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(-) Description

Title :  E. COLI P PILUS CHAPERONE-SUBUNIT COMPLEX PAPD-PAPH BOUND TO PILUS BIOGENESIS INHIBITOR, PILICIDE 5D
 
Authors :  H. Remaut, G. Phan, F. Buelens, E. Chorell, J. S. Pinkner, S. Edvinsson, F. Almqvist, S. J. Hultgren, G. Waksman
Date :  30 May 10  (Deposition) - 14 Jul 10  (Release) - 03 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chaperone, Chaperone-Surface Active Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Chorell, J. S. Pinkner, G. Phan, S. Edvinsson, F. Buelens, H. Remaut G. Waksman, S. J. Hultgren, F. Almqvist
Design And Synthesis Of C-2 Substituted Thiazolo And Dihydrothiazolo Ring-Fused 2-Pyridones: Pilicides With Increased Antivirulence Activity.
J. Med. Chem. V. 53 5690 2010
PubMed-ID: 20586493  |  Reference-DOI: 10.1021/JM100470T

(-) Compounds

Molecule 1 - CHAPERONE PROTEIN PAPD
    Atcc: 700336
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: C600
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: C-TERMINAL 6XHIS TAG
    Strain: J96
    Synonym: PAPD
 
Molecule 2 - PAP FIMBRIAL MINOR PILIN PROTEIN
    Atcc: 700336
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: C600
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: N-TERMINAL RESIDUES 1-22 DELETED
    Strain: J96
    Synonym: PAPH

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 5)

Asymmetric/Biological Unit (5, 5)
No.NameCountTypeFull Name
1CO1Ligand/IonCOBALT (II) ION
2EC21Ligand/Ion(2R,3R)-8-CYCLOPROPYL-7-(NAPHTHALEN-1-YLMETHYL)-5-OXO-2-PHENYL-2,3-DIHYDRO-5H-[1,3]THIAZOLO[3,2-A]PYRIDINE-3-CARBOXYLIC ACID
3EC51Ligand/Ion(2R)-2-[5-CYCLOPROPYL-6-(HYDROXYSULFANYL)-4-(NAPHTHALEN-1-YLMETHYL)-2-OXOPYRIDIN-1(2H)-YL]-3-PHENYLPROPANOIC ACID
4GOL1Ligand/IonGLYCEROL
5PGO1Ligand/IonS-1,2-PROPANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE B:85 , ASP B:120 , VAL B:121 , LEU B:137 , LEU B:144 , ASP B:145 , TYR B:146 , HOH B:2064BINDING SITE FOR RESIDUE PGO B1174
2AC2SOFTWARETRP A:36 , GLU A:38 , ASN A:89 , GLN A:108 , LYS A:110 , HOH A:2032 , ARG B:169BINDING SITE FOR RESIDUE GOL A1218
3AC3SOFTWAREHIS B:28BINDING SITE FOR RESIDUE CO B1175
4AC4SOFTWAREPRO A:30 , TYR A:31 , LEU A:32 , THR A:53 , VAL A:56 , ARG A:58 , SER A:70 , ILE A:93 , PRO A:94 , PRO A:95 , HOH A:2137 , HOH A:2138BINDING SITE FOR RESIDUE EC2 A1219
5AC5SOFTWARELEU A:32 , THR A:53 , VAL A:56 , ARG A:58 , ARG A:68 , SER A:70 , THR A:71 , PRO A:73 , ILE A:93 , PRO A:94 , PRO A:95 , HOH A:2138BINDING SITE FOR RESIDUE EC5 A1220

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:207 -A:212
2B:36 -B:75

(-) 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 2XG5)

(-) 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 2XG5)

(-) 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:217
 aligned with PAPD_ECOLX | P15319 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:217
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           PAPD_ECOLX    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 238
               SCOP domains d2xg5a1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d2xg5a2 A:125-217 PapD                                                                        SCOP domains
               CATH domains 2xg5A01 A:1-121 PapD-like                                                                                                2xg5A02 A:122-213  [code=2.60.40.1070, no name defined]                                     ---- CATH domains
               Pfam domains Pili_assembly_N-2xg5A01 A:1-121                                                                                          -------------------Pili_assembly_C-2xg5A02 A:141-204                               ------------- Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee.....ee....eeee..eeee....eeeeeeee.hhhhhh.......................eeeeeeeeeeeeeeehhhhh......hhhhheeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeeee.......eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------PILI_CHAPERONE    -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xg5 A   1 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 217
                                    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:147
 aligned with PAPH_ECOLX | P07111 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:149
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186         
           PAPH_ECOLX    47 AAFHGEVVRPACTLAMEDAWQIIDMGETPVRDLQNGFSGPERKFSLRLRNCEFNSQGGNLFSDSRIRVTFDGVRGETPDKFNLSGQAKGINLQIADVRGNIARAGKVMPAIPLTGNEEALDYTLRIVRNGKKLEAGNYFAVLGFRVDYE 195
               SCOP domains d2xg5b_ B: PAP fimbrial minor pilin protein PapH                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Fimbrial-2xg5B01 B:25-173                                                                                                                             Pfam domains
         Sec.struct. author ............eee......eee....hhhhhhh......eeeeeeee................eeeeee............ee....eeeeeee..................--..eeeeeeeeee.........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xg5 B  25 AAFHGEVVRPACTLAMEDAWQIIDMGETPVRDLQNGFSGPERKFSLRLRNCEFNSQGGNLFSDSRIRVTFDGVRGETPDKFNLSGQAKGINLQIADVRGNIARAGKVMPAIPLT--EEALDYTLRIVRNGKKLEAGNYFAVLGFRVDYE 173
                                    34        44        54        64        74        84        94       104       114       124       134   |  |144       154       164         
                                                                                                                                           138  |                                
                                                                                                                                              141
   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  (2, 2)

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   (PAPH_ECOLX | P07111)
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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  PAPH_ECOLX | P07111
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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 2wmp 2xg4 3dpa 3me0 5k93
        PAPH_ECOLX | P07111: 2j2z 2xg4

(-) 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
2wmp STRUCTURE OF THE E. COLI CHAPERONE PAPD IN COMPLEX WITH THE PILIN DOMAIN OF THE PAPGII ADHESIN
2xg4 E. COLI P PILUS CHAPERONE-SUBUNIT COMPLEX PAPD-PAPH BOUND TO PILUS BIOGENESIS INHIBITOR, PILICIDE 2C
3dpa PAPD