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(-) Description

Title :  CRYSTAL STRUCTURE OF DCTP6, A BORDETELLA PERTUSSIS EXTRACYTOPLASMIC SOLUTE RECEPTOR BINDING PYROGLUTAMIC ACID
 
Authors :  P. Rucktooa
Date :  06 Apr 07  (Deposition) - 12 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Extracytoplasmic Solute Receptor, Tripartite Atp Independent Periplasmic Transport, Pyroglutamic Acid, Ligand Binding, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Rucktooa, R. Antoine, J. Herrou, I. Huvent, C. Locht, F. Jacob-Dubuisson, V. Villeret, C. Bompard
Crystal Structures Of Two Bordetella Pertussis Periplasmic Receptors Contribute To Defining A Novel Pyroglutamic Acid Binding Dctp Subfamily.
J. Mol. Biol. V. 370 93 2007
PubMed-ID: 17499270  |  Reference-DOI: 10.1016/J.JMB.2007.04.047
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE EXPORTED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PQE30
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BP1887
    Organism Scientific: BORDETELLA PERTUSSIS TOHAMA I
    Organism Taxid: 257313
    Strain: TOHAMA I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PCA1Ligand/IonPYROGLUTAMIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:120 , GLN A:123 , ARG A:143 , TYR A:145 , GLN A:165 , SER A:182 , SER A:183 , THR A:186 , HOH A:319BINDING SITE FOR RESIDUE PCA A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PFZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PFZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PFZ)

(-) Exons   (0, 0)

(no "Exon" information available for 2PFZ)

(-) 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:301
 aligned with Q7VXB3_BORPE | Q7VXB3 from UniProtKB/TrEMBL  Length:324

    Alignment length:301
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323 
         Q7VXB3_BORPE    24 TKWDLPTAYPASNLHVENLTQFVKDVDSLSGGKLKITLHNNASLYKAPEIKRAVQGNQAQIGEILLTNFANEDPVYELDGLPFLATGYDASFKLYQAQKPFLEKKLASQGMMLLYSVAWPPQGIFANRDIKQVSDMKGLKWRAYSPVTAKIAELVGAQPVTVQQAELAQAMATGVIDSYMSSGSTGFDTKTYEYIKKFYDTEAWLPKNAVLVNKKAFDALDPATQQALKKAGAQAEERGWKLSQEKNSWYKEQLAKNGMAIIAPTAELKSGLTEVGKRMLDDWLKKAGADGQAMIDAYRKQ 324
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----SBP_bac_7-2pfzA01 A:7-287                                                                                                                                                                                                                                                                --------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhh....eeeee.hhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeee.....hhhhhh..eeee.hhhhhhhhhhh..eeee.hhhhhhhhhhh....eeeehhhhhhhhhhhhh..eee.......eeeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pfz A   2 TKWDLPTAYPASNLHVENLTQFVKDVDSLSGGKLKITLHNNASLYKAPEIKRAVQGNQAQIGEILLTNFANEDPVYELDGLPFLATGYDASFKLYQAQKPFLEKKLASQGMMLLYSVAWPPQGIFANRDIKQVSDMKGLKWRAYSPVTAKIAELVGAQPVTVQQAELAQAMATGVIDSYMSSGSTGFDTKTYEYIKKFYDTEAWLPKNAVLVNKKAFDALDPATQQALKKAGAQAEERGWKLSQEKNSWYKEQLAKNGMAIIAPTAELKSGLTEVGKRMLDDWLKKAGADGQAMIDAYRKQ 302
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
   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  (0, 0)

(no "SCOP Domain" information available for 2PFZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PFZ)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q7VXB3_BORPE | Q7VXB3)
biological process
    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: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.

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2pfy