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(-) Description

Title :  DEUBIQUITINATING ENZYME UCH-L3 (HUMAN) AT 1.8 ANGSTROM RESOLUTION
 
Authors :  S. C. Johnston, C. N. Larsen, W. J. Cook, K. D. Wilkinson, C. P. Hill
Date :  06 Oct 97  (Deposition) - 28 Jan 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Cysteine Protease, Deubiquitinating Enzyme, Ubiquitin, C- Terminal Hydrolase, Ubiquitin Conjugation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. C. Johnston, C. N. Larsen, W. J. Cook, K. D. Wilkinson, C. P. Hill
Crystal Structure Of A Deubiquitinating Enzyme (Human Uch-L3) At 1. 8 A Resolution.
Embo J. V. 16 3787 1997
PubMed-ID: 9233788  |  Reference-DOI: 10.1093/EMBOJ/16.13.3787
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN C-TERMINAL HYDROLASE UCH-L3
    Cellular LocationCYTOPLASM
    Cell LineB834 (DE3)
    ChainsA
    EC Number3.1.2.15
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cell LineB834 (DE3)
    Expression System PlasmidPRSL3
    Expression System StrainBL21
    Expression System Taxid562
    Expression System VariantGAL-MET- AUXOTROPH
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUCH-L3,DUB
    TissueHEMATOPOETIC

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1CATUNKNOWNGLN A:89 , CYS A:95 , HIS A:169 , ASP A:184ACTIVE SITE RESIDUES.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:47 -Pro A:48

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UCH_1PS00140 Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site.UCHL3_HUMAN89-105  1A:89-105

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003775952ENSE00002160775chr13:76123927-7612399872UCHL3_HUMAN1-14141A:5-1410
1.3ENST000003775953ENSE00001785432chr13:76124112-7612412312UCHL3_HUMAN15-1841A:15-184
1.4ENST000003775954ENSE00001596545chr13:76134889-76135017129UCHL3_HUMAN19-61431A:19-6143
1.5aENST000003775955aENSE00000684200chr13:76140831-76140987157UCHL3_HUMAN62-114531A:62-11453
1.6ENST000003775956ENSE00000684198chr13:76141363-7614144886UCHL3_HUMAN114-142291A:114-14229
1.7ENST000003775957ENSE00001349979chr13:76143596-7614364348UCHL3_HUMAN143-158161A:143-1464
1.9ENST000003775959ENSE00000684194chr13:76169051-7616912676UCHL3_HUMAN159-184261A:167-18418
1.10ENST0000037759510ENSE00000684192chr13:76178905-7617896359UCHL3_HUMAN184-203201A:184-20320
1.11bENST0000037759511bENSE00001853190chr13:76179865-76180069205UCHL3_HUMAN204-230271A:204-23027

(-) 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:206
 aligned with UCHL3_HUMAN | P15374 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:226
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224      
          UCHL3_HUMAN     5 RWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA 230
               SCOP domains d1ucha_ A: Ubiquitin carboxyl-terminal hydrolase UCH-l3                                                                                                                                                                            SCOP domains
               CATH domains 1uchA00 A:5-230 Ubiquitin C-terminal Hydrolase Uch-l3                                                                                                                                                                              CATH domains
               Pfam domains Peptidase_C12-1uchA01 A:5-216                                                                                                                                                                                       -------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh......eeeeee....hhhhhh....eeeeeeeee..hhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhh.......hhhhhhhh.....hhhhhhhhhh......--------------------.eeeeeeeee..eeeee.................hhhhhhhhhhhhhhhh......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------UCH_1            ----------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  1.3 Exon 1.4  PDB: A:19-61 UniProt: 19-61      Exon 1.5a  PDB: A:62-114 UniProt: 62-114             ----------------------------Exon 1.7        -------------------------Exon 1.10           Exon 1.11b  PDB: A:204-230  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:114-142     ----------------Exon 1.9  PDB: A:167-184  ---------------------------------------------- Transcript 1 (2)
                 1uch A   5 RWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRV--------------------DLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA 230
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144 |       -         -  |    174       184       194       204       214       224      
                                                                                                                                                                       146                  167                                                               

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  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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UCHL3_HUMAN | P15374)
molecular function
    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: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: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.
biological process
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    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: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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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)

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        UCHL3_HUMAN | P153741xd3

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