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(-) Description

Title :  STRUCTURE OF THE E. COLI CHAPERONE PAPD IN COMPLEX WITH THE PILIN DOMAIN OF THE PAPGII ADHESIN
 
Authors :  B. A. Ford, D. Verger, J. S. Elam, K. W. Dodson, J. S. Pinkner, S. J. Hultgr
Date :  02 Jul 09  (Deposition) - 25 Aug 10  (Release) - 26 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chaperone, Cell Adhesion, Donor Strand Complementation, Pilin Domain, Immunoglobulin Domain, Bacterial Attachment And Invasion, Donor Strand Exchange, Chaperone Usher Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. A. Ford, D. Verger, K. W. Dodson, E. Volkan, M. Kostakioti, J. S. Elam J. S. Pinkner, G. Waksman, S. J. Hultgren
Structure Of The Papd-Papgii Pilin Complex Reveals An Open And Flexible P5 Pocket.
J. Bacteriol. V. 194 6390 2012
PubMed-ID: 23002225  |  Reference-DOI: 10.1128/JB.06651-11
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHAPERONE PROTEIN PAPD
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: C600
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 22-239
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 364106
    Other Details: C TERMINUS 6-HISTIDINE TAG
    Other Details - Source: GENOMIC DNA
    Strain: UTI89
    Synonym: PAPD
 
Molecule 2 - PAPG PROTEIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: C600
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PILIN DOMAIN, RESIDUES 214-336
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: ADHESIN DOMAIN DELETED (RESIDUES 1 TO 193)
    Other Details - Source: GENOMIC DNA
    Strain: AD110
    Synonym: PAPGII

 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 2WMP)

(-) Sites  (0, 0)

(no "Site" information available for 2WMP)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:207 -A:212
2B:197 -B:229

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological 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 2WMP)

(-) 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 2WMP)

(-) 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:216
 aligned with PAPD_ECOLX | P15319 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:216
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      
           PAPD_ECOLX    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKK 237
               SCOP domains d2wmpa1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d2wmpa2 A:125-216 PapD                                                                       SCOP domains
               CATH domains 2wmpA01 A:1-121 PapD-like                                                                                                2wmpA02 A:122-212  [code=2.60.40.1070, no name defined]                                    ---- CATH domains
               Pfam domains Pili_assembly_N-2wmpA01 A:1-121                                                                                          -------------------Pili_assembly_C-2wmpA02 A:141-204                               ------------ Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee...........eeee..........eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh.....hhhhhheeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeeee.......eeeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------PILI_CHAPERONE    ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wmp A   1 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKK 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      


Chain A from PDB  Type:PROTEIN  Length:216
 aligned with Q1R2W9_ECOUT | Q1R2W9 from UniProtKB/TrEMBL  Length:239

    Alignment length:216
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      
         Q1R2W9_ECOUT    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKK 237
               SCOP domains d2wmpa1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d2wmpa2 A:125-216 PapD                                                                       SCOP domains
               CATH domains 2wmpA01 A:1-121 PapD-like                                                                                                2wmpA02 A:122-212  [code=2.60.40.1070, no name defined]                                    ---- CATH domains
               Pfam domains Pili_assembly_N-2wmpA01 A:1-121                                                                                          -------------------Pili_assembly_C-2wmpA02 A:141-204                               ------------ Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee...........eeee..........eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh.....hhhhhheeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeeee.......eeeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wmp A   1 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKK 216
                                    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:123
 aligned with Q47445_ECOLX | Q47445 from UniProtKB/TrEMBL  Length:336

    Alignment length:123
                                   223       233       243       253       263       273       283       293       303       313       323       333   
         Q47445_ECOLX   214 IGGCRPSAQSLEIKHGDLSINSANNHYAAQTLSVSCDVPANIRFMLLRNTTPTYSHGKKFSVGLGHGWDSIVSVNGVDTGETTMRWYKAGTQNLTIGSRLYGESSKIQPGVLSGSATLLMILP 336
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains PapG_N-2wmpB0-PapG_C-2wmpB02 B:208-316                                                                                      Pfam domains
         Sec.struct. author ....ee....................eeeeeeeeee...eeeeeeeee............eeeee..eeeeeee......eeeeee...eeeeeeeeeee............eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wmp B 194 IGGCRPSAQSLEIKHGDLSINSANNHYAAQTLSVSCDVPANIRFMLLRNTTPTYSHGKKFSVGLGHGWDSIVSVNGVDTGETTMRWYKAGTQNLTIGSRLYGESSKIQPGVLSGSATLLMILP 316
                                   203       213       223       233       243       253       263       273       283       293       303       313
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Clan: Adhesin (36)
(-)
Clan: E-set (290)
(-)
Clan: no clan defined [family: PapG_C] (2)
(-)
Clan: no clan defined [family: Pili_assembly_C] (20)

(-) Gene Ontology  (7, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q1R2W9_ECOUT | Q1R2W9)
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   (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   (Q47445_ECOLX | Q47445)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
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.

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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 2j7l 2uy6 2uy7 2w07 2xg4 2xg5 3dpa 3me0 5k93
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        Q1R2W9_ECOUT | Q1R2W9: 2uy6 2uy7 2w07

(-) 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
3dpa PAPD
3me0 STRUCTURE OF THE E. COLI CHAPERONE PAPD IN COMPLEX WITH THE PILIN DOMAIN OF THE PAPGII ADHESIN