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(-) Description

Title :  STRUCTURAL DETERMINANTS OF POLYMERIZATION REACTIVITY OF THE P PILUS ADAPTOR SUBUNIT PAPF
 
Authors :  D. Verger, R. J. Rose, E. Paci, G. Costakes, T. Daviter, S. Hultgren, H. Remaut, A. E. Ashcroft, S. E. Radford, G. Waksman
Date :  12 Aug 08  (Deposition) - 25 Nov 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Donor Strand Complementation, Nte, Papd, Papf, Pili, Pilin, Groove, Subunit, Immunoglobulin Domain, Donor-Strand Exchange, Secreted, Fimbrium, Periplasm, P5 Pocket, Chaperone, Cell Adhesion, Cell Projection, Pilus Biogenesis, Order Of Assembly, N-Terminal Extension (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Verger, R. J. Rose, E. Paci, G. Costakes, T. Daviter, S. Hultgren, H. Remaut, A. E. Ashcroft, S. E. Radford, G. Waksman
Structural Determinants Of Polymerization Reactivity Of The P Pilus Adaptor Subunit Papf.
Structure V. 16 1724 2008
PubMed-ID: 19000824  |  Reference-DOI: 10.1016/J.STR.2008.08.012

(-) 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
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 364106
    Strain: UTI89
    Synonym: PAPD
 
Molecule 2 - MINOR PILIN SUBUNIT PAPF
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: C600
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 364106
    Strain: UTI89
    Synonym: PAPF

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:82 , TYR A:150 , SER A:174BINDING SITE FOR RESIDUE SO4 A1217
2AC2SOFTWAREARG A:82 , ARG A:176BINDING SITE FOR RESIDUE SO4 A1218

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:207 -A:212
2B:15 -B:50

(-) 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 2W07)

(-) 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 2W07)

(-) 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 d2w07a1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d2w07a2 A:125-216 PapD                                                                       SCOP domains
               CATH domains 2w07A01 A:1-121 PapD-like                                                                                                2w07A02 A:122-213  [code=2.60.40.1070, no name defined]                                     --- CATH domains
               Pfam domains Pili_assembly_N-2w07A01 A:1-121                                                                                          -------------------Pili_assembly_C-2w07A02 A:141-204                               ------------ Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee...........eeee..........eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh......hhhh.eeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeeee.......eeeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------PILI_CHAPERONE    ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2w07 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 d2w07a1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d2w07a2 A:125-216 PapD                                                                       SCOP domains
               CATH domains 2w07A01 A:1-121 PapD-like                                                                                                2w07A02 A:122-213  [code=2.60.40.1070, no name defined]                                     --- CATH domains
               Pfam domains Pili_assembly_N-2w07A01 A:1-121                                                                                          -------------------Pili_assembly_C-2w07A02 A:141-204                               ------------ Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee...........eeee..........eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh......hhhh.eeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeeee.......eeeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2w07 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:121
 aligned with PRSF_ECOLX | P42187 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:140
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167
           PRSF_ECOLX    28 NVYIPPCTINNGQNIVVDFGNINPEHVDNSRGEVTKNISISCPYKSGSLWIKVTGNTMGVGQNNVLATNITHFGIALYQGKGMSTPLTLGNGSGNGYRVTAGLDTARSTFTFTSVPFRNGSGILNGGDFRTTASMSMIYN 167
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Fimbrial-2w07B01 B:9-148                                                                                                                     Pfam domains
         Sec.struct. author .......ee.hhh....................eeeeeeee...--..................eee.....eeeeeee..........-----------------.eeeeeeeeeee...................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w07 B   9 NVYIPPCTINNGQNIVVDFGNINPEHVDNSRGEVTKTISISCPY--GSLWIKVTGNTMGGGQNNVLATNITHFGIALYQGKGMSTPLTL-----------------RSTFTFTSVPFRNGSGILNGGDFRTTASMSMIYN 148
                                    18        28        38        48   |  | 58        68        78        88        |-         -      |118       128       138       148
                                                                      52 55                                        97               115                                 


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with Q1R2X3_ECOUT | Q1R2X3 from UniProtKB/TrEMBL  Length:167

    Alignment length:140
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167
         Q1R2X3_ECOUT    28 NVYIPPCTINNGQNIVVDFGNINPEHVDNSRGEVTKTISISCPYKSGSLWIKVTGNTMGGGQNNVLATNITHFGIALYQGKGMSTPLTLGNGSGNGYRVTAGLDTARSTFTFTSVPFRNGSGILNGGDFRTTASMSMIYN 167
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Fimbrial-2w07B01 B:9-148                                                                                                                     Pfam domains
         Sec.struct. author .......ee.hhh....................eeeeeeee...--..................eee.....eeeeeee..........-----------------.eeeeeeeeeee...................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w07 B   9 NVYIPPCTINNGQNIVVDFGNINPEHVDNSRGEVTKTISISCPY--GSLWIKVTGNTMGGGQNNVLATNITHFGIALYQGKGMSTPLTL-----------------RSTFTFTSVPFRNGSGILNGGDFRTTASMSMIYN 148
                                    18        28        38        48   |  | 58        68        78        88        |-         -      |118       128       138       148
                                                                      52 55                                        97               115
   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  (3, 3)

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

(-) Gene Ontology  (9, 17)

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   (Q1R2X3_ECOUT | Q1R2X3)
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.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0009289    pilus    A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

Chain B   (PRSF_ECOLX | P42187)
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.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
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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  2w07
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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 2wmp 2xg4 2xg5 3dpa 3me0 5k93
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        Q1R2W9_ECOUT | Q1R2W9: 2uy6 2uy7 2wmp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2W07)