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(-) Description

Title :  PAPD-PAPK CHAPERONE-PILUS SUBUNIT COMPLEX FROM E.COLI P PILUS
 
Authors :  K. Fuetterer, F. G. Sauer, S. J. Hultgren, G. Waksman
Date :  29 Mar 99  (Deposition) - 17 Aug 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chaperone, Pilus, Bacterial Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. G. Sauer, K. Futterer, J. S. Pinkner, K. W. Dodson, S. J. Hultgren, G. Waksman
Structural Basis Of Chaperone Function And Pilus Biogenesis.
Science V. 285 1058 1999
PubMed-ID: 10446050  |  Reference-DOI: 10.1126/SCIENCE.285.5430.1058
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (CHAPERONE PROTEIN PAPD)
    Cellular Location: PERIPLASM
    Chains: A
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - PROTEIN (PROTEIN PAPK)
    Cellular Location: PERIPLASM
    Chains: B
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1PDK)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:207 -A:212
2B:14 -B:54

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:48 -Pro A:49
2Thr A:53 -Pro A:54
3Pro B:38 -Pro B:39

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PILI_CHAPERONEPS00635 Gram-negative pili assembly chaperone signature.PAPD_ECOLX99-116  1A:78-95

(-) Exons   (0, 0)

(no "Exon" information available for 1PDK)

(-) 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:215
 aligned with PAPD_ECOLX | P15319 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:215
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     
           PAPD_ECOLX    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVK 236
               SCOP domains d1pdka1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d1pdka2 A:125-215 PapD                                                                      SCOP domains
               CATH domains 1pdkA01 A:1-121 PapD-like                                                                                                1pdkA02 A:122-213  [code=2.60.40.1070, no name defined]                                     -- CATH domains
               Pfam domains Pili_assembly_N-1pdkA01 A:1-121                                                                                          -------------------Pili_assembly_C-1pdkA02 A:141-204                               ----------- Pfam domains
         Sec.struct. author .......eeeee....eeeeeee.......eeeeeeeee..........eeee..eeee....eeeeeeee.hhhhh......eeeeeeeeee.............eeeeeeeeee.hhh.......hhhh.eeeee..eeeeee.....eeeeeee..hhhhh......eee...eeeeee.......eeeee.......eeeeeee..eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------PILI_CHAPERONE    ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pdk A   1 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVK 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain B from PDB  Type:PROTEIN  Length:149
 aligned with PAPK_ECOLX | P62532 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:149
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169         
           PAPK_ECOLX    30 LLDRPCHVSGDSLNKHVVFKTRASRDFWYPPGRSPTESFVIRLENCHATAVGKIVTLTFKGTEEAALPGHLKVTGVNAGRLGIALLDTDGSSLLKPGTSHNKGQGEKVTGNSLELPFGAYVVATPEALRTKSVVPGDYEATATFELTYR 178
               SCOP domains d1pdkb_ B: PapK pilus subunit                                                                                                                         SCOP domains
               CATH domains 1pdkB00 B:9-157  [code=2.60.40.1090, no name defined]                                                                                                 CATH domains
               Pfam domains Fimbrial-1pdkB01 B:9-157                                                                                                                              Pfam domains
         Sec.struct. author ......................hhhhh.........eeeeeee.......hhhheeeeee....................eeeeee..........................eeeeeeeeeee.hhhhh.............eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pdk B   9 LLDRPCHVSGDSLNKHVVFKTRASRDFWYPPGRSPTESFVIRLENCHATAVGKIVTLTFKGTEEAALPGHLKVTGVNAGRLGIALLDTDGSSLLKPGTSHNKGQGEKVTGNSLELPFGAYVVATPEALRTKSVVPGDYEATATFELTYR 157
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: Adhesin (36)
(-)
Clan: E-set (290)
(-)
Clan: no clan defined [family: Pili_assembly_C] (20)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PAPD_ECOLX | P15319)
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0061077    chaperone-mediated protein folding    The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
    GO:0043711    pilus organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pilus, a short filamentous structure on a bacterial cell, flagella-like in structure and generally present in many copies.
cellular component
    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).

Chain B   (PAPK_ECOLX | P62532)
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
cellular component
    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:0009289    pilus    A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

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  Cis Peptide Bonds
    Gly A:48 - Pro A:49   [ RasMol ]  
    Pro B:38 - Pro B:39   [ RasMol ]  
    Thr A:53 - Pro A:54   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PAPD_ECOLX | P15319: 1n0l 1qpp 1qpx 2j2z 2j7l 2uy6 2uy7 2w07 2wmp 2xg4 2xg5 3dpa 3me0 5k93
        PAPK_ECOLX | P62532: 1n12

(-) Related Entries Specified in the PDB File

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