Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 6 (YFR010W) FROM SACCHAROMYCES CEREVISIAE AT 1.74 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  29 Mar 04  (Deposition) - 21 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym./Biol. Unit :  A
Keywords :  Yfr010W, Ubiquitin Carboxyl-Terminal Hydrolase 6, Structural Genomics, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Ubiquitin Carboxyl-Terminal Hydrolase (Yfr010W) From Saccharomyces Cerevisiae At 1. 74 A Resolutio
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 6
    Chains: A
    EC Number: 3.1.2.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 97-499
    Gene: UBP6, YFR010W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: UBIQUITIN THIOLESTERASE 6, UBIQUITIN-SPECIFIC PROCESSING PROTEASE 6, DEUBIQUITINATING ENZYME 6

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1VJV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VJV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1USP_3PS50235 Ubiquitin specific protease (USP) domain profile.UBP6_YEAST109-497  1A:109-497
2USP_1PS00972 Ubiquitin specific protease (USP) domain signature 1.UBP6_YEAST110-125  1A:110-125
3USP_2PS00973 Ubiquitin specific protease (USP) domain signature 2.UBP6_YEAST430-448  1A:430-448

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YFR010W1YFR010W.1VI:165060-1665591500UBP6_YEAST1-4994991A:103-499 (gaps)397

(-) 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:367
 aligned with UBP6_YEAST | P43593 from UniProtKB/Swiss-Prot  Length:499

    Alignment length:397
                                   112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       
           UBP6_YEAST   103 QFAQLPVGFKNMGNTCYLNATLQALYRVNDLRDMILNYNPSQGVSNSGAQDEEIHKQIVIEMKRCFENLQNKSFKSVLPIVLLNTLRKCYPQFAERDSQGGFYKQQDAEELFTQLFHSMSIVFGDKFSEDFRIQFKTTIKDTANDNDITVKENESDSKLQCHISGTTNFMRNGLLEGLNEKIEKRSDLTGANSIYSVEKKISRLPKFLTVQYVRFFWKRSTNKKSKILRKVVFPFQLDVADMLTPEYAAEKVKVRDELRKVEKEKNEKEREIKRRKFDPSSSENVMTPREQYETQVALNESEKDQWLEEYKKHFPPNLEKGENPSCVYNLIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDKVSVVEKEKIESLAGGGESDSALILMYKGFGL 499
               SCOP domains d1vjva_ A: Ubiquitin carboxyl-terminal hydrolase 6                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---UCH-1vjvA01 A:106-494                                                                                                                                                                                                                                                                                                                                                                                ----- Pfam domains
         Sec.struct. author .......ee.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhh.......hhhhhhhhhhhhhhhhhhhhh.-..ee.hhhhhhhhhhhhhhhhh..----.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee...ee..eee.......hhhhhhhhhhee.---------....eeeeeeeee...eeeeee..eeee....eeee.........eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh----------------..hhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeeeeeee.......eeeeeee.......eeeee..eeeeehhhhhhhhhh.....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------USP_3  PDB: A:109-497 UniProt: 109-497                                                                                                                                                                                                                                                                                                                                                               -- PROSITE (1)
                PROSITE (2) -------USP_1           ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------USP_2              --------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:103-499 (gaps) UniProt: 1-499 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                   Transcript 1
                 1vjv A 103 QFAQLPVGFKNmGNTCYLNATLQALYRVNDLRDmILNYNPSQGVSNSGAQDEEIHKQIVIEmKRCFENLQNK-FKSVLPVVLLNTLRKCYPQFAERD----FYKQQDAEELFTQLFHSmSIVFGDKFSEDFRIQFKTTIKDTANDNDITVKENESDSKLQCHISGTTNFmRNGLLEGLNEK---------ANSIYSVEKKISRLPKFLTVQYVRFFWKRSTNKKSKILRKVVFPFQLDVADmLTPEYAAEKVKVRDELRKVEKEKNEK----------------VmTPREQYETQVALNESEKDQWLEEYKKHFPPNLEKGENPSCVYNLIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDKVSVVEKEKIESLAGGGESDSALILmYKGFGL 499
                                   112 |     122       132   |   142       152       162 |     172 | |   182       192      |  - |     212       222       232       242       252       262       272       282|        -|      302       312       322       332       342 |     352       362       | -         -    || 392       402       412       422       432       442       452       462       472       482       492|      
                                     114-MSE               136-MSE                     164-MSE   174 |                    199  204              221-MSE                                            272-MSE    283       293                                                344-MSE                   370              387|                                                                                                      493-MSE  
                                                                                                   176                                                                                                                                                                                                                 388-MSE                                                                                                           

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VJV)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UBP6_YEAST | P43593)
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: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.
biological process
    GO:1901799    negative regulation of proteasomal protein catabolic process    Any process that stops, prevents or reduces the frequency, rate or extent of proteasomal protein catabolic process.
    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: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:0000502    proteasome complex    A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.
    GO:0005838    proteasome regulatory particle    A multisubunit complex, which caps one or both ends of the proteasome core complex. This complex recognizes and unfolds ubiquitinated proteins, and translocates them to the proteasome core complex.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1vjv)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1vjv)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1vjv
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  UBP6_YEAST | P43593
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.2.15
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  UBP6_YEAST | P43593
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        UBP6_YEAST | P43593: 5a5b 5mpc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VJV)