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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PERIPLASMIC CHAPERONE SKP
 
Authors :  I. P. Korndorfer, M. K. Dommel, A. Skerra
Date :  23 Feb 04  (Deposition) - 14 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein Folding, Outer Membrane Protein, Molecular Dipole, Hydrophobic Surface, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. P. Korndorfer, M. K. Dommel, A. Skerra
Structure Of The Periplasmic Chaperone Skp Suggests Functional Similarity With Cytosolic Chaperones Despite Differing Architecture.
Nat. Struct. Mol. Biol. V. 11 1015 2004
PubMed-ID: 15361861  |  Reference-DOI: 10.1038/NSMB828
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SEVENTEEN KILODALTON PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASK75-IBA4-SKP
    Expression System Strain: JM83
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HLPA, SKP, OMPH, B0178, C0215, Z0190, ECS0180, SF0168, S0171
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1SG2)

(-) Sites  (0, 0)

(no "Site" information available for 1SG2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SG2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SG2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SG2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SG2)

(-) Exons   (0, 0)

(no "Exon" information available for 1SG2)

(-) 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:141
 aligned with SKP_ECOLI | P0AEU7 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:141
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160 
            SKP_ECOLI    21 ADKIAIVNMGSLFQQVAQKTGVSNTLENEFKGRASELQRMETDLQAKMKKLQSMKAGSDRTKLEKDVMAQRQTFAQKAQAFEQDRARRSNEERGKLVTRIQTAVKSVANSQDIDLVVDANAVAYNSSDVKDITADVLKQVK 161
               SCOP domains d1sg2a_ A: Periplasmic chaperon skp (HlpA)                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...eeee....eehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sg2 A  13 ADKIAIVNMGSLFQQVAQKTGVSNTLENEFKGRASELQRMETDLQAKMKKLQSMKAGSDRTKLEKDVMAQRQTFAQKAQAFEQDRARRSNEERGKLVTRIQTAVKSVANSQDIDLVVDANAVAYNSSDVKDITADVLKQVK 153
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152 


Chain B from PDB  Type:PROTEIN  Length:109
 aligned with SKP_ECOLI | P0AEU7 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:143
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158   
            SKP_ECOLI    19 QAADKIAIVNMGSLFQQVAQKTGVSNTLENEFKGRASELQRMETDLQAKMKKLQSMKAGSDRTKLEKDVMAQRQTFAQKAQAFEQDRARRSNEERGKLVTRIQTAVKSVANSQDIDLVVDANAVAYNSSDVKDITADVLKQVK 161
               SCOP domains d1sg2b_ B: Periplasmic chaperon skp (HlpA)                                                                                                      SCOP domains
               CATH domains 1sg2B00 B:11-153 OmpH-like (Pfam 03938)                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.----------------------------------......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee...eeee....eehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sg2 B  11 GAADKIAIVNMGSLFQQVAQKTGVSNTLENEFKGRASELQRM----------------------------------AQKAQAFEQDRARRSNEERGKLVTRIQTAVKSVANSQDIDLVVDANAVAYNSSDVKDITADVLKQVK 153
                                    20        30        40        50 |       -         -         -      | 90       100       110       120       130       140       150   
                                                                    52                                 87                                                                  


Chain C from PDB  Type:PROTEIN  Length:142
 aligned with SKP_ECOLI | P0AEU7 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:142
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159  
            SKP_ECOLI    20 AADKIAIVNMGSLFQQVAQKTGVSNTLENEFKGRASELQRMETDLQAKMKKLQSMKAGSDRTKLEKDVMAQRQTFAQKAQAFEQDRARRSNEERGKLVTRIQTAVKSVANSQDIDLVVDANAVAYNSSDVKDITADVLKQVK 161
               SCOP domains d1sg2c_ C: Periplasmic chaperon skp (HlpA)                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) OmpH-1sg2C01 C:12-153                                                                                                                          Pfam domains (1)
           Pfam domains (2) OmpH-1sg2C02 C:12-153                                                                                                                          Pfam domains (2)
           Pfam domains (3) OmpH-1sg2C03 C:12-153                                                                                                                          Pfam domains (3)
         Sec.struct. author ....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee...eeee......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sg2 C  12 AADKIAIVNMGSLFQQVAQKTGVSNTLENEFKGRASELQRMETDLQAKMKKLQSMKAGSDRTKLEKDVMAQRQTFAQKAQAFEQDRARRSNEERGKLVTRIQTAVKSVANSQDIDLVVDANAVAYNSSDVKDITADVLKQVK 153
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151
   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  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (SKP_ECOLI | P0AEU7)
molecular function
    GO:0001530    lipopolysaccharide binding    Interacting selectively and non-covalently with lipopolysaccharide.
    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:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0043165    Gram-negative-bacterium-type cell outer membrane assembly    The assembly of an outer membrane of the type formed in Gram-negative bacteria. This membrane is enriched in polysaccharide and protein, and the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0051085    chaperone mediated protein folding requiring cofactor    The process of assisting in the correct posttranslational noncovalent assembly of proteins, which is dependent on additional protein cofactors. This process occurs over one or several cycles of nucleotide hydrolysis-dependent binding and release.
    GO:0065002    intracellular protein transmembrane transport    The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0032978    protein insertion into membrane from inner side    The process in which a protein is incorporated into a lipid bilayer, e.g., the prokaryotic, mitochondrial, or chloroplast inner membrane, from the inner side.
    GO:0022417    protein maturation by protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that results in the attainment of the full functional capacity of a protein.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    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)

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        SKP_ECOLI | P0AEU7: 1u2m

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