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(-) Description

Title :  THE CATALYTIC DOMAIN OF HUMAN OTUD5
 
Authors :  J. R. Walker, A. E. Asinas, L. Crombet, A. Dong, J. Weigelt, C. Bountra, C. H. Arrowsmith, A. M. Edwards, S. Dhe-Paganon, Structural Genomic Consortium (Sgc)
Date :  29 Oct 10  (Deposition) - 15 Dec 10  (Release) - 15 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Peptidase C65 Otubain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Walker, A. E. Asinas, L. Crombet, A. Dong, J. Weigelt, C. Bountra, C. H. Arrowsmith, A. M. Edwards, S. Dhe-Paganon, Structural Genomics Consortium (Sgc)
The Catalytic Domain Of Human Otud5
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OTU DOMAIN-CONTAINING PROTEIN 5
    Chains: A
    EC Number: 3.4.19.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: OTU DOMAIN (UNP RESIDUES 172-339)
    Gene: OTUD5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEUBIQUITINATING ENZYME A, DUBA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
3PG41Ligand/IonTETRAETHYLENE GLYCOL
4SO41Ligand/IonSULFATE ION
5UNX1Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:238 , GLU A:241 , VAL A:242 , HOH A:404 , HOH A:417 , HOH A:460BINDING SITE FOR RESIDUE PEG A 400
2AC2SOFTWARELYS A:216 , ASP A:231 , GLN A:232 , GLY A:235 , VAL A:334 , HOH A:439 , HOH A:447BINDING SITE FOR RESIDUE PEG A 401
3AC3SOFTWAREGLU A:197 , GLN A:199 , TRP A:202 , TYR A:257BINDING SITE FOR RESIDUE PG4 A 402
4AC4SOFTWARELYS A:219 , ARG A:227 , HOH A:449 , HOH A:484BINDING SITE FOR RESIDUE SO4 A 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OTUPS50802 OTU domain profile.OTUD5_HUMAN213-341  1A:213-336

(-) Exons   (0, 0)

(no "Exon" information available for 3PFY)

(-) 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:129
 aligned with OTUD5_HUMAN | Q96G74 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:151
                                   200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 
          OTUD5_HUMAN   191 MDPATVEQQEHWFEKALRDKKGFIIKQMKEDGACLFRAVADQVYGDQDMHEVVRKHCMDYLMKNADYFSNYVTEDFTTYINRKRKNNCHGNHIEMQAMAEMYNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSYHRNIHYNSVVNP 341
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------OTU-3pfyA01 A:219-331                                                                                                 ----- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...-----------------.hhhhhhhhhhhhh..eeee....-----...eee..........eeeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------OTU  PDB: A:213-336 UniProt: 213-341                                                                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pfy A 191 mDPATVEQQEHWFEKALRDKKGFIIKQmKEDGACLFRAVADQVYGDQDmHEVVRKHCmDYLmKNADYFSNYV-----------------GNHIEmQAmAEmYNRPVEVYQYST-----EPINTFHGIHQNEDEPIRVSYHRNIHYNSVVNP 336
                            |      200       210       220       230       240       250 |     260 |       -       280    |  290|      300  |    305       315       325       335 
                            |                        218-MSE              239-MSE  248-MSE       262               280    |  |  |         303   304                                
                          191-MSE                                                      252-MSE                          285-MSE |                                                  
                                                                                                                           288-MSE                                                 
                                                                                                                              291-MSE                                              

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  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 3PFY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (OTUD5_HUMAN | Q96G74)
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:0032480    negative regulation of type I interferon production    Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0071108    protein K48-linked deubiquitination    A protein deubiquitination process in which a K48-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is removed from a protein.
    GO:0070536    protein K63-linked deubiquitination    A protein deubiquitination process in which a K63-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is removed from a protein.
    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:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  OTUD5_HUMAN | Q96G74
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 Related Entries

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

UniProtKB/Swiss-Prot
        OTUD5_HUMAN | Q96G74: 3tmo 3tmp

(-) Related Entries Specified in the PDB File

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