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

(-) Description

Title :  STRUCTURE OF THE PUP LIGASE PAFA OF THE PROKARYOTIC UBIQUITIN-LIKE MODIFICATION PATHWAY IN COMPLEX WITH ADP
 
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 :  2.16
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Pupylation, Depupylation, Prokaryotic Ubiquitin-Like Protein, 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 - PUP--PROTEIN LIGASE
    Atcc: 13032
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET EXPRESSION SYSTEM
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 1718
    Synonym: PAFA, PROTEASOME ACCESSORY FACTOR A, PUP-CONJUGATING ENZYME

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:60 , THR A:73 , GLU A:75 , ASN A:132 , LEU A:134 , ASP A:208 , PRO A:210 , HIS A:211 , ARG A:219 , ARG A:418 , TRP A:440 , PRO A:458 , MG A:1479 , HOH A:2053 , HOH A:2250 , HOH A:2251 , HOH A:2252 , ILE B:12 , GLY B:14 , ILE B:15 , GLU B:16 , LYS B:444 , ASN B:446 , PRO B:450BINDING SITE FOR RESIDUE ADP A1478
2AC2SOFTWAREADP A:1478 , HOH A:2053 , HOH A:2063 , HOH A:2250 , HOH A:2251 , GLU B:16BINDING SITE FOR RESIDUE MG A1479
3AC3SOFTWAREGLY A:14 , ILE A:15 , GLU A:16 , HOH A:2016 , HOH A:2235 , HOH A:2236 , ARG B:60 , THR B:73 , ALA B:74 , GLU B:75 , ASN B:132 , LEU B:134 , PRO B:210 , HIS B:211 , ARG B:219 , ARG B:418 , TRP B:440 , PRO B:458 , MG B:1480BINDING SITE FOR RESIDUE ADP B1479
4AC4SOFTWAREGLU A:16 , HOH A:2016 , HOH A:2017 , HOH A:2018 , HOH A:2235 , ADP B:1479BINDING SITE FOR RESIDUE MG B1480

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B0T)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:447 -Pro A:448
2Arg B:447 -Pro B:448

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B0T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B0T)

(-) Exons   (0, 0)

(no "Exon" information available for 4B0T)

(-) 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:470
 aligned with PAFA_CORGL | Q8NQE1 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:476
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471      
           PAFA_CORGL     2 STVESALTRRIMGIETEYGLTFVDGDSKKLRPDEIARRMFRPIVEKYSSSNIFIPNGSRLYLDVGSHPEYATAECDNLTQLINFEKAGDVIADRMAVDAEESLAKEDIAGQVYLFKNNVDSVGNSYGCHENYLVGRSMPLKALGKRLMPFLITRQLICGAGRIHHPNPLDKGESFPLGYCISQRSDHVWEGVSSATTRSRPIINTRDEPHADSHSYRRLHVIVGDANMAEPSIALKVGSTLLVLEMIEADFGLPSLELANDIASIREISRDATGSTLLSLKDGTTMTALQIQQVVFEHASKWLEQRPEPEFSGTSNTEMARVLDLWGRMLKAIESGDFSEVDTEIDWVIKKKLIDRFIQRGNLGLDDPKLAQVDLTYHDIRPGRGLFSVLQSRGMIKRWTTDEAILAAVDTAPDTTRAHLRGRILKAADTLGVPVTVDWMRHKVNRPEPQSVELGDPFSAVNSEVDQLIEYMTVHA 477
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.....eeeeee.eeeee.------.hhhhhhhhhhhhhhhhh..eee.....eee.......eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee............eeeeeeee.....hhhhhhhhhhhhhhhhhhh..eee.............eee...hhhhhhhhhhh........ee...........eeeeee.......hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhh......eee.....eeehhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.......hhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eee...eeee.....eeee........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b0t A   2 STVESALTRRIMGIETEYGLTFVD------RPDEIARRMFRPIVEKYSSSNIFIPNGSRLYLDVGSHPEYATAECDNLTQLINFEKAGDVIADRMAVDAEESLAKEDIAGQVYLFKNNVDSVGNSYGCHENYLVGRSMPLKALGKRLMPFLITRQLICGAGRIHHPNPLDKGESFPLGYCISQRSDHVWEGVSSATTRSRPIINTRDEPHADSHSYRRLHVIVGDANMAEPSIALKVGSTLLVLEMIEADFGLPSLELANDIASIREISRDATGSTLLSLKDGTTMTALQIQQVVFEHASKWLEQRPEPEFSGTSNTEMARVLDLWGRMLKAIESGDFSEVDTEIDWVIKKKLIDRFIQRGNLGLDDPKLAQVDLTYHDIRPGRGLFSVLQSRGMIKRWTTDEAILAAVDTAPDTTRAHLRGRILKAADTLGVPVTVDWMRHKVNRPEPQSVELGDPFSAVNSEVDQLIEYMTVHA 477
                                    11        21   |     -|       41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471      
                                                  25     32                                                                                                                                                                                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:472
 aligned with PAFA_CORGL | Q8NQE1 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:477
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       
           PAFA_CORGL     2 STVESALTRRIMGIETEYGLTFVDGDSKKLRPDEIARRMFRPIVEKYSSSNIFIPNGSRLYLDVGSHPEYATAECDNLTQLINFEKAGDVIADRMAVDAEESLAKEDIAGQVYLFKNNVDSVGNSYGCHENYLVGRSMPLKALGKRLMPFLITRQLICGAGRIHHPNPLDKGESFPLGYCISQRSDHVWEGVSSATTRSRPIINTRDEPHADSHSYRRLHVIVGDANMAEPSIALKVGSTLLVLEMIEADFGLPSLELANDIASIREISRDATGSTLLSLKDGTTMTALQIQQVVFEHASKWLEQRPEPEFSGTSNTEMARVLDLWGRMLKAIESGDFSEVDTEIDWVIKKKLIDRFIQRGNLGLDDPKLAQVDLTYHDIRPGRGLFSVLQSRGMIKRWTTDEAILAAVDTAPDTTRAHLRGRILKAADTLGVPVTVDWMRHKVNRPEPQSVELGDPFSAVNSEVDQLIEYMTVHAE 478
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.....eeeeee.eeeee.-----.hhhhhhhhhhhhhhhhhh..eee.....eee.......eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee............eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..eee.............eee...hhhhhhhhhh.........ee...........eeeeee.......hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhh.....eee.....eeehhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.......hhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhhhhh...ee...eeee.....eeee........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b0t B   2 STVESALTRRIMGIETEYGLTFVD-----LRPDEIARRMFRPIVEKYSSSNIFIPNGSRLYLDVGSHPEYATAECDNLTQLINFEKAGDVIADRMAVDAEESLAKEDIAGQVYLFKNNVDSVGNSYGCHENYLVGRSMPLKALGKRLMPFLITRQLICGAGRIHHPNPLDKGESFPLGYCISQRSDHVWEGVSSATTRSRPIINTRDEPHADSHSYRRLHVIVGDANMAEPSIALKVGSTLLVLEMIEADFGLPSLELANDIASIREISRDATGSTLLSLKDGTTMTALQIQQVVFEHASKWLEQRPEPEFSGTSNTEMARVLDLWGRMLKAIESGDFSEVDTEIDWVIKKKLIDRFIQRGNLGLDDPKLAQVDLTYHDIRPGRGLFSVLQSRGMIKRWTTDEAILAAVDTAPDTTRAHLRGRILKAADTLGVPVTVDWMRHKVNRPEPQSVELGDPFSAVNSEVDQLIEYMTVHAE 478
                                    11        21   |    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       
                                                  25    31
   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 4B0T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B0T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B0T)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PAFA_CORGL | Q8NQE1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0016879    ligase activity, forming carbon-nitrogen bonds    Catalysis of the joining of two molecules, or two groups within a single molecule, via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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:0019787    ubiquitin-like protein transferase activity    Catalysis of the transfer of a ubiquitin-like from one protein to another via the reaction X-ULP + Y --> Y-ULP + X, where both X-ULP and Y-ULP are covalent linkages. ULP represents a ubiquitin-like protein.
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.
    GO:0070490    protein pupylation    The process in which a Pup protein is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of Pup and the epsilon-amino group of a lysine residue of the target protein.

 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:447 - Pro A:448   [ RasMol ]  
    Arg B:447 - Pro B:448   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4b0t
    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
  PAFA_CORGL | Q8NQE1
    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)
  6.3.2.-
    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
  PAFA_CORGL | Q8NQE1
    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
        PAFA_CORGL | Q8NQE1: 4bjr

(-) Related Entries Specified in the PDB File

4b0r STRUCTURE OF THE DEAMIDASE-DEPUPYLASE DOP OF THE PROKARYOTIC UBIQUITIN-LIKE MODIFICATION PATHWAY
4b0s STRUCTURE OF THE DEAMIDASE-DEPUPYLASE DOP OF THE PROKARYOTIC UBIQUITIN-LIKE MODIFICATION PATHWAY IN COMPLEX WITH ATP