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(-) Description

Title :  Q118A MUTANT OF SO1698 PROTEIN, AN ASPARTIC PEPTIDASE FROM SHEWANELLA ONEIDENSIS
 
Authors :  J. Osipiuk, R. Mulligan, M. Bargassa, F. Collart, A. Joachimiak, Midwe For Structural Genomics (Mcsg)
Date :  17 Jun 10  (Deposition) - 21 Jul 10  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Biol. Unit 2:  A,B,C,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 4:  A,B  (1x)
Biol. Unit 5:  C,D  (1x)
Keywords :  Structural Genomics, Aspartic Peptidase, Autocatalysis, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, R. Mulligan, M. Bargassa, J. E. Hamilton, M. A. Cunningham A. Joachimiak
Characterization Of Member Of Duf1888 Protein Family, Self-Cleaving And Self-Assembling Endopeptidase.
J. Biol. Chem. V. 287 19452 2012
PubMed-ID: 22493430  |  Reference-DOI: 10.1074/JBC.M112.358069

(-) Compounds

Molecule 1 - PEPTIDASE
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN 1-116
    Gene: SO_1698
    Mutation: YES
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 70863
    Strain: MR-1
 
Molecule 2 - PEPTIDASE
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN 117-125
    Gene: SO_1698
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 70863
    Strain: MR-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD
Biological Unit 2 (1x): ABCD
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 4 (1x): AB  
Biological Unit 5 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MPD-1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MPD-1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:14 , GLN A:53 , HOH A:119 , HOH A:133BINDING SITE FOR RESIDUE MPD A 401
2AC2SOFTWARELEU A:17 , GLU A:18 , HOH A:146 , HOH A:269BINDING SITE FOR RESIDUE CA A 403
3AC3SOFTWAREASP C:52 , HOH C:142 , HOH C:152 , HOH C:166 , HOH C:177 , HOH C:180 , HOH C:210 , HOH C:276BINDING SITE FOR RESIDUE CA C 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NJN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NJN)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NJN)

(-) 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:114
 aligned with Q8EGA7_SHEON | Q8EGA7 from UniProtKB/TrEMBL  Length:125

    Alignment length:114
                                    12        22        32        42        52        62        72        82        92       102       112    
         Q8EGA7_SHEON     3 APQGLAQFIKVNVTLENGEPVFIYTDANGQVCQGDITVTQAGTITYLLNDQTLKGLKFVGVGFVTPFDGIIDAVTISSDGMLVQLVDLDKTPGTTKFQFVLSNTANTLLVLSPD 116
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeeee..eeeeeee.....ee...eee...eeeeeeeee......eeeeeee.........eeee.....eeeeee.....eeeeeeeeee......eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3njn A   3 APQGLAQFIKVNVTLENGEPVFIYTDANGQVCQGDITVTQAGTITYLLNDQTLKGLKFVGVGFVTPFDGIIDAVTISSDGMLVQLVDLDKTPGTTKFQFVLSNTANTLLVLSPD 116
                                    12        22        32        42        52        62        72        82        92       102       112    


Chain B from PDB  Type:PROTEIN  Length:8
 aligned with Q8EGA7_SHEON | Q8EGA7 from UniProtKB/TrEMBL  Length:125

    Alignment length:8
         Q8EGA7_SHEON   117 PQIINRPQ 124
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author .eeee... Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 3njn B 117 PAIINRPQ 124


Chain C from PDB  Type:PROTEIN  Length:114
 aligned with Q8EGA7_SHEON | Q8EGA7 from UniProtKB/TrEMBL  Length:125

    Alignment length:114
                                    12        22        32        42        52        62        72        82        92       102       112    
         Q8EGA7_SHEON     3 APQGLAQFIKVNVTLENGEPVFIYTDANGQVCQGDITVTQAGTITYLLNDQTLKGLKFVGVGFVTPFDGIIDAVTISSDGMLVQLVDLDKTPGTTKFQFVLSNTANTLLVLSPD 116
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeeee..eeeeeee.....ee...eee...eeeeeeeee......eeeeeee.........eeee.....eeeeee.....eeee.eeeee......eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3njn C   3 APQGLAQFIKVNVTLENGEPVFIYTDANGQVCQGDITVTQAGTITYLLNDQTLKGLKFVGVGFVTPFDGIIDAVTISSDGMLVQLVDLDKTPGTTKFQFVLSNTANTLLVLSPD 116
                                    12        22        32        42        52        62        72        82        92       102       112    


Chain D from PDB  Type:PROTEIN  Length:7
 aligned with Q8EGA7_SHEON | Q8EGA7 from UniProtKB/TrEMBL  Length:125

    Alignment length:7
         Q8EGA7_SHEON   117 PQIINRP 123
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
           Pfam domains (1) --DUF18 Pfam domains (1)
           Pfam domains (2) --DUF18 Pfam domains (2)
           Pfam domains (3) --DUF18 Pfam domains (3)
           Pfam domains (4) --DUF18 Pfam domains (4)
         Sec.struct. author .eeee.. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 3njn D 117 PAIINRP 123
   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 3NJN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: DUF1888] (9)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8EGA7_SHEON | Q8EGA7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8EGA7_SHEON | Q8EGA7: 3n55 3njf 3njg 3njh 3nji 3njj 3njk 3njl 3njm

(-) Related Entries Specified in the PDB File

3n55 WILD-TYPE SO1698 PROTEIN, AN ASPARTIC PEPTIDASE FROM SHEWANELLA ONEIDENSIS.
3njf
3njg
3njh
3nji
3njj
3njk
3njl
3njm RELATED ID: APC83618 RELATED DB: TARGETDB