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(-) Description

Title :  X-RAY STRUCTURE OF THE GENERAL SECRETION PATHWAY COMPLEX OF THE N-TERMINAL DOMAIN OF EPSE AND THE CYTOSOLIC DOMAIN OF EPSL OF VIBRIO CHOLERAE
 
Authors :  J. Abendroth, P. M. Murphy, A. Mushtaq, M. Bagdasarian, M. Sandkvist,
Date :  06 Jan 05  (Deposition) - 13 May 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,X,Y
Biol. Unit 1:  A,X  (1x)
Biol. Unit 2:  B,Y  (1x)
Keywords :  Transport Protein, Type Ii Secretion, Vibrio Cholerae, Eps, Gsp, Transmembrane, Transport, Atp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Abendroth, P. M. Murphy, A. Mushtaq, M. Bagdasarian, M. Sandkvist, W. G. J. Hol
The X-Ray Structure Of The Type Ii Secretion System Complex Formed By The N-Terminal Domain Of Epse And The Cytoplasmic Domain Of Epsl Of Vibrio Cholerae
J. Mol. Biol. V. 348 845 2005
PubMed-ID: 15843017  |  Reference-DOI: 10.1016/J.JMB.2005.02.061

(-) Compounds

Molecule 1 - GENERAL SECRETION PATHWAY PROTEIN L
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: CYTOPLASMIC DOMAIN, RESIDUES 5-246
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Synonym: CHOLERA TOXIN SECRETION PROTEIN, EPSL, GENERAL SECRETION PROTEIN EPSL
 
Molecule 2 - GENERAL SECRETION PATHWAY PROTEIN E,
    Chains: X, Y
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: DOMAIN N1, RESIDUES 1-96
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Synonym: TYPE II TRAFFIC WARDEN ATPASE, CHOLERA TOXIN SECRETION PROTEIN EPSE, GENERAL SECRETION PROTEIN EPSE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABXY
Biological Unit 1 (1x): A X 
Biological Unit 2 (1x):  B Y

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:180 , ASP B:92BINDING SITE FOR RESIDUE CA A1240

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BH1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala X:44 -Pro X:45
2Ala Y:44 -Pro Y:45

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BH1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BH1)

(-) Exons   (0, 0)

(no "Exon" information available for 2BH1)

(-) 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:238
 aligned with GSPL_VIBCH | P45782 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:238
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235        
           GSPL_VIBCH     6 SEFLTVRLSSQKEADIPWLVWSAEQQEVIASGQVAGWEALHEIESYADQRSVVVLLAASDLILTSVEIPPGASRQLENMLPYLLEDEIAQDVEDVHFCVLSKGRETADVVGVDRLWLRACLDHLKACGFDVKRVLPDVLAIPRPEHGLAALQLGDEWLVRKSTTQGMAVDAQWLSLLAASDWVQNEGEYLPLQALTPLPELSLAETQEWRYEPSGLVMQLLTQEALTSKFNLLTGSFK 243
               SCOP domains d2bh1a2 A:2-145 automated matches                                                                                                               d2bh1a1 A:146-239 automated matches                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......eeeeeeee....eeeeeeeee.hhhhhhhhhhh...eeeeee.hhh.eeeeee.....hhhhhhhhhhhhhhh....hhheeeeeeee...eeeeeeeehhhhhhhhhhhhh....eeeeeehhhh.......eeeeee..eeeeeee..eeeeeehhhhhhhh..hhhee..ee..eee..............eee.....hhhhhhhhh.........hhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bh1 A   2 SEFLTVRLSSQKEADIPWLVWSAEQQEVIASGQVAGWEALHEIESYADQRSVVVLLAASDLILTSVEIPPGASRQLENMLPYLLEDEIAQDVEDVHFCVLSKGRETADVVGVDRLWLRACLDHLKACGFDVKRVLPDVLAIPRPEHGLAALQLGDEWLVRKSTTQGMAVDAQWLSLLAASDWVQNEGEYLPLQALTPLPELSLAETQEWRYEPSGLVMQLLTQEALTSKFNLLTGSFK 239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with GSPL_VIBCH | P45782 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:238
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235        
           GSPL_VIBCH     6 SEFLTVRLSSQKEADIPWLVWSAEQQEVIASGQVAGWEALHEIESYADQRSVVVLLAASDLILTSVEIPPGASRQLENMLPYLLEDEIAQDVEDVHFCVLSKGRETADVVGVDRLWLRACLDHLKACGFDVKRVLPDVLAIPRPEHGLAALQLGDEWLVRKSTTQGMAVDAQWLSLLAASDWVQNEGEYLPLQALTPLPELSLAETQEWRYEPSGLVMQLLTQEALTSKFNLLTGSFK 243
               SCOP domains d2bh1b2 B:2-145 automated matches                                                                                                               d2bh1b1 B:146-239 automated matches                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeeeee....eeeeeeee..hhhhhhhhhhh...eeeeee.hhh.eeeeee........hhhhhhhhh.......hhheeeeeeee...eeeeeeeehhhhhhhhhhhhh....eeeeeehhhh.......eeeeee..eeeeeee..eeeeeehhhhhhhh..hhh........eee..............eee.....hhhhhhhhh.........hhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bh1 B   2 SEFLTVRLSSQKEADIPWLVWSAEQQEVIASGQVAGWEALHEIESYADQRSVVVLLAASDLILTSVEIPPGASRQLENMLPYLLEDEIAQDVEDVHFCVLSKGRETADVVGVDRLWLRACLDHLKACGFDVKRVLPDVLAIPRPEHGLAALQLGDEWLVRKSTTQGMAVDAQWLSLLAASDWVQNEGEYLPLQALTPLPELSLAETQEWRYEPSGLVMQLLTQEALTSKFNLLTGSFK 239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        


Chain X from PDB  Type:PROTEIN  Length:68
 aligned with GSPE_VIBCH | P37093 from UniProtKB/Swiss-Prot  Length:503

    Alignment length:68
                                    23        33        43        53        63        73        
           GSPE_VIBCH    14 IRRLPFSFANRFKLVLDWNEDFSQASIYYLAPLSMEALVETKRVVKHAFQLIELSQAEFESKLTQVYQ  81
               SCOP domains d2bh1x1 X:14-81 General secretion pathway protein E, EpsE            SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh.eeeee......eeeee.....hhhhhhhhhhh...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2bh1 X  14 IRRLPFSFANRFKLVLDWNEDFSQASIYYLAPLSMEALVETKRVVKHAFQLIELSQAEFESKLTQVYQ  81
                                    23        33        43        53        63        73        


Chain Y from PDB  Type:PROTEIN  Length:68
 aligned with GSPE_VIBCH | P37093 from UniProtKB/Swiss-Prot  Length:503

    Alignment length:68
                                    23        33        43        53        63        73        
           GSPE_VIBCH    14 IRRLPFSFANRFKLVLDWNEDFSQASIYYLAPLSMEALVETKRVVKHAFQLIELSQAEFESKLTQVYQ  81
               SCOP domains d2bh1y_ Y: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh.eeeee......eeeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2bh1 Y  14 IRRLPFSFANRFKLVLDWNEDFSQASIYYLAPLSMEALVETKRVVKHAFQLIELSQAEFESKLTQVYQ  81
                                    23        33        43        53        63        73
   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  (4, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BH1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BH1)

(-) Gene Ontology  (14, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GSPL_VIBCH | P45782)
molecular function
    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:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
    GO:0009306    protein secretion    The controlled release of proteins from a cell.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0009276    Gram-negative-bacterium-type cell wall    The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain X,Y   (GSPE_VIBCH | P37093)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
    GO:0015628    protein secretion by the type II secretion system    The process in which proteins are secreted across the outer membrane of Gram-negative bacteria by the type II secretion system. Proteins using this pathway are first translocated across the cytoplasmic membrane via the Sec or Tat pathways.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0015627    type II protein secretion system complex    A large protein complex, containing 12-15 subunits, that spans the cell envelope of Gram-negative bacteria and mediates the movement of proteins into the extracellular environment. The complex includes a component in the cytoplasm, an inner membrane subcomplex that reaches into the periplasmic compartment and a secretion pore in the outer membrane. Proteins using the Type II pathway are transported across the cytoplasmic membrane by the Sec or Tat complex.

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  2bh1
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  GSPE_VIBCH | P37093
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  GSPL_VIBCH | P45782
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 Related Entries

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

UniProtKB/Swiss-Prot
        GSPE_VIBCH | P37093: 1p9r 1p9w 4ksr 4kss
        GSPL_VIBCH | P45782: 1w97 1yf5

(-) Related Entries Specified in the PDB File

1p9r CRYSTAL STRUCTURE OF VIBRIO CHOLERAE PUTATIVE NTPASE EPSE
1p9w CRYSTAL STRUCTURE OF VIBRIO CHOLERAE PUTATIVE NTPASE EPSE
1w97 CYTO-EPSL: THE CYTOPLASMIC DOMAIN OF EPSL, AN INNER MEMBRANE COMPONENT OF THE TYPE II SECRETION SYSTEM OF VIBRIO CHOLERAE