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(-) Description

Title :  D37A 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) - 14 Jul 10  (Release) - 10 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (3x)
Biol. Unit 3:  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, B, C, 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
    Gene: SO_1698
    Mutation: YES
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 70863
    Strain: MR-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (3x):   CD
Biological Unit 3 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
3NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL-1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL3Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:71 , ILE A:72 , ASP A:74 , ASP A:89 , ASP A:91 , HOH A:180BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWAREGLY B:71 , ILE B:72 , ASP B:74 , ASP B:89 , ASP B:91 , HOH B:131BINDING SITE FOR RESIDUE CA B 502
3AC3SOFTWAREGLY C:71 , ILE C:72 , ASP C:74 , ASP C:89 , ASP C:91 , HOH C:235BINDING SITE FOR RESIDUE CA C 503
4AC4SOFTWAREGLY D:71 , ILE D:72 , ASP D:74 , ASP D:89 , ASP D:91 , HOH D:128BINDING SITE FOR RESIDUE CA D 504
5AC5SOFTWAREASP D:81 , THR D:106 , ALA D:107 , ASN D:108 , HOH D:141BINDING SITE FOR RESIDUE GOL D 505
6AC6SOFTWARETHR C:106 , HOH C:214 , HOH C:232 , HOH C:233 , HOH C:248 , HOH C:272 , HOH C:276BINDING SITE FOR RESIDUE NA C 506
7AC7SOFTWARETHR A:106 , HOH A:164 , HOH A:177 , HOH A:178 , HOH A:260 , HOH A:261 , HOH A:263BINDING SITE FOR RESIDUE NA A 507

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NJH)

(-) 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:121
 aligned with Q8EGA7_SHEON | Q8EGA7 from UniProtKB/TrEMBL  Length:125

    Alignment length:121
                                    13        23        33        43        53        63        73        83        93       103       113       123 
         Q8EGA7_SHEON     4 PQGLAQFIKVNVTLENGEPVFIYTDANGQVCQGDITVTQAGTITYLLNDQTLKGLKFVGVGFVTPFDGIIDAVTISSDGMLVQLVDLDKTPGTTKFQFVLSNTANTLLVLSPDPQIINRPQ 124
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee..eeeeeee..........ee....eeeeeeeee......eeeeeee.........eeee.....eeeeee.....eeeeeeeeee......eee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3njh A   4 PQGLAQFIKVNVTLENGEPVFIYTDANGQVCQGAITVTQAGTITYLLNDQTLKGLKFVGVGFVTPFDGIIDAVTISSDGMLVQLVDLDKTPGTTKFQFVLSNTANTLLVLSPDPQIINRPQ 124
                                    13        23        33        43        53        63        73        83        93       103       113       123 


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with Q8EGA7_SHEON | Q8EGA7 from UniProtKB/TrEMBL  Length:125

    Alignment length:121
                                    13        23        33        43        53        63        73        83        93       103       113       123 
         Q8EGA7_SHEON     4 PQGLAQFIKVNVTLENGEPVFIYTDANGQVCQGDITVTQAGTITYLLNDQTLKGLKFVGVGFVTPFDGIIDAVTISSDGMLVQLVDLDKTPGTTKFQFVLSNTANTLLVLSPDPQIINRPQ 124
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee..eeeeeee..........ee....eeeeeeeee......eeeeeee.........eeee.....eeeeee.....eeeeeeeeee......eee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3njh B   4 PQGLAQFIKVNVTLENGEPVFIYTDANGQVCQGAITVTQAGTITYLLNDQTLKGLKFVGVGFVTPFDGIIDAVTISSDGMLVQLVDLDKTPGTTKFQFVLSNTANTLLVLSPDPQIINRPQ 124
                                    13        23        33        43        53        63        73        83        93       103       113       123 


Chain C from PDB  Type:PROTEIN  Length:120
 aligned with Q8EGA7_SHEON | Q8EGA7 from UniProtKB/TrEMBL  Length:125

    Alignment length:120
                                    13        23        33        43        53        63        73        83        93       103       113       123
         Q8EGA7_SHEON     4 PQGLAQFIKVNVTLENGEPVFIYTDANGQVCQGDITVTQAGTITYLLNDQTLKGLKFVGVGFVTPFDGIIDAVTISSDGMLVQLVDLDKTPGTTKFQFVLSNTANTLLVLSPDPQIINRP 123
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeeeee..eeeeeee..........ee....eeeeeeeee......eeeeeee.........eeee.....eeeeee.....eeeeeeeeee......eee....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3njh C   4 PQGLAQFIKVNVTLENGEPVFIYTDANGQVCQGAITVTQAGTITYLLNDQTLKGLKFVGVGFVTPFDGIIDAVTISSDGMLVQLVDLDKTPGTTKFQFVLSNTANTLLVLSPDPQIINRP 123
                                    13        23        33        43        53        63        73        83        93       103       113       123


Chain D from PDB  Type:PROTEIN  Length:122
 aligned with Q8EGA7_SHEON | Q8EGA7 from UniProtKB/TrEMBL  Length:125

    Alignment length:122
                                    13        23        33        43        53        63        73        83        93       103       113       123  
         Q8EGA7_SHEON     4 PQGLAQFIKVNVTLENGEPVFIYTDANGQVCQGDITVTQAGTITYLLNDQTLKGLKFVGVGFVTPFDGIIDAVTISSDGMLVQLVDLDKTPGTTKFQFVLSNTANTLLVLSPDPQIINRPQN 125
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) DUF1888-3njhD01 D:4-124                                                                                                  - Pfam domains (1)
           Pfam domains (2) DUF1888-3njhD02 D:4-124                                                                                                  - Pfam domains (2)
           Pfam domains (3) DUF1888-3njhD03 D:4-124                                                                                                  - Pfam domains (3)
           Pfam domains (4) DUF1888-3njhD04 D:4-124                                                                                                  - Pfam domains (4)
         Sec.struct. author ....eeeeeeeeeee..eeeeeee..........ee....eeeeeeeee......eeeeeee.........eeee.....eeeeee.....eeeeeeeeee......eee....eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3njh D   4 PQGLAQFIKVNVTLENGEPVFIYTDANGQVCQGAITVTQAGTITYLLNDQTLKGLKFVGVGFVTPFDGIIDAVTISSDGMLVQLVDLDKTPGTTKFQFVLSNTANTLLVLSPDPQIINRPQN 125
                                    13        23        33        43        53        63        73        83        93       103       113       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 3NJH)

(-) CATH Domains  (0, 0)

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

(-) 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 3nji 3njj 3njk 3njl 3njm 3njn

(-) Related Entries Specified in the PDB File

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