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(-) Description

Title :  CRYSTAL STRUCTURE OF AF2198, A JAB1/MPN DOMAIN PROTEIN FROM ARCHAEOGLOBUS FULGIDUS
 
Authors :  H. J. T. T. Tran, M. D. Allen, J. Lowe, M. Bycroft
Date :  04 Jun 03  (Deposition) - 14 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Proteasome, Deubiquitination, Archaea, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. J. T. T. Tran, M. D. Allen, J. Lowe, M. Bycroft
The Structure Of The Jab1/Mpn Domain And Its Implications For Proteasome Function
Biochemistry V. 42 11460 2003
PubMed-ID: 14516197  |  Reference-DOI: 10.1021/BI035033G

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN AF2198
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainC41
    Expression System Taxid562
    Expression System VectorPRSETA
    Organism ScientificARCHAEOGLOBUS FULGIDUS
    Organism Taxid2234
    SynonymAF2198

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
11442Ligand/IonTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
11441Ligand/IonTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1144-1Ligand/IonTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1144-1Ligand/IonTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
11441Ligand/IonTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:70 , HIS A:72 , ASP A:83 , 144 A:1123BINDING SITE FOR RESIDUE ZN A1122
2AC2SOFTWAREHIS B:70 , HIS B:72 , ASP B:83 , HOH B:2070 , HOH B:2071BINDING SITE FOR RESIDUE ZN B1123
3AC3SOFTWAREHIS C:70 , HIS C:72 , ASP C:83 , HOH C:2078 , ARG D:89BINDING SITE FOR RESIDUE ZN C1123
4AC4SOFTWAREHIS D:70 , HIS D:72 , ASP D:83 , 144 D:1124BINDING SITE FOR RESIDUE ZN D1123
5AC5SOFTWAREGLU A:25 , HIS A:70 , HIS A:72 , SER A:80 , GLU A:82 , ASP A:83 , ZN A:1122 , HOH A:2065 , ARG B:89BINDING SITE FOR RESIDUE 144 A1123
6AC6SOFTWAREARG C:89 , GLU D:25 , HIS D:70 , HIS D:72 , SER D:80 , GLU D:82 , ASP D:83 , ZN D:1123BINDING SITE FOR RESIDUE 144 D1124

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:77 -A:98
2B:77 -B:98
3C:77 -C:98
4D:77 -D:98

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1His A:22 -Pro A:23
2Tyr A:99 -Pro A:100
3His B:22 -Pro B:23
4Tyr B:99 -Pro B:100
5His C:22 -Pro C:23
6Tyr C:99 -Pro C:100
7His D:22 -Pro D:23
8Tyr D:99 -Pro D:100

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OI0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OI0)

(-) Exons   (0, 0)

(no "Exon" information available for 1OI0)

(-) Sequences/Alignments

Asymmetric 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:108
 aligned with O28085_ARCFU | O28085 from UniProtKB/TrEMBL  Length:121

    Alignment length:121
                               1                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117 
         O28085_ARCFU     - ---MKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFLPFVSGSVSAVIHLDMLPIGMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVV 118
               SCOP domains d1oi0a_ A: Hypothetical protein AF2198                                                                                    SCOP domains
               CATH domains 1oi0A00 A:1-121 Cytidine Deaminase, domain 2                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeehhhhhhhhhhhhhhh....eeeeee...ee.eeee.....-------------...eeeeeeeee.......hhhhhhhhhhh..eeeeee.......eeeee....ee..eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oi0 A   1 GSSMKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFLPFVS-------------IGMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVV 121
                                    10        20        30        40      |  -         -|       70        80        90       100       110       120 
                                                                         47            61                                                            

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with O28085_ARCFU | O28085 from UniProtKB/TrEMBL  Length:121

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
         O28085_ARCFU     1 MKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFLPFVSGSVSAVIHLDMLPIGMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVVE 119
               SCOP domains d1oi0b_ B: Hypothetical protein AF2198                                                                                  SCOP domains
               CATH domains 1oi0B00 B:4-122 Cytidine Deaminase, domain              2                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhh....eeeeeee..eeeeeee...-------------.....eeeeeeeee.......hhhhhhhhhhh..eeeeee.......eeee.........eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1oi0 B   4 MKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFLPF-------------LPIGMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVVE 122
                                    13        23        33        43 |       -     |  63        73        83        93       103       113         
                                                                    45            59                                                               

Chain C from PDB  Type:PROTEIN  Length:104
 aligned with O28085_ARCFU | O28085 from UniProtKB/TrEMBL  Length:121

    Alignment length:122
                               1                                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97       107       117  
         O28085_ARCFU     - ---MKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFLPFVSGSVSAVIHLDMLPIGMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVVE 119
               SCOP domains d1oi0c_ C: Hypothetical protein AF2198                                                                                     SCOP domains
               CATH domains 1oi0C00 C:1-122 Cytidine Deaminase, domain                   2                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeehhhhhhhhhhhhhhh....eeeeee...ee.eeee.------------------..eeeeeeeee.......hhhhhhhhhhh..eeeeee.......eeee.....ee..eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oi0 C   1 GSSMKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFL------------------GMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVVE 122
                                    10        20        30        40  |      -         - |      70        80        90       100       110       120  
                                                                     43                 62                                                            

Chain D from PDB  Type:PROTEIN  Length:108
 aligned with O28085_ARCFU | O28085 from UniProtKB/TrEMBL  Length:121

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
         O28085_ARCFU     1 MKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFLPFVSGSVSAVIHLDMLPIGMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVVE 119
               SCOP domains d1oi0d_ D: Hypothetical protein AF2198                                                                                  SCOP domains
               CATH domains 1oi0D00 D:4-122 Cytidine Deaminase, domain 2                                                                            CATH domains
           Pfam domains (1) ---Prok-JAB-1oi0D01 D:7-109                                                                               ------------- Pfam domains (1)
           Pfam domains (2) ---Prok-JAB-1oi0D02 D:7-109                                                                               ------------- Pfam domains (2)
           Pfam domains (3) ---Prok-JAB-1oi0D03 D:7-109                                                                               ------------- Pfam domains (3)
           Pfam domains (4) ---Prok-JAB-1oi0D04 D:7-109                                                                               ------------- Pfam domains (4)
         Sec.struct. author .eeehhhhhhhhhhhhhhh....eeeeeee..eeeeeee......-----------....eeeeeeeee.......hhhhhhhhh....eeeeee.......eeee.........eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1oi0 D   4 MKISRGLLKTILEAAKSAHPDEFIALLSGSKDVMDELIFLPFVSG-----------PIGMKVFGTVHSHPSPSCRPSEEDLSLFTRFGKYHIIVCYPYDENSWKCYNRKGEEVELEVVE 122
                                    13        23        33        43    |    -      | 63        73        83        93       103       113         
                                                                       48          60                                                              

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: JAB (8)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O28085_ARCFU | O28085)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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