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(-) Description

Title :  PERIPLASMIC DOMAIN OF EPSL FROM VIBRIO PARAHAEMOLYTICUS
 
Authors :  J. Abendroth, A. C. Kreger, H. Abendroth, M. Sandkvist, W. G. J. Hol
Date :  06 Jan 09  (Deposition) - 31 Mar 10  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Transport, Type Ii Secretion, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Abendroth, A. C. Kreger, W. G. J. Hol
The Dimer Formed By The Periplasmic Domain Of Epsl From The Type 2 Secretion System Of Vibrio Parahaemolyticus.
J. Struct. Biol. V. 168 313 2009
PubMed-ID: 19646531  |  Reference-DOI: 10.1016/J.JSB.2009.07.022

(-) Compounds

Molecule 1 - GENERAL SECRETION PATHWAY PROTEIN L
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJA-080
    Expression System Strain: BL21GOLD(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET21A
    Fragment: PERIPLASMIC DOMAIN, RESIDUES 319-404
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS
    Organism Taxid: 670

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:338 , GLY A:339 , VAL A:341 , LEU A:344 , HOH A:2005 , HOH A:2024BINDING SITE FOR RESIDUE EDO A 1405
2AC2SOFTWARELEU B:338 , GLY B:339 , VAL B:341 , LEU B:344 , HOH B:2005 , HOH B:2025BINDING SITE FOR RESIDUE EDO B 1405
3AC3SOFTWARELYS A:350 , ARG A:359 , HOH A:2025 , LYS B:350 , ARG B:359 , PO4 B:1406BINDING SITE FOR RESIDUE PO4 A 1406
4AC4SOFTWARELYS A:350 , PO4 A:1406 , LYS B:350BINDING SITE FOR RESIDUE PO4 B 1406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W7V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W7V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W7V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W7V)

(-) Exons   (0, 0)

(no "Exon" information available for 2W7V)

(-) 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:82
 aligned with Q87TC9_VIBPA | Q87TC9 from UniProtKB/TrEMBL  Length:404

    Alignment length:83
                                   331       341       351       361       371       381       391       401   
         Q87TC9_VIBPA   322 STDVAMLSWLAALPATLGQVKDLEITSFKYDGQRGEVRIHARSSDFQPFEQARVKLAEKFNVEQGQLNRSDNVVMGSFVLKRQ 404
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.hhhhhhhh....eeeeeeee....eeeeeeee..hhhhhhhhhhhhh.eeeee...ee.-..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 2w7v A 322 STDVAmLSWLAALPATLGQVKDLEITSFKYDGQRGEVRIHARSSDFQPFEQARVKLAEKFNVEQGQLNRS-NVVmGSFVLKRQ 404
                                 | 331       341       351       361       371       381       391 |  |  401   
                                 |                                                             391 |  |        
                               327-MSE                                                           393  |        
                                                                                                    396-MSE    


Chain B from PDB  Type:PROTEIN  Length:82
 aligned with Q87TC9_VIBPA | Q87TC9 from UniProtKB/TrEMBL  Length:404

    Alignment length:83
                                   331       341       351       361       371       381       391       401   
         Q87TC9_VIBPA   322 STDVAMLSWLAALPATLGQVKDLEITSFKYDGQRGEVRIHARSSDFQPFEQARVKLAEKFNVEQGQLNRSDNVVMGSFVLKRQ 404
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) GspL_C-2w7vB01 B:322-404                                                            Pfam domains (1)
           Pfam domains (2) GspL_C-2w7vB02 B:322-404                                                            Pfam domains (2)
         Sec.struct. author ..hhhhhhhh.hhhhhhhh....eeeeeeee....eeeeeeee..hhhhhhhhhhhhh.eeeee...ee.-..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 2w7v B 322 STDVAmLSWLAALPATLGQVKDLEITSFKYDGQRGEVRIHARSSDFQPFEQARVKLAEKFNVEQGQLNRS-NVVmGSFVLKRQ 404
                                 | 331       341       351       361       371       381       391 |  |  401   
                               327-MSE                                                         391 |  |        
                                                                                                 393  |        
                                                                                                    396-MSE
   Legend:   → Mismatch (orange background)
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  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 2W7V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W7V)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: EpsM (2)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q87TC9_VIBPA | Q87TC9)
molecular function
    GO:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
    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.

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