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(-) Description

Title :  CRYSTAL STRUCTURE OF DCTP7, 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 :  1.95
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 :  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, B, C, D
    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: BP1891
    Organism Scientific: BORDETELLA PERTUSSIS TOHAMA I
    Organism Taxid: 257313
    Strain: TOHAMA I

 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  (2, 28)

Asymmetric Unit (2, 28)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
2PCA4Ligand/IonPYROGLUTAMIC ACID
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PCA1Ligand/IonPYROGLUTAMIC ACID
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PCA1Ligand/IonPYROGLUTAMIC ACID
Biological Unit 3 (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PCA1Ligand/IonPYROGLUTAMIC ACID
Biological Unit 4 (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PCA1Ligand/IonPYROGLUTAMIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:48 , TRP A:120 , GLN A:123 , ARG A:143 , TYR A:145 , THR A:165 , THR A:182 , SER A:183 , THR A:186BINDING SITE FOR RESIDUE PCA A 302
2AC2SOFTWAREARG B:48 , TRP B:120 , GLN B:123 , ARG B:143 , TYR B:145 , THR B:165 , THR B:182 , SER B:183 , THR B:186BINDING SITE FOR RESIDUE PCA B 302
3AC3SOFTWAREARG C:48 , TRP C:120 , GLN C:123 , ARG C:143 , TYR C:145 , THR C:165 , THR C:182 , SER C:183 , THR C:186BINDING SITE FOR RESIDUE PCA C 302
4AC4SOFTWAREARG D:48 , TRP D:120 , GLN D:123 , ARG D:143 , TYR D:145 , THR D:165 , THR D:182 , SER D:183 , THR D:186BINDING SITE FOR RESIDUE PCA D 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr C:299 -Arg C:300

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PFY)

(-) 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:301
 aligned with Q7VXB1_BORPE | Q7VXB1 from UniProtKB/TrEMBL  Length:321

    Alignment length:301
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320 
         Q7VXB1_BORPE    21 ATSWTMTAEQPDANYLTQNARQFADEVKAATAGALEIKVQSNSTLLKRPEVKRGVQQGVVQIGEVLVSALGNEDPLFEIDSVPFLASSFNESEKLWKATRPLLAQRLDKQGIVLVYGSPWPPQGIYTKKPVAALADLKGTRFRAYSASTSHMAALMGAVPTTVQTPEVPQAFSTGVIDAMLTSPATGVDSQAWDYVKYYYDAQAFIPQSFVIANKRAFQRLPAEVRQAVLDAGAKAEIRGWQTARAKTRELTDTLARNGMSVEPLPPQLAKELQAIGATMVSDWSKKAGADGQQLLDAYRK 321
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhh....eeeee.hhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeee.....hhhhhh..eeee.hhhhhhhhhhh..eeee.hhhhhhhhhhh.....eeehhhhhhhhhhhhh..eeee......eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pfy A   1 ATSWTmTAEQPDANYLTQNARQFADEVKAATAGALEIKVQSNSTLLKRPEVKRGVQQGVVQIGEVLVSALGNEDPLFEIDSVPFLASSFNESEKLWKATRPLLAQRLDKQGIVLVYGSPWPPQGIYTKKPVAALADLKGTRFRAYSASTSHmAALmGAVPTTVQTPEVPQAFSTGVIDAmLTSPATGVDSQAWDYVKYYYDAQAFIPQSFVIANKRAFQRLPAEVRQAVLDAGAKAEIRGWQTARAKTRELTDTLARNGmSVEPLPPQLAKELQAIGATmVSDWSKKAGADGQQLLDAYRK 301
                                 |  10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 |   | 160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
                                 6-MSE                                                                                                                                           152-MSE                     180-MSE                                                                         260-MSE             280-MSE                 
                                                                                                                                                                                     156-MSE                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:301
 aligned with Q7VXB1_BORPE | Q7VXB1 from UniProtKB/TrEMBL  Length:321

    Alignment length:301
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320 
         Q7VXB1_BORPE    21 ATSWTMTAEQPDANYLTQNARQFADEVKAATAGALEIKVQSNSTLLKRPEVKRGVQQGVVQIGEVLVSALGNEDPLFEIDSVPFLASSFNESEKLWKATRPLLAQRLDKQGIVLVYGSPWPPQGIYTKKPVAALADLKGTRFRAYSASTSHMAALMGAVPTTVQTPEVPQAFSTGVIDAMLTSPATGVDSQAWDYVKYYYDAQAFIPQSFVIANKRAFQRLPAEVRQAVLDAGAKAEIRGWQTARAKTRELTDTLARNGMSVEPLPPQLAKELQAIGATMVSDWSKKAGADGQQLLDAYRK 321
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhh...eeeee.hhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee....eeee.....hhhhhh..eeee.hhhhhhhhhhh..eeee.hhhhhhhhhhh....eeeehhhhhhhhhhhhh..eee.......eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pfy B   1 ATSWTmTAEQPDANYLTQNARQFADEVKAATAGALEIKVQSNSTLLKRPEVKRGVQQGVVQIGEVLVSALGNEDPLFEIDSVPFLASSFNESEKLWKATRPLLAQRLDKQGIVLVYGSPWPPQGIYTKKPVAALADLKGTRFRAYSASTSHmAALmGAVPTTVQTPEVPQAFSTGVIDAmLTSPATGVDSQAWDYVKYYYDAQAFIPQSFVIANKRAFQRLPAEVRQAVLDAGAKAEIRGWQTARAKTRELTDTLARNGmSVEPLPPQLAKELQAIGATmVSDWSKKAGADGQQLLDAYRK 301
                                 |  10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 |   | 160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
                                 6-MSE                                                                                                                                           152-MSE                     180-MSE                                                                         260-MSE             280-MSE                 
                                                                                                                                                                                     156-MSE                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:301
 aligned with Q7VXB1_BORPE | Q7VXB1 from UniProtKB/TrEMBL  Length:321

    Alignment length:301
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320 
         Q7VXB1_BORPE    21 ATSWTMTAEQPDANYLTQNARQFADEVKAATAGALEIKVQSNSTLLKRPEVKRGVQQGVVQIGEVLVSALGNEDPLFEIDSVPFLASSFNESEKLWKATRPLLAQRLDKQGIVLVYGSPWPPQGIYTKKPVAALADLKGTRFRAYSASTSHMAALMGAVPTTVQTPEVPQAFSTGVIDAMLTSPATGVDSQAWDYVKYYYDAQAFIPQSFVIANKRAFQRLPAEVRQAVLDAGAKAEIRGWQTARAKTRELTDTLARNGMSVEPLPPQLAKELQAIGATMVSDWSKKAGADGQQLLDAYRK 321
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhh...eeeee.hhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeee.....hhhhhh..eeee.hhhhhhhhhhh..eeee.hhhhhhhhhhh....eeeehhhhhhhhhhhhh..eee.......eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pfy C   1 ATSWTmTAEQPDANYLTQNARQFADEVKAATAGALEIKVQSNSTLLKRPEVKRGVQQGVVQIGEVLVSALGNEDPLFEIDSVPFLASSFNESEKLWKATRPLLAQRLDKQGIVLVYGSPWPPQGIYTKKPVAALADLKGTRFRAYSASTSHmAALmGAVPTTVQTPEVPQAFSTGVIDAmLTSPATGVDSQAWDYVKYYYDAQAFIPQSFVIANKRAFQRLPAEVRQAVLDAGAKAEIRGWQTARAKTRELTDTLARNGmSVEPLPPQLAKELQAIGATmVSDWSKKAGADGQQLLDAYRK 301
                                 |  10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 |   | 160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
                                 6-MSE                                                                                                                                           152-MSE                     180-MSE                                                                         260-MSE             280-MSE                 
                                                                                                                                                                                     156-MSE                                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:301
 aligned with Q7VXB1_BORPE | Q7VXB1 from UniProtKB/TrEMBL  Length:321

    Alignment length:301
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320 
         Q7VXB1_BORPE    21 ATSWTMTAEQPDANYLTQNARQFADEVKAATAGALEIKVQSNSTLLKRPEVKRGVQQGVVQIGEVLVSALGNEDPLFEIDSVPFLASSFNESEKLWKATRPLLAQRLDKQGIVLVYGSPWPPQGIYTKKPVAALADLKGTRFRAYSASTSHMAALMGAVPTTVQTPEVPQAFSTGVIDAMLTSPATGVDSQAWDYVKYYYDAQAFIPQSFVIANKRAFQRLPAEVRQAVLDAGAKAEIRGWQTARAKTRELTDTLARNGMSVEPLPPQLAKELQAIGATMVSDWSKKAGADGQQLLDAYRK 321
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----SBP_bac_7-2pfyD01 D:6-287                                                                                                                                                                                                                                                                 -------------- Pfam domains (1)
           Pfam domains (2) -----SBP_bac_7-2pfyD02 D:6-287                                                                                                                                                                                                                                                                 -------------- Pfam domains (2)
           Pfam domains (3) -----SBP_bac_7-2pfyD03 D:6-287                                                                                                                                                                                                                                                                 -------------- Pfam domains (3)
           Pfam domains (4) -----SBP_bac_7-2pfyD04 D:6-287                                                                                                                                                                                                                                                                 -------------- Pfam domains (4)
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhh....eeeee.hhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee....eeee.....hhhhhh..eeee.hhhhhhhhhhh..eeee.hhhhhhhhhhh.....eeehhhhhhhhhhhhh..eeee......eeeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pfy D   1 ATSWTmTAEQPDANYLTQNARQFADEVKAATAGALEIKVQSNSTLLKRPEVKRGVQQGVVQIGEVLVSALGNEDPLFEIDSVPFLASSFNESEKLWKATRPLLAQRLDKQGIVLVYGSPWPPQGIYTKKPVAALADLKGTRFRAYSASTSHmAALmGAVPTTVQTPEVPQAFSTGVIDAmLTSPATGVDSQAWDYVKYYYDAQAFIPQSFVIANKRAFQRLPAEVRQAVLDAGAKAEIRGWQTARAKTRELTDTLARNGmSVEPLPPQLAKELQAIGATmVSDWSKKAGADGQQLLDAYRK 301
                                 |  10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 |   | 160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
                                 6-MSE                                                                                                                                           152-MSE                     180-MSE                                                                         260-MSE             280-MSE                 
                                                                                                                                                                                     156-MSE
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  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 2PFY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q7VXB1_BORPE | Q7VXB1)
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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2pfz