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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF THE MONOMERIC SUBUNIT-FREE CAF1M CHAPERONE
 
Authors :  X. D. Yu, A. Dubnovitsky, A. F. Pudney, S. Macintyre, S. D. Knight, A. V. Z
Date :  16 Jun 12  (Deposition) - 26 Sep 12  (Release) - 21 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.52
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chaperone, Amino Acid Motifs, Bacterial Capsules, Bacterial Proteins, Gene Expression Regulation, Molecular Chaperones, Protein Binding, Protein Conformation (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 - CHAPERONE PROTEIN CAF1M
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTCA1/CAF1MD2-11, D113-129
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PTRC99A
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 24-258
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Synonym: CAPSULE PROTEIN FRACTION 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4AY0)

(-) Sites  (0, 0)

(no "Site" information available for 4AY0)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:98 -A:120
2B:98 -B:120

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:64 -Pro A:65
2Thr B:64 -Pro B:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AY0)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PILI_CHAPERONEPS00635 Gram-negative pili assembly chaperone signature.CAF1M_YERPE110-127
 		  2A:87-104
B:87-104

(-) Exons   (0, 0)

(no "Exon" information available for 4AY0)

(-) 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:188
 aligned with CAF1M_YERPE | P26926 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:222
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255  
          CAF1M_YERPE    36 GVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDENKEKESEDPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPPKDEDIWVDDATNKQKFNPDKDVGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLPKGLAGARNVSWRIINDQGGLDRLYSKNVT 257
               SCOP domains d4ay0a1 A:13-130 automated matches                                                                                                     d4ay0a2 A:131-217 automated matches                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee...eeeee.....eeeeee......eeeeeeee...........eeee..eeee....eeeeeeee..........eeeeeeeeee..-------------------------------.eeeeeee......hhhhhhhhheeeee..eeeeee.....eeeeeeee..ee....ee...eeeeee.---.....eeeeee..........eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------PILI_CHAPERONE    ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ay0 A  13 GVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDENKEKESEDPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPP-------------------------------NCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDL---LAGARNVSWRIINDQGGLDRLYSKNVT 217
                                    22        32        42        52        62        72        82        92       102 |       -         -         -   |   125       135       145       155       165       175       185 |   | 195       205       215  
                                                                                                                     104                             119                                                                 187 191                          


Chain B from PDB  Type:PROTEIN  Length:189
 aligned with CAF1M_YERPE | P26926 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:222
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256  
          CAF1M_YERPE    37 VTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDENKEKESEDPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPPKDEDIWVDDATNKQKFNPDKDVGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLPKGLAGARNVSWRIINDQGGLDRLYSKNVTL 258
               SCOP domains d4ay0b1 B:14-130 automated matches                                                                                                    d4ay0b2 B:131-218 automated matches                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee...eeeee.....eeeeeee.....eeeeeeee............eee..eeee....eeeeeee..---......eeeeeeeeee..------------------------------.eeeeeeee......hhhhhhhhheeeee..eeeeee.....eeeeeeee..ee....ee...eeeeee.........eeeeee..........eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------PILI_CHAPERONE    ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ay0 B  14 VTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDENKEKESEDPFVVTPPLFRLDAKQQNSLRIAQA---FPRDKESLKWLCVKGIPP------------------------------NNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLPKGLAGARNVSWRIINDQGGLDRLYSKNVTL 218
                                    23        33        43        53        63        73        83   |    93       103|        -         -         - |     126       136       146       156       166       176       186       196       206       216  
                                                                                                83  87              104                            118
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AY0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AY0)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CAF1M_YERPE | P26926)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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).

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  Cis Peptide Bonds
    Thr A:64 - Pro A:65   [ RasMol ]  
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  4ay0
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  CAF1M_YERPE | P26926
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 Related Entries

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

UniProtKB/Swiss-Prot
        CAF1M_YERPE | P26926: 1p5u 1p5v 1z9s 2os7 3dos 3dpb 3dsn 4ayf 4az8 4b0m

(-) Related Entries Specified in the PDB File

1p5u X-RAY STRUCTURE OF THE TERNARY CAF1M:CAF1: CAF1CHAPERONE:SUBUNIT:SUBUNIT COMPLEX
1p5v X-RAY STRUCTURE OF THE CAF1M:CAF1 CHAPERONE: SUBUNITPREASSEMBLY COMPLEX
1z9s CRYSTAL STRUCTURE OF THE NATIVE CHAPERONE:SUBUNIT: SUBUNITCAF1M:CAF1:CAF1 COMPLEX
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
4b0e CRYSTAL STRUCTURE OF THE CAF1A USHER PROTEIN N- TERMINAL DOMAIN FROM YERSINIA PESTIS
4b0m COMPLEX OF THE CAF1AN USHER DOMAIN, CAF1M CHAPERONE AND CAF1 SUBUNIT FROM YERSINIA PESTIS