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(-) Description

Title :  CRYSTAL STRUCTURE OF ENTEROPATHOGENIC E.COLI (EPEC) TYPE III SECRETION SYSTEM PROTEIN ESCJ
 
Authors :  C. K. Yip, T. G. Kimbrough, H. B. Felise, M. Vuckovic, N. A. Thomas, R. A. P E. A. Frey, B. B. Finlay, S. I. Miller, N. C. J. Strynadka
Date :  13 Jan 05  (Deposition) - 07 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Mixed Alpha/Beta, Extended Linker, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. K. Yip, T. G. Kimbrough, H. B. Felise, M. Vuckovic, N. A. Thomas, R. A. Pfuetzner, E. A. Frey, B. B. Finlay, S. I. Miller, N. C. Strynadka
Structural Characterization Of The Molecular Platform For Type Iii Secretion System Assembly.
Nature V. 435 702 2005
PubMed-ID: 15931226  |  Reference-DOI: 10.1038/NATURE03554

(-) Compounds

Molecule 1 - ESCJ
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET41A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SIGNAL PEPTIDE-REMOVED AND NON-LIPIDATED, RESIDUES 21-190
    Gene: ESCJ
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:120 , GLN B:112 , GLU B:115 , HOH B:776 , HOH B:783 , LYS C:81BINDING SITE FOR RESIDUE PO4 B 701
2AC2SOFTWAREARG B:116 , LYS B:120 , GLN C:112 , GLU C:115 , HOH C:749 , HOH C:770 , HOH C:822 , LYS D:81BINDING SITE FOR RESIDUE PO4 C 702
3AC3SOFTWAREGLN A:112 , GLU A:115 , HOH A:849 , HOH A:907 , HOH A:938 , HOH A:939 , LYS D:120BINDING SITE FOR RESIDUE PO4 A 703
4AC4SOFTWARELYS A:81 , LYS C:120 , GLN D:112 , GLU D:115 , HOH D:843 , HOH D:872 , HOH D:942BINDING SITE FOR RESIDUE PO4 D 704
5AC5SOFTWAREMET A:20 , ALA A:62 , ALA A:63 , ALA A:64 , SER D:149 , VAL D:153 , ASN D:154 , LEU D:155 , ILE D:182 , HOH D:808BINDING SITE FOR RESIDUE GOL A 800
6AC6SOFTWARELYS D:163 , ILE D:178 , SER D:179 , VAL D:180 , HOH D:924BINDING SITE FOR RESIDUE GOL D 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YJ7)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:78 -Pro A:79
2Phe B:78 -Pro B:79
3Phe C:78 -Pro C:79
4Phe D:78 -Pro D:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YJ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YJ7)

(-) Exons   (0, 0)

(no "Exon" information available for 1YJ7)

(-) 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:154
 aligned with Q8VQD3_ECOLX | Q8VQD3 from UniProtKB/TrEMBL  Length:190

    Alignment length:167
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       
         Q8VQD3_ECOLX    20 CKEQLYTGLTEKEANQMQALLLSNDVNVSKEMDKSGNMTLSVEKEDFVRAITILNNNGFPKKKFADIEVIFPPSQLVASPSQENAKINYLKEQDIERLLSKIPGVIDCSVSLNVNNNESQPSSAAVLVISSPEVNLAPSVIQIKNLVKNSVDDLKLENISVVIKSSS 186
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhhhhhhhhh....eeee.....eeeeee..hhhhhhhhhhhh........hhhhhh.------hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.-------.eeeeeeee.....hhhhhhhhhhhhhhhh...hhh.eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yj7 A  20 MKEQLYTGLTEKEANQMQALLLSNDVNVSKEMDKSGNMTLSVAAADFVRAITILNNNGFPKKKFADIEVIFP------SPSQENAKINYLKEQDIERLLSKIPGVIDCSVSLNV-------SSAAVLVISSPEVNLAPSVIQIKNLVKNSVDDLKLENISVVIKSSS 186
                                    29        39        49        59        69        79        89 |      99       109       119       129   |     - |     149       159       169       179       
                                                                                                  91     98                                133     141                                             


Chain B from PDB  Type:PROTEIN  Length:154
 aligned with Q8VQD3_ECOLX | Q8VQD3 from UniProtKB/TrEMBL  Length:190

    Alignment length:166
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      
         Q8VQD3_ECOLX    21 KEQLYTGLTEKEANQMQALLLSNDVNVSKEMDKSGNMTLSVEKEDFVRAITILNNNGFPKKKFADIEVIFPPSQLVASPSQENAKINYLKEQDIERLLSKIPGVIDCSVSLNVNNNESQPSSAAVLVISSPEVNLAPSVIQIKNLVKNSVDDLKLENISVVIKSSS 186
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh...eeeee.....eeeee...hhhhhhhhhhhh........hhhhhh.------hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.------..eeeeeeee.....hhhhhhhhhhhhhhhh...hhh.eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yj7 B  21 KEQLYTGLTEKEANQMQALLLSNDVNVSKEMDKSGNMTLSVAAADFVRAITILNNNGFPKKKFADIEVIFP------SPSQENAKINYLKEQDIERLLSKIPGVIDCSVSLNV------PSSAAVLVISSPEVNLAPSVIQIKNLVKNSVDDLKLENISVVIKSSS 186
                                    30        40        50        60        70        80        90|      100       110       120       130  |    140       150       160       170       180      
                                                                                                 91     98                                133    140                                              


Chain C from PDB  Type:PROTEIN  Length:153
 aligned with Q8VQD3_ECOLX | Q8VQD3 from UniProtKB/TrEMBL  Length:190

    Alignment length:165
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     
         Q8VQD3_ECOLX    21 KEQLYTGLTEKEANQMQALLLSNDVNVSKEMDKSGNMTLSVEKEDFVRAITILNNNGFPKKKFADIEVIFPPSQLVASPSQENAKINYLKEQDIERLLSKIPGVIDCSVSLNVNNNESQPSSAAVLVISSPEVNLAPSVIQIKNLVKNSVDDLKLENISVVIKSS 185
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh...eeeee.....eeeee...hhhhhhhhhhhh........hhhhhh.------hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.------..eeeeeeee.....hhhhhhhhhhhhhhhh...hhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yj7 C  21 KEQLYTGLTEKEANQMQALLLSNDVNVSKEMDKSGNMTLSVAAADFVRAITILNNNGFPKKKFADIEVIFP------SPSQENAKINYLKEQDIERLLSKIPGVIDCSVSLNV------PSSAAVLVISSPEVNLAPSVIQIKNLVKNSVDDLKLENISVVIKSS 185
                                    30        40        50        60        70        80        90|      100       110       120       130  |    140       150       160       170       180     
                                                                                                 91     98                                133    140                                             


Chain D from PDB  Type:PROTEIN  Length:158
 aligned with Q8VQD3_ECOLX | Q8VQD3 from UniProtKB/TrEMBL  Length:190

    Alignment length:170
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
         Q8VQD3_ECOLX    21 KEQLYTGLTEKEANQMQALLLSNDVNVSKEMDKSGNMTLSVEKEDFVRAITILNNNGFPKKKFADIEVIFPPSQLVASPSQENAKINYLKEQDIERLLSKIPGVIDCSVSLNVNNNESQPSSAAVLVISSPEVNLAPSVIQIKNLVKNSVDDLKLENISVVIKSSSGQDG 190
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) YscJ_FliF-1yj7D01 D:21-189                                                                                                                                               - Pfam domains (1)
           Pfam domains (2) YscJ_FliF-1yj7D02 D:21-189                                                                                                                                               - Pfam domains (2)
           Pfam domains (3) YscJ_FliF-1yj7D03 D:21-189                                                                                                                                               - Pfam domains (3)
           Pfam domains (4) YscJ_FliF-1yj7D04 D:21-189                                                                                                                                               - Pfam domains (4)
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh...eeeee.....eeeee...hhhhhhhhhhhh........hhhhhh.------hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.------..eeeeeeee.....hhhhhhhhhhhhhhhh...hhh.eeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yj7 D  21 KEQLYTGLTEKEANQMQALLLSNDVNVSKEMDKSGNMTLSVAAADFVRAITILNNNGFPKKKFADIEVIFP------SPSQENAKINYLKEQDIERLLSKIPGVIDCSVSLNV------PSSAAVLVISSPEVNLAPSVIQIKNLVKNSVDDLKLENISVVIKSSSGQDG 190
                                    30        40        50        60        70        80        90|      100       110       120       130  |    140       150       160       170       180       190
                                                                                                 91     98                                133    140
   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 1YJ7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YJ7)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: YscJ_FliF] (2)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q8VQD3_ECOLX | Q8VQD3)
biological process
    GO:0009306    protein secretion    The controlled release of proteins from a cell.

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