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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CAF1A USHER PROTEIN N-TERMINAL DOMAIN FROM YERSINIA PESTIS
 
Authors :  A. Dubnovitsky, X. D. Yu, A. F. Pudney, S. Macintyre, S. D. Knight, A. V. Z
Date :  02 Jul 12  (Deposition) - 26 Sep 12  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Transport Protein, Chaperone-Usher Pathway, Pili Assembly (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Di Yu, A. Dubnovitsky, A. F. Pudney, S. Macintyre, S. D. Knight, A. V. Zavialov
Allosteric Mechanism Controls Traffic In The Chaperone/Usher Pathway.
Structure V. 20 1861 2012
PubMed-ID: 22981947  |  Reference-DOI: 10.1016/J.STR.2012.08.016

(-) Compounds

Molecule 1 - F1 CAPSULE-ANCHORING PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCAF1AN
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN, RESIDUES 23-158
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Synonym: CAF1A USHER PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4B0E)

(-) Sites  (0, 0)

(no "Site" information available for 4B0E)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:64 -A:91
2B:64 -B:91
3C:64 -C:91
4D:64 -D:91

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B0E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B0E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B0E)

(-) Exons   (0, 0)

(no "Exon" information available for 4B0E)

(-) 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:96
 aligned with CAF1A_YERPE | P26949 from UniProtKB/Swiss-Prot  Length:833

    Alignment length:96
                                    59        69        79        89        99       109       119       129       139      
          CAF1A_YERPE    50 LPGNYFVNVFVNGRKVDSGNIDFRLEKHNGKELLWPCLSSLQLTKYGIDIDKYPDLIKSGTEQCVDLLAIPHSDVQFYFNQQKLSLIVPPQALLPR 145
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeee..eeeeeeeeeeeeeee..eeeeee..hhhhhhhh..hhhhhhhhhhh......hhhhh...eeeeehhh.eeeee.hhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4b0e A  28 LPGNYFVNVFVNGRKVDSGNIDFRLEKHNGKELLWPCLSSLQLTKYGIDIDKYPDLIKSGTEQCVDLLAIPHSDVQFYFNQQKLSLIVPPQALLPR 123
                                    37        47        57        67        77        87        97       107       117      


Chain B from PDB  Type:PROTEIN  Length:98
 aligned with CAF1A_YERPE | P26949 from UniProtKB/Swiss-Prot  Length:833

    Alignment length:98
                                    58        68        78        88        98       108       118       128       138        
          CAF1A_YERPE    49 QLPGNYFVNVFVNGRKVDSGNIDFRLEKHNGKELLWPCLSSLQLTKYGIDIDKYPDLIKSGTEQCVDLLAIPHSDVQFYFNQQKLSLIVPPQALLPRF 146
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee..eeeeeeeeeeeeeee..eeeeeee.hhhhhhhh..hhhhhhhhhhh......hhhhh...eeeee....eeeee.hhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4b0e B  27 QLPGNYFVNVFVNGRKVDSGNIDFRLEKHNGKELLWPCLSSLQLTKYGIDIDKYPDLIKSGTEQCVDLLAIPHSDVQFYFNQQKLSLIVPPQALLPRF 124
                                    36        46        56        66        76        86        96       106       116        


Chain C from PDB  Type:PROTEIN  Length:91
 aligned with CAF1A_YERPE | P26949 from UniProtKB/Swiss-Prot  Length:833

    Alignment length:95
                                    59        69        79        89        99       109       119       129       139     
          CAF1A_YERPE    50 LPGNYFVNVFVNGRKVDSGNIDFRLEKHNGKELLWPCLSSLQLTKYGIDIDKYPDLIKSGTEQCVDLLAIPHSDVQFYFNQQKLSLIVPPQALLP 144
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..eeeeeeeeeeeeeee..eeeeeee.hhhhhhhh..hhhhhhhhh----....hhhhh...eeeee....eeeee.hhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 4b0e C  28 LPGNYFVNVFVNGRKVDSGNIDFRLEKHNGKELLWPCLSSLQLTKYGIDIDKYPDLI----EQCVDLLAIPHSDVQFYFNQQKLSLIVPPQALLP 122
                                    37        47        57        67        77      |  - |      97       107       117     
                                                                                   84   89                                 


Chain D from PDB  Type:PROTEIN  Length:100
 aligned with CAF1A_YERPE | P26949 from UniProtKB/Swiss-Prot  Length:833

    Alignment length:105
                                    49        59        69        79        89        99       109       119       129       139     
          CAF1A_YERPE    40 DVSLFNQGLQLPGNYFVNVFVNGRKVDSGNIDFRLEKHNGKELLWPCLSSLQLTKYGIDIDKYPDLIKSGTEQCVDLLAIPHSDVQFYFNQQKLSLIVPPQALLP 144
               SCOP domains d4b0ed_ D: automated matches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.....eeeeeeeee..eeeeeeeeeeeeeee..eeeeee..hhhhhhhh..hhhhhhhhh-----...hhhhh...eeeeehhh.eeeee.hhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 4b0e D  18 DVSLFNQGLQLPGNYFVNVFVNGRKVDSGNIDFRLEKHNGKELLWPCLSSLQLTKYGIDIDKYPDLI-----QCVDLLAIPHSDVQFYFNQQKLSLIVPPQALLP 122
                                    27        37        47        57        67        77      |  -  |     97       107       117     
                                                                                             84    90
   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  (1, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B0E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B0E)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CAF1A_YERPE | P26949)
molecular function
    GO:0015473    fimbrial usher porin activity    A porin that acts in the assembly of fimbria together with fimbrial chaperone.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0009297    pilus assembly    The assembly of a pilus, a short filamentous structure on a bacterial cell, flagella-like in structure and generally present in many copies. Pili are variously involved in transfer of nucleic acids, adherence to surfaces, and formation of pellicles. Is required for bacterial conjugation, or can play a role in adherence to surfaces (when it is called a fimbrium), and in the formation of pellicles.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CAF1A_YERPE | P26949: 2xet 3fcg 4b0m

(-) Related Entries Specified in the PDB File

2xet CONSERVED HYDROPHOBIC CLUSTERS ON THE SURFACE OF THE CAF1A USHER C-TERMINAL DOMAIN ARE IMPORTANT FOR F1 ANTIGEN ASSEMBLY
4ay0 HIGH RESOLUTION CRYSTAL STRUCTURE OF THE MONOMERIC SUBUNIT-FREE CAF1M CHAPERONE
4ayf CRYSTAL STRUCTURE OF THE COMPLEX OF THE CAF1M:CAF1 CHAPERONE:SUBUNIT PREASSEMBLY COMPLEX CARRYING THE TYR40ALA MUTATION IN THE CAF1M CHAPERONE
4az8 CRYSTAL STRUCTURE OF THE COMPLEX OF THE CAF1M:CAF1 CHAPERONE:SUBUNIT PREASSEMBLY COMPLEX CARRYING THE KDKDTN INSERTION AT THE F1G1 LOOP REGION
4b0m COMPLEX OF THE CAF1AN USHER DOMAIN, CAF1M CHAPERONE AND CAF1 SUBUNIT FROM YERSINIA PESTIS