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(-) Description

Title :  CRYSTAL STRUCTURE OF DEN1 IN COMPLEX WITH NEDD8
 
Authors :  D. Reverter, K. Wu, T. G. Erdene, Z. Q. Pan, K. D. Wilkinson, C. D. Lima
Date :  21 Oct 04  (Deposition) - 21 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cysteine Protease, Ubiquitin-Like, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Reverter, K. Wu, T. G. Erdene, Z. Q. Pan, K. D. Wilkinson, C. D. Lima
Structure Of A Complex Between Nedd8 And The Ulp/Senp Protease Family Member Den1.
J. Mol. Biol. V. 345 141 2005
PubMed-ID: 15567417  |  Reference-DOI: 10.1016/J.JMB.2004.10.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SENTRIN-SPECIFIC PROTEASE 8
    ChainsA
    EC Number3.4.22.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneSENP8, FKSG8, PRSC2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsGLUTATHIONE S-TRANSFERASE FUSION, CLEAVED WITH THROMBIN
    SynonymSENTRIN/SUMO-SPECIFIC PROTEASE SENP8, CYSTEINE PROTEASE FKSG8, PROTEASE, CYSTEINE 2, DEN1 PROTEASE
 
Molecule 2 - NEDDYLIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneNEDD8
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsGLUTATHIONE S-TRANSFERASE FUSION, CLEAVED WITH THROMBIN
    SynonymUBIQUITIN-LIKE PROTEIN NEDD8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1XT9)

(-) Sites  (0, 0)

(no "Site" information available for 1XT9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XT9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:23 -Pro A:24

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_023705T207ASENP8_HUMANPolymorphism930871AT207A

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.NEDD8_HUMAN1-76  1B:1-76
2ULP_PROTEASEPS50600 Ubiquitin-like protease family profile.SENP8_HUMAN11-174  1A:11-174
3UBIQUITIN_1PS00299 Ubiquitin domain signature.NEDD8_HUMAN27-52  1B:27-52

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002504951aENSE00001101093chr14:24701660-24701456205NEDD8_HUMAN1-661B:1-66
1.4ENST000002504954ENSE00002175755chr14:24687637-2468759048NEDD8_HUMAN7-22161B:7-2216
1.5aENST000002504955aENSE00002178617chr14:24687421-2468733983NEDD8_HUMAN23-50281B:23-5028
1.6eENST000002504956eENSE00001549615chr14:24686429-24686058372NEDD8_HUMAN50-81321B:50-7627

2.1ENST000003409121ENSE00001521305chr15:72410637-72410805169SENP8_HUMAN-00--
2.2ENST000003409122ENSE00001386768chr15:72431918-724333041387SENP8_HUMAN1-2282281A:2-211 (gaps)210

(-) 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:208
 aligned with SENP8_HUMAN | Q96LD8 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
          SENP8_HUMAN     2 DPVVLSYMDSLLRQSDVSLLDPPSWLNDHIIGFAFEYFANSQFHDCSDHVSFISPEVTQFIKCTSNPAEIAMFLEPLDLPNKRVVFLAINDNSNQAAGGTHWSLLVYLQDKNSFFHYDSHSRSNSVHAKQVAEKLEAFLGRKGDKLAFVEEKAPAQQNSYDCGMYVICNTEALCQNFFRQQTESLLQLLTPAYITKKRGEWKDLITTLAK 211
               SCOP domains d1xt9a_ A: Sentrin-specific protease 8, SENP8                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------------Peptidase_C48-1xt9A01 A:25-211                                                                                                                                                              Pfam domains
         Sec.struct. author ..eeeee..eeeehhhhhh......eehhhhhhhhhhhhhh.hhhhh..eeeehhhhhhhhhhh..--hhhhhhhhhhhhhh.eeeeeee...........eeeeeee....eeeee......hhhhhhhhhhh............eeee..........hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A---- SAPs(SNPs)
                PROSITE (2) ---------ULP_PROTEASE  PDB: A:11-174 UniProt: 11-174                                                                                                                         ------------------------------------- PROSITE (2)
               Transcript 2 Exon 2.2  PDB: A:2-211 (gaps) UniProt: 1-228 [INCOMPLETE]                                                                                                                                                          Transcript 2
                 1xt9 A   2 DPVVLSYMDSLLRQSDVSLLDPPSWLNDHIIGFAFEYFANSQFHDCSDHVSFISPEVTQFIKCTSN--EIAMFLEPLDLPNKRVVFLAINDNSNQAAGGTHWSLLVYLQDKNSFFHYDSHSRSNSVHAKQVAEKLEAFLGRKGDKLAFVEEKAPAQQNSYDCGMYVICNTEALCQNFFRQQTESLLQLLTPAYITKKRGEWKDLITTLAK 211
                                    11        21        31        41        51        61     |  71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
                                                                                            67 70                                                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:76
 aligned with NEDD8_HUMAN | Q15843 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:76
                                    10        20        30        40        50        60        70      
          NEDD8_HUMAN     1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG  76
               SCOP domains d1xt9b_ B: Nedd8                                                             SCOP domains
               CATH domains 1xt9B00 B:1-76                                                               CATH domains
               Pfam domains -----ubiquitin-1xt9B01 B:6-74                                             -- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee..ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: B:1-76 UniProt: 1-76                                       PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------UBIQUITIN_1  PDB: B:27-52 ------------------------ PROSITE (3)
           Transcript 1 (1) 1.1a  Exon 1.4        Exon 1.5a  PDB: B:23-50     -------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.6e  PDB: B:50-76     Transcript 1 (2)
                 1xt9 B   1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG  76
                                    10        20        30        40        50        60        70      

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (17, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SENP8_HUMAN | Q96LD8)
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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Chain B   (NEDD8_HUMAN | Q15843)
molecular function
    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:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0009653    anatomical structure morphogenesis    The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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: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
        NEDD8_HUMAN | Q158431ndd 1r4m 1r4n 2bkr 2ko3 2n7k 2nvu 3dbh 3dbl 3dbr 3dqv 3gzn 4f8c 4fbj 4hcp 4p5o
        SENP8_HUMAN | Q96LD82bkq 2bkr

(-) Related Entries Specified in the PDB File

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