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(-) Description

Title :  E.COLI P PILUS CHAPERONE PAPD IN COMPLEX WITH A PILUS BIOGENESIS INHIBITOR, PILICIDE 2C
 
Authors :  H. Remaut, J. S. Pinkner, S. J. Hultgren, F. Almqvist, G. Waksman
Date :  12 Oct 06  (Deposition) - 01 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Fimbria, Inhibitor, Chaperone, Periplasmic, Immunoglobulin Domain, Chaperone/Surface Active Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Pinkner, H. Remaut, F. Buelens, E. Miller, V. Aberg, N. Pemberton, M. Hedenstrom, A. Larsson, P. Seed, G. Waksman, S. J. Hultgren, F. Almqvist
Rationally Designed Small Compounds Inhibit Pilus Biogenesis In Uropathogenic Bacteria.
Proc. Natl. Acad. Sci. Usa V. 103 17897 2006
PubMed-ID: 17098869  |  Reference-DOI: 10.1073/PNAS.0606795103

(-) Compounds

Molecule 1 - CHAPERONE PROTEIN PAPD
    Atcc: 700336
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMMB91
    Expression System Strain: C600
    Expression System Taxid: 562
    Fragment: RESIDUES 22-239
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: J96
    Synonym: PAPD

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1XC21Ligand/Ion(3R)-8-CYCLOPROPYL-6-(MORPHOLIN-4-YLMETHYL)-7-(1-NAPHTHYLMETHYL)-5-OXO-2,3-DIHYDRO-5H-[1,3]THIAZOLO[3,2-A]PYRIDINE-3-CARBOXYLIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1XC22Ligand/Ion(3R)-8-CYCLOPROPYL-6-(MORPHOLIN-4-YLMETHYL)-7-(1-NAPHTHYLMETHYL)-5-OXO-2,3-DIHYDRO-5H-[1,3]THIAZOLO[3,2-A]PYRIDINE-3-CARBOXYLIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:32 , ILE A:46 , THR A:47 , ALA A:52 , THR A:53 , PRO A:55 , ARG A:58 , PRO A:94 , PRO A:95 , ARG A:96BINDING SITE FOR RESIDUE XC2 A1216

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:207 -A:212

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:48 -Pro A:49
2Thr A:53 -Pro A:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J7L)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PILI_CHAPERONEPS00635 Gram-negative pili assembly chaperone signature.PAPD_ECOLX99-116  1A:78-95
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PILI_CHAPERONEPS00635 Gram-negative pili assembly chaperone signature.PAPD_ECOLX99-116  2A:78-95

(-) Exons   (0, 0)

(no "Exon" information available for 2J7L)

(-) 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:210
 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 d2j7la1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d2j7la2 A:125-215 PapD                                                                      SCOP domains
               CATH domains 2j7lA01 A:1-121 PapD-like                                                                                                2j7lA02 A:122-213  [code=2.60.40.1070, no name defined]                                     -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee...........eeee..eeee....eeeeeeee.hhhhhh.....eeeeeeeeee.....-----.....eeeeeeeehhhhh......hhhhh.eeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeee........eeeeeee..eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------PILI_CHAPERONE    ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j7l A   1 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLDPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSE-----QIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVK 215
                                    10        20        30        40        50        60        70        80        90       | -   |   110       120       130       140       150       160       170       180       190       200       210     
                                                                                                                            98   104                                                                                                               


Chain A from PDB  Type:PROTEIN  Length:210
 aligned with Q7ATU9_ECOLX | Q7ATU9 from UniProtKB/TrEMBL  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     
         Q7ATU9_ECOLX    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVK 236
               SCOP domains d2j7la1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d2j7la2 A:125-215 PapD                                                                      SCOP domains
               CATH domains 2j7lA01 A:1-121 PapD-like                                                                                                2j7lA02 A:122-213  [code=2.60.40.1070, no name defined]                                     -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee...........eeee..eeee....eeeeeeee.hhhhhh.....eeeeeeeeee.....-----.....eeeeeeeehhhhh......hhhhh.eeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeee........eeeeeee..eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j7l A   1 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLDPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSE-----QIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVK 215
                                    10        20        30        40        50        60        70        80        90       | -   |   110       120       130       140       150       160       170       180       190       200       210     
                                                                                                                            98   104
   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  (2, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J7L)

(-) Gene Ontology  (5, 10)

Asymmetric 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 A   (Q7ATU9_ECOLX | Q7ATU9)
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).

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  2j7l
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  PAPD_ECOLX | P15319
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 Related Entries

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

UniProtKB/Swiss-Prot
        PAPD_ECOLX | P15319: 1n0l 1pdk 1qpp 1qpx 2j2z 2uy6 2uy7 2w07 2wmp 2xg4 2xg5 3dpa 3me0 5k93
UniProtKB/TrEMBL
        Q7ATU9_ECOLX | Q7ATU9: 2j2z

(-) Related Entries Specified in the PDB File

1n0l CRYSTAL STRUCTURE OF THE PAPD CHAPERONE (C- TERMINALLY 6XHISTIDINE-TAGGED) BOUND TO THE PAPE PILUS SUBUNIT (N-TERMINAL-DELETED) FROM UROPATHOGENIC E. COLI
1pdk PAPD-PAPK CHAPERONE-PILUS SUBUNIT COMPLEX FROM E.COLI P PILUS
1qpp CRYSTAL STRUCTURES OF SELF CAPPING PAPD CHAPERONE HOMODIMERS
1qpx CRYSTAL STRUCTURES OF SELF-CAPPING PAPD CHAPERONE HOMODIMERS
2j2z X-RAY STRUCTURE OF THE CHAPERONE PAPD IN COMPLEX WITH THE PILUS TERMINATOR SUBUNIT PAPH AT 2.3 ANGSTROM RESOLUTION
3dpa PAPD