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(-) Description

Title :  STRUCTURE OF N-TERMINAL DUSP-UBL DOMAINS OF HUMAN USP15
 
Authors :  S. Harper, T. M. D. Besong, J. Emsley, D. J. Scott, I. Dreveny
Date :  03 Aug 11  (Deposition) - 28 Sep 11  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Domain Present In Ubiquitin Specific Proteases (Dusp), Ubiquitin-Like Domain (Ubl), Hydrolase, Protease, Deubiquitinating Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Harper, T. M. Besong, J. Emsley, D. J. Scott, I. Dreveny
Structure Of The Usp15 N-Terminal Domains: A Beta-Hairpin Mediates Close Association Between The Dusp And Ubl Domains
Biochemistry V. 50 7995 2011
PubMed-ID: 21848306  |  Reference-DOI: 10.1021/BI200726E

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 15
    ChainsA
    EC Number3.4.19.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET26B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1-222
    GeneKIAA0529, USP15, USP15 (1-222)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDEUBIQUITINATING ENZYME 15, UBIQUITIN THIOLESTERASE 15, UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 15, UNPH-2, UNPH4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:75 , ARG A:150 , ARG A:151 , HOH A:402 , HOH A:454BINDING SITE FOR RESIDUE SO4 A 231

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T9L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3T9L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T9L)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DUSPPS51283 DUSP domain profile.UBP15_HUMAN7-118  1A:7-118

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002803771ENSE00001358609chr12:62654187-6265428498UBP15_HUMAN1-30301A:6-3025
1.2ENST000002803772ENSE00001141626chr12:62687960-62688087128UBP15_HUMAN30-73441A:30-7344
1.3ENST000002803773ENSE00000937158chr12:62696571-62696701131UBP15_HUMAN73-116441A:73-11644
1.4ENST000002803774ENSE00000937159chr12:62708571-62708697127UBP15_HUMAN117-159431A:117-15943
1.5aENST000002803775aENSE00000937160chr12:62715245-62715390146UBP15_HUMAN159-207491A:159-20749
1.8aENST000002803778aENSE00000937161chr12:62719653-6271971462UBP15_HUMAN208-228211A:208-22215
1.10ENST0000028037710ENSE00000996340chr12:62743002-6274308887UBP15_HUMAN228-257301A:223-2275
1.11ENST0000028037711ENSE00000937162chr12:62749112-62749256145UBP15_HUMAN257-305490--
1.12ENST0000028037712ENSE00000937163chr12:62775271-62775444174UBP15_HUMAN306-363580--
1.13ENST0000028037713ENSE00000937164chr12:62777621-62777779159UBP15_HUMAN364-416530--
1.14ENST0000028037714ENSE00000937165chr12:62777859-62778083225UBP15_HUMAN417-491750--
1.15ENST0000028037715ENSE00000937166chr12:62783211-6278329484UBP15_HUMAN492-519280--
1.16ENST0000028037716ENSE00000937167chr12:62783385-6278347995UBP15_HUMAN520-551320--
1.17ENST0000028037717ENSE00000937168chr12:62783577-62783768192UBP15_HUMAN551-615650--
1.18ENST0000028037718ENSE00000937169chr12:62784644-62784759116UBP15_HUMAN615-654400--
1.19ENST0000028037719ENSE00000937170chr12:62784937-62785209273UBP15_HUMAN654-745920--
1.20ENST0000028037720ENSE00000937171chr12:62785596-6278566671UBP15_HUMAN745-768240--
1.21ENST0000028037721ENSE00000937172chr12:62786052-62786167116UBP15_HUMAN769-807390--
1.22ENST0000028037722ENSE00000937173chr12:62786833-62786982150UBP15_HUMAN807-857510--
1.23ENST0000028037723ENSE00000937174chr12:62790075-62790178104UBP15_HUMAN857-892360--
1.24ENST0000028037724ENSE00000937175chr12:62794967-6279505589UBP15_HUMAN892-921300--
1.25ENST0000028037725ENSE00001358543chr12:62797973-627998981926UBP15_HUMAN922-981600--

(-) 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:222
 aligned with UBP15_HUMAN | Q9Y4E8 from UniProtKB/Swiss-Prot  Length:981

    Alignment length:245
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245     
          UBP15_HUMAN     6 AADLDTQRSDIATLLKTSLRKGDTWYLVDSRWFKQWKKYVGFDSWDKYQMGDQNVYPGPIDNSGLLKDGDAQSLKEHLIDELDYILLPTEGWNKLVSWYTLMEGQEPIARKVVEQGMFVKHCKVEVYLTELKLCENGNMNNVVTRRFSKADTIDTIEKEIRKIFSIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNEDGTWPRGPSTPKSPGASNFSTLPKISPSSLSNNY 250
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhh..........hhhhh.....hhhhh.................eeeeehhhhhhhhhhhh........eeeeeee.....eeeee...eeeeeee.......eeeee....hhhhhhhhhhhhh.......eeeeeeehhheeee................eeeeeee.........-----------------------..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -DUSP  PDB: A:7-118 UniProt: 7-118                                                                               ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:6-30    ------------------------------------------Exon 1.3  PDB: A:73-116 UniProt: 73-116     Exon 1.4  PDB: A:117-159 UniProt: 117-159  --------------------------------------------------------------------Exon 1.10 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.2  PDB: A:30-73 UniProt: 30-73       -------------------------------------------------------------------------------------Exon 1.5a  PDB: A:159-207 UniProt: 159-207       Exon 1.8a            ---------------------- Transcript 1 (2)
                 3t9l A   6 AADLDTQRSDIATLLKTSLRKGDTWYLVDSRWFKQWKKYVGFDSWDKYQMGDQNVYPGPIDNSGLLKDGDAQSLKEHLIDELDYILLPTEGWNKLVSWYTLMEGQEPIARKVVEQGMFVKHCKVEVYLTELKLCENGNMNNVVTRRFSKADTIDTIEKEIRKIFSIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNEDGTWPR-----------------------LEHHH 227
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215      |  -         -         -|    
                                                                                                                                                                                                                                                  222                     223    

   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  (0, 0)

(no "SCOP Domain" information available for 3T9L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T9L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T9L)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UBP15_HUMAN | Q9Y4E8)
molecular function
    GO:0046332    SMAD binding    Interacting selectively and non-covalently with a SMAD signaling protein.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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:0004843    thiol-dependent ubiquitin-specific protease activity    Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein.
    GO:0036459    thiol-dependent ubiquitinyl hydrolase activity    Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
    GO:0005160    transforming growth factor beta receptor binding    Interacting selectively and non-covalently with the transforming growth factor beta receptor.
    GO:0061649    ubiquitin modification-dependent histone binding    Interacting selectively and non-covalently with a histone protein in which a residue has been modified by ubiquitination. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
biological process
    GO:0030509    BMP signaling pathway    A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0035616    histone H2B conserved C-terminal lysine deubiquitination    A histone deubiquitination process in which a ubiquitin monomer is removed from a conserved lysine residue in the C-terminus of histone H2B. The conserved lysine residue is K119 in fission yeast, K123 in budding yeast, or K120 in mammals.
    GO:0035520    monoubiquitinated protein deubiquitination    The removal of the ubiquitin group from a monoubiquitinated protein.
    GO:0060389    pathway-restricted SMAD protein phosphorylation    The process of introducing a phosphate group on to a pathway restricted SMAD protein. A pathway restricted SMAD protein is an effector protein that acts directly downstream of the transforming growth factor family receptor.
    GO:0016579    protein deubiquitination    The removal of one or more ubiquitin groups from a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    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: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
        UBP15_HUMAN | Q9Y4E81w6v 3lmn 3ppa 3pv1 4a3o 4a3p 5jjw

(-) Related Entries Specified in the PDB File

1w6v SOLUTION STRUCTURE OF THE HUMAN UBIQUITIN-SPECIFIC PROTEASE 15 DUSP DOMAIN