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(-) Description

Title :  STRUCTURE OF THE DEAMIDASE-DEPUPYLASE DOP OF THE PROKARYOTIC UBIQUITIN-LIKE MODIFICATION PATHWAY
 
Authors :  D. Ozcelik, J. Barandun, N. Schmitz, M. Sutter, E. Guth, F. F. Damberger F. H. -T. Allain, N. Ban, E. Weber-Ban
Date :  04 Jul 12  (Deposition) - 12 Sep 12  (Release) - 12 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Pupylation, Depupylation, Proteasome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Ozcelik, J. Barandun, N. Schmitz, M. Sutter, E. Guth, F. F. Damberger, F. H. -T. Allain, N. Ban, E. Weber-Ban
Structures Of Pup Ligase Pafa And Depupylase Dop From The Prokaryotic Ubiquitin-Like Modification Pathway.
Nat. Commun. V. 3 1014 2012
PubMed-ID: 22910360  |  Reference-DOI: 10.1038/NCOMMS2009

(-) Compounds

Molecule 1 - DEAMIDASE-DEPUPYLASE DOP
    Atcc: 43068
    Chains: A
    EC Number: 3.4.-.-, 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Organism Scientific: ACIDOTHERMUS CELLULOLYTICUS
    Organism Taxid: 351607
    Strain: 11B

 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 4B0R)

(-) Sites  (0, 0)

(no "Site" information available for 4B0R)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B0R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B0R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B0R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B0R)

(-) Exons   (0, 0)

(no "Exon" information available for 4B0R)

(-) 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:456
 aligned with DOP_ACIC1 | A0LU48 from UniProtKB/Swiss-Prot  Length:503

    Alignment length:500
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500
            DOP_ACIC1     1 MHRVMGIETEYGISVPHQPNANAMAASSQVVNAYAPIGAPAQRQARWDFEEENPLRDARGFEVAREAADPSQLTDEDLGLANVILTNGARLYVDHAHPEYSTPEVTNPRDAVLWDKAGERIMAEAARRAADLPMGWTIQLYKNNTDNKGASYGCHENYLMNRSTPFADIVRHLIPFFVTRQVFCGAGRVGIGADGRGEGFQLSQRADFFEVEVGLETTLKRPIINTRDEPHADPEKYRRLHVIIGDANMSEIATYLKLGTTALVLAMIEDGFLSQDFSVESPVGALRAVSHDPTLRYQLRLHDGRRLTAVQLQMEYLEQARKYVEDRFGTDVDDMTRDVLDRWETTLVRLADDPMQLSRDLDWVAKLSILEGYRQRENLPWSAHKLQLVDLQYHDVRPDRGLYNRLVARGRMNLLVDEAAVRTAMHEPPNDTRAYFRGRCLAKFGAEIAAASWDSVIFDLPGRDSLQRVPTLEPLRGTRAHVGDLLDRCRSATELVAALT 500
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.eee.......hhhhhhhhhhhhhh.--------------------------------------------..ee.....eeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh........eee............eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..eeee.....eeeee...hhhhh.eeee.......eeee...........eeeeee.......hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh......eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.......hhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhh...eeee...eeee........eeee.......hhhhhhhhhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b0r A   1 MHRVMGIETEYGISVPHQPNANAMAASSQVVNAYAP--------------------------------------------ANVILTNGARLYVDHAHPEYSTPEVTNPRDAVLWDKAGERIMAEAARRAADLPMGWTIQLYKNNTDNKGASYGCHENYLMNRSTPFADIVRHLIPFFVTRQVFCGAGRVGIGADGRGEGFQLSQRADFFEVEVGLETTLKRPIINTRDEPHADPEKYRRLHVIIGDANMSEIATYLKLGTTALVLAMIEDGFLSQDFSVESPVGALRAVSHDPTLRYQLRLHDGRRLTAVQLQMEYLEQARKYVEDRFGTDVDDMTRDVLDRWETTLVRLADDPMQLSRDLDWVAKLSILEGYRQRENLPWSAHKLQLVDLQYHDVRPDRGLYNRLVARGRMNLLVDEAAVRTAMHEPPNDTRAYFRGRCLAKFGAEIAAASWDSVIFDLPGRDSLQRVPTLEPLRGTRAHVGDLLDRCRSATELVAALT 500
                                    10        20        30     |   -         -         -         -         -|       90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500
                                                              36                                           81
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4B0R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B0R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B0R)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DOP_ACIC1 | A0LU48)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0016811    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0019941    modification-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 modification of the target protein.
    GO:0010498    proteasomal protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DOP_ACIC1 | A0LU48: 4b0s 5lrt

(-) Related Entries Specified in the PDB File

4b0s STRUCTURE OF THE DEAMIDASE-DEPUPYLASE DOP OF THE PROKARYOTIC UBIQUITIN-LIKE MODIFICATION PATHWAY IN COMPLEX WITH ATP
4b0t STRUCTURE OF THE PUP LIGASE PAFA OF THE PROKARYOTIC UBIQUITIN-LIKE MODIFICATION PATHWAY IN COMPLEX WITH ADP