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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OTU DOMAIN OF OTULIN D336A MUTANT
 
Authors :  K. Keusekotten, P. R. Elliott, L. Glockner, Y. Kulathu, T. Wauer, D. Kra K. Hofmann, D. Komander
Date :  18 Feb 13  (Deposition) - 26 Jun 13  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Keusekotten, P. R. Elliott, L. Glockner, B. K. Fiil, R. B. Damgaard, Y. Kulathu, T. Wauer, M. K. Hospenthal, M. Gyrd-Hansen, D. Krappmann, K. Hofmann, D. Komander
Otulin Antagonizes Lubac Signaling By Specifically Hydrolyzing Met1-Linked Polyubiquitin.
Cell(Cambridge, Mass. ) V. 153 1312 2013
PubMed-ID: 23746843  |  Reference-DOI: 10.1016/J.CELL.2013.05.014

(-) Compounds

Molecule 1 - PROTEIN FAM105B
    ChainsA
    EC Number3.4.19.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VariantROSETTA PLACI
    Expression System VectorPOPINF
    Expression System Vector TypePLASMID
    FragmentOTU DOMAIN, RESIDUES 80-352
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:163 , GLU A:209 , HOH A:2208 , HOH A:2212BINDING SITE FOR RESIDUE CA A1346
2AC2SOFTWARELYS A:94 , VAL A:318BINDING SITE FOR RESIDUE CL A1347
3AC3SOFTWARETRP A:167 , ASP A:268 , PRO A:269 , GLY A:270 , GLN A:271 , ARG A:274 , HOH A:2161 , HOH A:2327BINDING SITE FOR RESIDUE GOL A1348
4AC4SOFTWARELEU A:235 , ASN A:238 , ARG A:239 , GLU A:242 , HOH A:2123 , HOH A:2230 , HOH A:2329BINDING SITE FOR RESIDUE GOL A1349
5AC5SOFTWAREHIS A:276 , GLN A:279 , VAL A:280 , GLY A:285 , GLU A:287 , GLU A:290 , HOH A:2269BINDING SITE FOR RESIDUE GOL A1350

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:319 -Pro A:320

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_053819M155LOTUL_HUMANPolymorphism11953822AM155L
2UniProtVAR_029469S227NOTUL_HUMANPolymorphism9312870AS227N
3UniProtVAR_076865Y244COTUL_HUMANDisease (AIPDS)  ---AY244C
4UniProtVAR_076866L272POTUL_HUMANDisease (AIPDS)  ---AL272P
5UniProtVAR_053820N311SOTUL_HUMANPolymorphism9312870AN311S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZNX)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZNX)

(-) 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:260
 aligned with OTUL_HUMAN | Q96BN8 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:272
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343  
           OTUL_HUMAN    74 GASEPRLSVAPEMDIMDYCKKEWRGNTQKATCMKMGYEEVSQKFTSIRRVRGDNYCALRATLFQAMSQAVGLPPWLQDPELMLLPEKLISKYNWIKQWKLGLKFDGKNEDLVDKIKESLTLLRKKWAGLAEMRTAEARQIACDELFTNEAEEYSLYEAVKFLMLNRAIELYNDKEKGKEVPFFSVLLFARDTSNDPGQLLRNHLNQVGHTGGLEQVEMFLLAYAVRHTIQVYRLSKYNTEEFITVYPTDPPKDWPVVTLIAEDDRHYNIPVR 345
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----......eehhhhhhhhh...hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...--------hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhhh.eeeeee.hhh.hhh.eeee.........eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------L-----------------------------------------------------------------------N----------------C---------------------------P--------------------------------------S---------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3znx A  78 GP----LSVAPEMDIMDYCKKEWRGNTQKATCMKMGYEEVSQKFTSIRRVRGDNYCALRATLFQAMSQAVGLPPWLQDPELMLLPEKLISKYNWIKQWKLG--------DLVDKIKESLTLLRKKWAGLAEMRTAEARQIACDELFTNEAEEYSLYEAVKFLMLNRAIELYNDKEKGKEVPFFSVLLFARDTSNDPGQLLRNHLNQVGHTGGLEQVEMFLLAYAVRHTIQVYRLSKYNTEEFITVYPTDPPKDWPVVTLIAEADRHYNIPVR 345
                             |    | 83        93       103       113       123       133       143       153       163       173|      183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343  
                             |   80                                                                                           174      183                                                                                                                                                                  
                            79                                                                                                                                                                                                                                                                              

   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 3ZNX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (OTUL_HUMAN | Q96BN8)
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.
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0060070    canonical Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0032088    negative regulation of NF-kappaB transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0070431    nucleotide-binding oligomerization domain containing 2 signaling pathway    Any series of molecular signals generated as a consequence of binding to nucleotide-binding oligomerization domain containing 2 (NOD2).
    GO:1990108    protein linear deubiquitination    A protein deubiquitination process in which a linear polymer of ubiquitin, formed by the amino-terminal methionine (M1) of one ubiquitin molecule and by the carboxy-terminal glycine (G76) of the next, is removed from a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0010803    regulation of tumor necrosis factor-mediated signaling pathway    Any process that modulates the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor.
    GO:0002040    sprouting angiogenesis    The extension of new blood vessels from existing capillaries into avascular tissues resulting from the proliferation of blood vessel endothelial cells.
cellular component
    GO:0071797    LUBAC complex    A ubiquitin ligase complex that catalyzes linear head-to-tail polyubiquitin conjugation on its targets. In human the complex consists of RBCK1, RNF31 and SHARPIN, and has an MW of approximately 600 kDa, suggesting a heteromultimeric assembly of its subunits. LUBAC stands for Linear Ubiquitin Chain Assembly Complex.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        OTUL_HUMAN | Q96BN83znv 3znz 4ksj 4ksk 4ksl 4oyk 4p0b

(-) Related Entries Specified in the PDB File

3znv CRYSTAL STRUCTURE OF THE OTU DOMAIN OF OTULIN AT 1.3 ANGSTROMS.