2UY6 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE P PILUS ROD SUBUNIT PAPA

Authors :   D. Verger, E. Bullitt, S. J. Hultgren, G. Waksman

Date :   02 Apr 07 (Deposition) - 29 May 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Donor Strand Complementation, Pili/N-Terminal Extension, Pilus Biogenesis, Donor-Strand Exchange, Nte, Dsc, Dse, Papa, Papd, Fimbria, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Verger, E. Bullitt, S. J. Hultgren, G. Waksman
Crystal Structure Of The P Pilus Rod Subunit Papa.
Plos Pathog. V. 3 E73 2007
PubMed-ID: 17511517 | Reference-DOI: 10.1371/JOURNAL.PPAT.0030073

Molecule 1 - PERIPLASMID CHAPERONE PAPD PROTEIN
	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	:	364106
	Other Details	:	HIS-TAGGED C TERMINUS
	Strain	:	UTI89

Molecule 2 - PAP FIMBRIAL MAJOR PILIN PROTEIN
	Chains	:	B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRC99A
	Expression System Strain	:	C600
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	J96
	Synonym	:	PAP PILI

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2UY6)

(no "Site" information available for 2UY6)

Asymmetric/Biological Unit

No.	Residues
1	A:207	-	A:212
2	B:22	-	B:61
3	C:22	-	C:61

Asymmetric/Biological Unit

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

(no "SAP(SNP)/Variant" information available for 2UY6)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PILI_CHAPERONE	PS00635	Gram-negative pili assembly chaperone signature.	PAPD_ECOLX	99-116	1	A:78-95

(no "Exon" information available for 2UY6)

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 d2uy6a1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d2uy6a2 A:125-217 PapD                                                                        SCOP domains
               CATH domains 2uy6A01 A:1-121 PapD-like                                                                                                2uy6A02 A:122-213  [code=2.60.40.1070, no name defined]                                     ---- CATH domains
               Pfam domains Pili_assembly_N-2uy6A01 A:1-121                                                                                          -------------------Pili_assembly_C-2uy6A02 A:141-204                               ------------- Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee...........eeee..........eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh......hhhhheeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeee........eeeeee...eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------PILI_CHAPERONE    -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uy6 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 Q1R2W9_ECOUT | Q1R2W9 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       
         Q1R2W9_ECOUT    22 AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKE 238
               SCOP domains d2uy6a1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d2uy6a2 A:125-217 PapD                                                                        SCOP domains
               CATH domains 2uy6A01 A:1-121 PapD-like                                                                                                2uy6A02 A:122-213  [code=2.60.40.1070, no name defined]                                     ---- CATH domains
               Pfam domains Pili_assembly_N-2uy6A01 A:1-121                                                                                          -------------------Pili_assembly_C-2uy6A02 A:141-204                               ------------- Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeee...........eeee..........eeeeeeee.hhhhhh.....eeeeeeeeee........eeeeeeeeeeeeeeehhhhh......hhhhheeeee..eeeeee.....eeeeeee.hhhhhhhh....eee...eeeeee.......eeee........eeeeee...eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uy6 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 PAPA_ECOLX | P04127 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:154
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181    
           PAPA_ECOLX    32 KVTFNGTVVDAPCSISQKSADQSIDFGQLSKSFLEAGGVSKPMDLDIELVNCDITAFKGGNGAKKGTVKLAFTGPIVNGHSDELDTNGGTGTAIVVQGAGKNVVFDGSEGDANTLKDGENVLHYTAVVKKSSAVGAAVTEGAFSAVANFNLTYQ 185
               SCOP domains d2uy6b1 B:10-163 Pap fimbrial major pilin protein PapA                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eee.............hhhhhhhh.....eeeeeeee..........----...eeeeee..ee..eeeeee......eeeeee........eeee...........eeeeeeeeee.............eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uy6 B  10 KVTFNNTVVDAPCSISQKSADQSIDFGQLSKSFLEAGGVSKPMDLDIELVNCDITAFKGG----KGTVKLAFTGPIVNGHSDELDTNGGTGLAIVVQGAGKNVVFDGSEGDANTLKDGENVLHYTAVVKKSSAVGAAVTEGAFSAVANFNLTYQ 163
                                    19        29        39        49        59        69    |   79        89        99       109       119       129       139       149       159    
                                                                                      69   74

Chain C from PDB  Type:PROTEIN  Length:144
 aligned with PAPA_ECOLX | P04127 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:144
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181    
           PAPA_ECOLX    42 APCSISQKSADQSIDFGQLSKSFLEAGGVSKPMDLDIELVNCDITAFKGGNGAKKGTVKLAFTGPIVNGHSDELDTNGGTGTAIVVQGAGKNVVFDGSEGDANTLKDGENVLHYTAVVKKSSAVGAAVTEGAFSAVANFNLTYQ 185
               SCOP domains d2uy6c_ C: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Fimbrial-2uy6C01 C:20-163                                                                                                                        Pfam domains (1)
           Pfam domains (2) Fimbrial-2uy6C02 C:20-163                                                                                                                        Pfam domains (2)
         Sec.struct. author ...eehhhhhheeeeeeeeehhhhhh......eeeeeeeeee..............eeeeeee..ee..eeeeee......eeeeeee..ee..........ee...eeeeeeeeeeeee..........eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2uy6 C  20 APCSISQKSADQSIDFGQLSKSFLEAGGVSKPMDLDIELVNCDITAFKGGNGAKKGTVKLAFTGPIVNGHSDELDTNGGTGLAIVVQGAGKNVVFDGSEGDANTLKDGENVLHYTAVVKKSSAVGAAVTEGAFSAVANFNLTYQ 163
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.1070, no name defined] (29)

Escherichia coli. Organism_taxid: 364106. Strain: uti89. (4)

2uy6A02

A:122-213

Homologous Superfamily: PapD-like (38)

Escherichia coli. Organism_taxid: 364106. Strain: uti89. (4)

2uy6A01

A:1-121

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Adhesin (36)

Family: Fimbrial (23)

Escherichia coli (15)

1a	Fimbrial-2uy6C01	C:20-163
1b	Fimbrial-2uy6C02	C:20-163

Clan: E-set (290)

Family: Pili_assembly_N (20)

Escherichia coli (strain UTI89 / UPEC) (3)

Pili_assembly_N-2uy6A01

A:1-121

Clan: no clan defined [family: Pili_assembly_C] (20)

Family: Pili_assembly_C (20)

Escherichia coli (strain UTI89 / UPEC) (3)

Pili_assembly_C-2uy6A02

A:141-204

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,C (PAPA_ECOLX | P04127)

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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2uy6)

	Sites
(no "Sites" information available for 2uy6)

	Cis Peptide Bonds
		Gly A:48 - Pro A:49	[ RasMol ]
		Thr A:53 - Pro A:54	[ RasMol ]

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	2uy6
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	PAPA_ECOLX \| P04127
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	PAPD_ECOLX \| P15319
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	Q1R2W9_ECOUT \| Q1R2W9
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	PAPA_ECOLX \| P04127
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	PAPD_ECOLX \| P15319
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Q1R2W9_ECOUT \| Q1R2W9
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UniProtKB/Swiss-Prot
	PAPA_ECOLX \| P04127	:	2uy7 5flu
	PAPD_ECOLX \| P15319	:	1n0l 1pdk 1qpp 1qpx 2j2z 2j7l 2uy7 2w07 2wmp 2xg4 2xg5 3dpa 3me0 5k93
UniProtKB/TrEMBL
	Q1R2W9_ECOUT \| Q1R2W9	:	2uy7 2w07 2wmp

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
2j7l	E. COLI P PILUS CHAPERONE PAPD IN COMPLEX WITH A PILUS BIOGENESIS INHIBITOR, PILICIDE 2C
3dpa	PAPD

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (3, 3)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (4, 4)

CATH Domains (2, 2)

Pfam Domains (3, 4)

Gene Ontology (8, 13)

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