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Title :   STRUCTURE OF THE E. COLI CHAPERONE PAPD IN COMPLEX WITH THE PILIN DOMAIN OF THE PAPGII ADHESIN

Authors :   B. A. Ford, J. S. Elam, K. W. Dodson, J. S. Pinkner, S. J. Hultgren

Date :   31 Mar 10 (Deposition) - 27 Apr 11 (Release) - 27 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.03

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

Keywords :   Immunoglobulin Pilin Chaperone, Chaperone, Fimbrium, Immunoglobulin Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. A. Ford, D. Verger, J. S. Elam, K. W. Dodson, J. S. Pinkner, G. Waksman S. J. Hultgren
Structure Of The E. Coli Chaperone Papd In Complex With The Pilin Domain Of The Papgii Adhesin
To Be Published
PubMed: search

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
	Gene	:	PAPD
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - PAPG PROTEIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	PILIN DOMAIN (UNP RESIDUES 215-336)
	Gene	:	C3583, PAPG, PAPGII
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3ME0)

Asymmetric/Biological Unit

No.	Residues
1	A:207	-	A:212
2	B:197	-	B:229

Asymmetric/Biological Unit

No.	Residues
1	Gly A:48	-	Pro A:49
2	Thr A:53	-	Pro A:54
3	Arg A:96	-	Ser A:97

(no "SAP(SNP)/Variant" information available for 3ME0)

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 3ME0)

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 d3me0a1 A:1-124 Pilus chaperone PapD, N-domain                                                                              d3me0a2 A:125-216 PapD                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains Pili_assembly_N-3me0A01 A:1-121                                                                                          -------------------Pili_assembly_C-3me0A02 A:141-204                               ------------ Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee......eeeeeeeee....ee....eeee..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
                 3me0 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      
                                            18-MSE                                          66-MSE                                                                                                   172-MSE

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with Q47450_ECOLX | Q47450 from UniProtKB/TrEMBL  Length:336

    Alignment length:128
                                   218       228       238       248       258       268       278       288       298       308       318       328        
         Q47450_ECOLX   209 FLFKNIGGCRPSAQSLEIKHGDLSINSANNHYAAQTLSVSCDVPANIRFMLLRNTTPTYSHGKKFSVGLGHGWDSIVSVNGVDTGETTMRWYKAGTQNLTIGSRLYGESSKIQPGVLSGSATLLMILP 336
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------PapG_N-3me0B-PapG_C-3me0B02 B:208-316                                                                                      Pfam domains
         Sec.struct. author ........eee.....eee............eeeeeeeeee...eeeeeeeee............eeeee..eeeeeee......eeeeee...eeeeeeeeeeeee..........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3me0 B 189 HHHHHHGGCRPSAQSLEIKHGDLSINSANNHYAAQTLSVSCDVPANIRFMLLRNTTPTYSHGKKFSVGLGHGWDSIVSVNGVDTGETTMRWYKAGTQNLTIGSRLYGESSKIQPGVLSGSATLLMILP 316
                                   198       208       218       228       238       248       258       268       278       288       298       308

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: C2 domain-like (198)

Superfamily: Periplasmic chaperone C-domain (38)

Family: Periplasmic chaperone C-domain (33)

Protein domain: PapD (14)

Escherichia coli [TaxId: 562] (14)

d3me0a2

A:125-216

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: PapD-like (47)

Family: Pilus chaperone (36)

Protein domain: Pilus chaperone PapD, N-domain (14)

Escherichia coli [TaxId: 562] (14)

d3me0a1

A:1-124

(no "CATH Domain" information available for 3ME0)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Adhesin (36)

Family: PapG_N (2)

Escherichia coli (2)

PapG_N-3me0B01

B:195-206

Clan: E-set (290)

Family: Pili_assembly_N (20)

Escherichia coli (8)

Pili_assembly_N-3me0A01

A:1-121

Clan: no clan defined [family: PapG_C] (2)

Family: PapG_C (2)

Escherichia coli (2)

PapG_C-3me0B02

B:208-316

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

Family: Pili_assembly_C (20)

Escherichia coli (8)

Pili_assembly_C-3me0A02

A:141-204

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 (Q47450_ECOLX | Q47450)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Arg A:96 - Ser A:97	[ RasMol ]
		Gly A:48 - Pro A:49	[ RasMol ]
		Thr A:53 - Pro A:54	[ RasMol ]

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UniProtKB/Swiss-Prot
	PAPD_ECOLX \| P15319	:	1n0l 1pdk 1qpp 1qpx 2j2z 2j7l 2uy6 2uy7 2w07 2wmp 2xg4 2xg5 3dpa 5k93
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	Q47450_ECOLX \| Q47450	:	1j8r 1j8s

2wmp	STRUCTURE OF THE E. COLI CHAPERONE PAPD IN COMPLEX WITH THE PILIN DOMAIN OF THE PAPGII ADHESIN, FORM 2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (4, 4)

Gene Ontology (7, 7)

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