUGATING ENZYME E2-25 KDA (HUNTINGTON INTERACTING PROTEIN 2)
3e46 CRYSTAL STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME E2-25KDA (HUNTINGTON INTERACTING PROTEIN 2) M172A MUTANT