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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE E.COLI ESPP AUTOTRANSPORTER BETA-DOMAIN.
 
Authors :  T. J. Barnard, N. Dautin, P. Lukacik, H. D. Bernstein, S. K. Buchanan
Date :  20 Jul 07  (Deposition) - 13 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.66
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Outer Membrane Protein, Beta-Barrel, Beta-Domain, Autotransporter, Hydrolase, Protease, Secreted, Serine Protease, Transmembrane, Virulence, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. J. Barnard, N. Dautin, P. Lukacik, H. D. Bernstein, S. K. Buchanan
Autotransporter Structure Reveals Intra-Barrel Cleavage Followed By Conformational Changes.
Nat. Struct. Mol. Biol. V. 14 1214 2007
PubMed-ID: 17994105  |  Reference-DOI: 10.1038/NSMB1322

(-) Compounds

Molecule 1 - SERINE PROTEASE ESPP
    ChainsA, B
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPTRC99A
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneESPP
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83334
    SynonymEXTRACELLULAR SERINE PROTEASE PLASMID-ENCODED ESPP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2QOM)

(-) Sites  (0, 0)

(no "Site" information available for 2QOM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QOM)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Thr A:1133 -Ala A:1134
2Asn A:1236 -Gly A:1237
3Asn B:1236 -Gly B:1237
4Phe B:1300 -Gly B:1301

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QOM)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AUTOTRANSPORTERPS51208 Autotransporter beta-domain profile.ESPP_ECO571034-1300
 
  2A:1034-1300
B:1034-1300
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AUTOTRANSPORTERPS51208 Autotransporter beta-domain profile.ESPP_ECO571034-1300
 
  1A:1034-1300
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AUTOTRANSPORTERPS51208 Autotransporter beta-domain profile.ESPP_ECO571034-1300
 
  1-
B:1034-1300

(-) Exons   (0, 0)

(no "Exon" information available for 2QOM)

(-) 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:265
 aligned with ESPP_ECO57 | Q7BSW5 from UniProtKB/Swiss-Prot  Length:1300

    Alignment length:278
                                                                                                                                                                                                                                                                                                             1300 
                                  1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      | 
          ESPP_ECO57   1024 NLNKRMGDLRDINGEAGAWARIMSGTGSASGGFSDNYTHVQVGVDKKHELDGLDLFTGFTVTHTDSSASADVFSGKTKSVGAGLYASAMFDSGAYIDLIGKYVHHDNEYTATFAGLGTRDYSTHSWYAGAEAGYRYHVTEDAWIEPQAELVYGSVSGKQFAWKDQGMHLSMKDKDYNPLIGRTGVDVGKSFSGKDWKVTARAGLGYQFDLLANGETVLRDASGEKRIKGEKDSRMLMSVGLNAEIRDNVRFGLEFEKSAFGKYNVDNAVNANFRYSF-    -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qomA00 A:1024-1301 autotransporter esta                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.........eeeeeeeeeeeee.....eeeeeeeeeeeee....--.eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeee.---....eeeeeeeeeeeeeeee.ee....eeeeeeeeeeeeeeeeee.--------...eeeeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeee..................eeeeeeeeeeeeeee...eee.eeeeeee....eeeeeeee..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------AUTOTRANSPORTER  PDB: A:1034-1300 UniProt: 1034-1300                                                                                                                                                                                                                       - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qom A 1024 NLNKRMGDLRDINGEAGAWARIMSGTGSASGGFSDNYTHVQVGVDKKHEL--LDLFTGFTVTHTDSSASADVFSGKTKSVGAGLYASAMFDSGAYIDLIGKYVHHDNEYTA---GLGTRDYSTHSWYAGAEAGYRYHVTEDAWIEPQAELVYGSVSGKQF--------LSMKDKDYNPLIGRTGVDVGKSFSGKDWKVTARAGLGYQFDLLANGETVLRDASGEKRIKGEKDSRMLMSVGLNAEIRDNVRFGLEFEKSAFGKYNVDNAVNANFRYSFG 1301
                                  1033      1043      1053      1063      1073  |   1083      1093      1103      1113      1123      1133|   | 1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293        
                                                                          1073  |                                                      1134   |                                         1183     1192                                                                                                             
                                                                             1076                                                          1138                                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:269
 aligned with ESPP_ECO57 | Q7BSW5 from UniProtKB/Swiss-Prot  Length:1300

    Alignment length:278
                                                                                                                                                                                                                                                                                                             1300 
                                  1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      | 
          ESPP_ECO57   1024 NLNKRMGDLRDINGEAGAWARIMSGTGSASGGFSDNYTHVQVGVDKKHELDGLDLFTGFTVTHTDSSASADVFSGKTKSVGAGLYASAMFDSGAYIDLIGKYVHHDNEYTATFAGLGTRDYSTHSWYAGAEAGYRYHVTEDAWIEPQAELVYGSVSGKQFAWKDQGMHLSMKDKDYNPLIGRTGVDVGKSFSGKDWKVTARAGLGYQFDLLANGETVLRDASGEKRIKGEKDSRMLMSVGLNAEIRDNVRFGLEFEKSAFGKYNVDNAVNANFRYSF-    -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qomB00 B:1   024-1301 autotransporter esta                                                                                                                                                                                                                                            CATH domains
           Pfam domains (1) -----------   Autotransporter-2qomB01 B:1038-1290                                                                                                                                                                                                                          ----------- Pfam domains (1)
           Pfam domains (2) -----------   Autotransporter-2qomB02 B:1038-1290                                                                                                                                                                                                                          ----------- Pfam domains (2)
         Sec.struct. author hhhhhh.....---.eeeeeeeeeeeee.....eeeeeeeeeeeeeeee.-.eeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee...---..eeeeeeeeeeeeeee.eeee..eeeeeeeeeeeeeeeeee.....-......eeeeeeeeeeeeeeeeeeeee..-.eeeeeeeeeeeeeeee..................eeeeeeeeeeeeeee...eeee..eeeee....eeeeeeee..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------AUTOTRANSPORTER  PDB: B:1034-1300 UniProt: 1034-1300                                                                                                                                                                                                                       - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qom B 1024 NLNKRMGDLRD---EAGAWARIMSGTGSASGGFSDNYTHVQVGVDKKHEL-GLDLFTGFTVTHTDSSASADVFSGKTKSVGAGLYASAMFDSGAYIDLIGKYVHHDNEYTATFA---TRDYSTHSWYAGAEAGYRYHVTEDAWIEPQAELVYGSVSGKQFAWKD-GMHLSMKDKDYNPLIGRTGVDVGKSFSGK-WKVTARAGLGYQFDLLANGETVLRDASGEKRIKGEKDSRMLMSVGLNAEIRDNVRFGLEFEKSAFGKYNVDNAVNANFRYSFG 1301
                                  1033|   | 1043      1053      1063      1073 |    1083      1093      1103      1113      1123      1133   |  1143      1153      1163      1173      1183   | |1193      1203      1213   | |1223      1233      1243      1253      1263      1273      1283      1293        
                                   1034   |                               1073 |                                                          1137   |                                          1187 |                        1217 |                                                                                  
                                       1038                                 1075                                                              1141                                            1189                          1219                                                                                  

   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 2QOM)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: MBB (97)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ESPP_ECO57 | Q7BSW5)
molecular function
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019867    outer membrane    The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        ESPP_ECO57 | Q7BSW53slj 3slo 3slt 3sze

(-) Related Entries Specified in the PDB File

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