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(-) Description

Title :  X-RAY STRUCTURE OF THE CHAPERONE PAPD IN COMPLEX WITH THE PILUS TERMINATOR SUBUNIT PAPH AT 2.3 ANGSTROM RESOLUTION
 
Authors :  D. Verger, E. Miller, H. Remaut, G. Waksman, S. Hultgren
Date :  17 Aug 06  (Deposition) - 08 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Chaperone/Surface Active Protein, Periplasmic, Pilus Termination, Immunoglobulin Domain, Paph, Papd, Fimbria, Chaperone, P5 Pocket, Chaperone/ Surface Active Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Verger, E. Miller, H. Remaut, G. Waksman, S. Hultgren
Molecular Mechanism Of P Pilus Termination In Uropathogenic Escherichia Coli.
Embo Rep. V. 7 1228 2006
PubMed-ID: 17082819  |  Reference-DOI: 10.1038/SJ.EMBOR.7400833

(-) 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
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: UTI 89
    Synonym: PERIPLASMIC CHAPERONE PAPD
 
Molecule 2 - PAP FIMBRIAL MINOR PILIN 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
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: RESIDUES 2 TO 22 DELETED (NON DONOR STRAND EXCHANGE REGION). N_TERMINAL EXTENSION 1 DELETED (NTD1).
    Strain: J96
    Synonym: PAPH

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1CO1Ligand/IonCOBALT (II) ION
2SO411Ligand/IonSULFATE ION
Biological Unit 1 (1, 22)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2SO422Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:39 , GLU A:40 , LEU A:85BINDING SITE FOR RESIDUE SO4 A1218
02AC2SOFTWARELYS A:44 , THR A:47 , ASP A:74 , ARG A:91 , HOH A:2042BINDING SITE FOR RESIDUE SO4 A1219
03AC3SOFTWAREARG A:82 , SER A:174 , HOH A:2039BINDING SITE FOR RESIDUE SO4 A1220
04AC4SOFTWAREILE A:206 , LYS A:216 , ARG B:122BINDING SITE FOR RESIDUE SO4 A1221
05AC5SOFTWAREARG A:82 , ARG A:176BINDING SITE FOR RESIDUE SO4 A1222
06AC6SOFTWAREPRO A:79 , GLN A:80 , ASP A:81 , HOH A:2167 , HOH A:2168 , HOH A:2169BINDING SITE FOR RESIDUE SO4 A1223
07AC7SOFTWAREHIS B:28 , HOH B:2099BINDING SITE FOR RESIDUE CO B1174
08AC8SOFTWARESER A:159 , LYS A:161 , PHE B:61 , SER B:62 , ARG B:149BINDING SITE FOR RESIDUE SO4 B1175
09AC9SOFTWAREGLN B:58 , ARG B:152 , LEU B:157BINDING SITE FOR RESIDUE SO4 B1176
10BC1SOFTWAREGLY A:199 , ARG A:200 , ALA B:26 , PHE B:27BINDING SITE FOR RESIDUE SO4 B1177
11BC2SOFTWAREARG B:73 , ASN B:74 , GLU B:142 , HOH B:2102 , HOH B:2103 , HOH B:2104BINDING SITE FOR RESIDUE SO4 B1178
12BC3SOFTWAREPHE B:85 , ASP B:120 , VAL B:121 , LEU B:137 , LEU B:144 , ASP B:145 , TYR B:146 , HOH B:2105BINDING SITE FOR RESIDUE SO4 B1179

(-) SS Bonds  (2, 2)

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

(-) 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 2J2Z)

(-) 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 2J2Z)

(-) 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: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 d2j2za1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d2j2za2 A:125-217 PapD                                                                        SCOP domains
               CATH domains 2j2zA01 A:1-121 PapD-like                                                                                                2j2zA02 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..........eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh......hhhh.eeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeee........eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------PILI_CHAPERONE    -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j2z 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 A from PDB  Type:PROTEIN  Length:217
 aligned with Q7ATU9_ECOLX | Q7ATU9 from UniProtKB/TrEMBL  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       
         Q7ATU9_ECOLX    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 238
               SCOP domains d2j2za1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d2j2za2 A:125-217 PapD                                                                        SCOP domains
               CATH domains 2j2zA01 A:1-121 PapD-like                                                                                                2j2zA02 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..........eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh......hhhh.eeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeee........eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j2z 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:150
 aligned with PAPH_ECOLX | P07111 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:150
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195
           PAPH_ECOLX    46 RAAFHGEVVRPACTLAMEDAWQIIDMGETPVRDLQNGFSGPERKFSLRLRNCEFNSQGGNLFSDSRIRVTFDGVRGETPDKFNLSGQAKGINLQIADVRGNIARAGKVMPAIPLTGNEEALDYTLRIVRNGKKLEAGNYFAVLGFRVDYE 195
               SCOP domains d2j2zb1 B:24-173 PAP fimbrial minor pilin protein PapH                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eee.............hhhhhhh......eeeeeeee....ee..ee..............................eeeeee.......................eeeeeeeeee.........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2j2z B  24 RAAFHGEVVRPACTLAMEDAWQIIDMGETPVRDLQNGFSGPERKFSLRLRNCEFNSQGGNLFSDSRIRVTFDGVRGETPDKFNLSGQAKGINLQIADVRGNIARAGKVMPAIPLTGNEEALDYTLRIVRNGKKLEAGNYFAVLGFRVDYE 173
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
   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 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 2J2Z)

(-) Gene Ontology  (8, 13)

Asymmetric Unit(hide GO term definitions)
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).

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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  2j2z
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  PAPD_ECOLX | P15319
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  PAPH_ECOLX | P07111
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  Q7ATU9_ECOLX | Q7ATU9
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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 2j7l 2uy6 2uy7 2w07 2wmp 2xg4 2xg5 3dpa 3me0 5k93
        PAPH_ECOLX | P07111: 2xg4 2xg5
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        Q7ATU9_ECOLX | Q7ATU9: 2j7l

(-) 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