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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COLICIN I RECEPTOR CIR FROM E.COLI IN COMPLEX WITH RECEPTOR BINDING DOMAIN OF COLICIN IA.
 
Authors :  S. K. Buchanan, L. Esser, P. Lukacik
Date :  20 Jun 06  (Deposition) - 08 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Outer Membrane, Iron Transport, Tonb Box, Signal Transduction, Colicin I Receptor, Receptor Ligand, Membrane Protein, Protein Transport, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. K. Buchanan, P. Lukacik, S. Grizot, R. Ghirlando, M. M. Ali, T. J. Barnard, K. S. Jakes, P. K. Kienker, L. Esser
Structure Of Colicin I Receptor Bound To The R-Domain Of Colicin Ia: Implications For Protein Import.
Embo J. V. 26 2594 2007
PubMed-ID: 17464289  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601693

(-) Compounds

Molecule 1 - COLICIN I RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET20B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: COLICIN I RECEPTOR
    Gene: CIRA
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - COLICIN-IA
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET17B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: R DOMAIN OF COLICIN IA
    Gene: CIA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1LDA2Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:338 , TYR A:362BINDING SITE FOR RESIDUE LDA A 664
2AC2SOFTWAREGLN A:187 , SER A:206 , ASP A:236BINDING SITE FOR RESIDUE LDA A 665

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:435 -A:439

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:82 -Gly A:83
2Asn A:85 -Arg A:86
3Thr A:353 -Ser A:354

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TONB_DEPENDENT_REC_2PS01156 TonB-dependent receptor proteins signature 2.CIRA_ECOLI646-663  1A:649-663

(-) Exons   (0, 0)

(no "Exon" information available for 2HDI)

(-) 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:598
 aligned with CIRA_ECOLI | P17315 from UniProtKB/Swiss-Prot  Length:663

    Alignment length:633
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660   
           CIRA_ECOLI    31 ETMVVTASSVEQNLKDAPASISVITQEDLQRKPVQNLKDVLKEVPGVQLTNEGDNRKGVSIRGLDSSYTLILVDGKRVNSRNAVFRHNDFDLNWIPVDSIERIEVVRGPMSSLYGSDALGGVVNIITKKIGQKWSGTVTVDTTIQEHRDRGDTYNGQFFTSGPLIDGVLGMKAYGSLAKREKDDPQNSTTTDTGETPRIEGFSSRDGNVEFAWTPNQNHDFTAGYGFDRQDRDSDSLDKNRLERQNYSVSHNGRWDYGTSELKYYGEKVENKNPGNSSPITSESNTVDGKYTLPLTAINQFLTVGGEWRHDKLSDAVNLTGGTSSKTSASQYALFVEDEWRIFEPLALTTGVRMDDHETYGEHWSPRAYLVYNATDTVTVKGGWATAFKAPSLLQLSPDWTSNSCRGACKIVGSPDLKPETSESWELGLYYMGEEGWLEGVESSVTVFRNDVKDRISISRTSDVNAAPGYQNFVGFETGANGRRIPVFSYYNVNKARIQGVETELKIPFNDEWKLSINYTYNDGRDVSNGENKPLSDLPFHTANGTLDWKPLALEDWSFYVSGHYTGQKRADSATAKTPGGYTIWNTGAAWQVTKDVKLRAGVLNLGDKDLSRDDYSYNEDGRRYFMAVDYRF 663
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2hdiA01 A:31-157 Ferric Hydroxamate Uptake Protein; Chain A, domain 1                                                          -----2hdiA02 A:163-663  [code=2.40.170.20, no name define               d]                                                                                                                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.......ee.hhh..eeeeehhhhhhh.....hhhhhh....eeeee.....eeeee...hhh.eeeee..ee...........hhhhh..hhh.eeeeeeee..hhhhhh.....eeeeeee.......eeeeeeeeeee.......eeeeeeeeeeeee...eeeeeeeeeeee....---------------.eeeeeeeeeeeee.....eeeeeeeeeeeeeee.-----.eeeeeeeeeeeeee....eeeeeeeeeeeeee.......eeeeeeeeeeeeeeeehhh.eeeeeeeeeeeeeeehhhhh.......eeeeeeeeeeeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeee....eeeeeeeeeeee..hhhhhh...eeeehhhheeee.......eeeeeeeeeeeee..hhhhh..eeeeeeeeeeeeeeee..ee....hhhhh..eeeeee.....eeeeee.eeeeeeeeeeeeeeeeee....eeeeeeeeeeeeee......eeeeeeeeeeeeeeeee.......eeeeeeeeee...----------..eeeeeeeeeeeee..eeeeeeee.........-----.....eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TONB_DEPENDENT_REC PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hdi A  31 ETMVVTASSVEQNLKDAPASISVITQEDLQRKPVQNLKDVLKEVPGVQLTNEGDNRKGVSIRGLDSSYTLILVDGKRVNSRNAVFRHNDFDLNWIPVDSIERIEVVRGPMSSLYGSDALGGVVNIITKKIGQKWSGTVTVDTTIQEHRDRGDTYNGQFFTSGPLIDGVLGMKAYGSLAKREKDD---------------EGFSSRDGNVEFAWTPNQNHDFTAGYGFDRQDRDS-----NRLERQNYSVSHNGRWDYGTSELKYYGEKVENKNPGNSSPITSESNTVDGKYTLPLTAINQFLTVGGEMRHDKMSDAVNLTGGTSSKTSASQYALFVEDEWRIFEPLALTTGVRMDDHETYGEHWSPRAYLVYNATDTVTVKGGWATAFKAPSLLQLSPDWTSNSCRGACKIVGSPDLKPETSESWELGLYYMGEEGWLEGVESSVTVFRNDVKDRISISRTSDVNAAPGYQNFVGFETGANGRRIPVFSYYNVNKARIQGVETELKIPFNDEWKLSINYTYNDGRDVSNGENKPLSDLPFHTANGTLDWKPLALEDWSMYMSGHYTGQK----------GGYTIWNTGAAWQVTKDVKLRAGVLNLGDKDLSR-----NEDGRRYFMAVDYRF 663
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   |     -       230       240       250       260   |   270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590        |-       610       620       630       640  |    650       660   
                                                                                                                                                                                                                 214             230                               264   270                                                                                                                                                                                                                                                                                                                                      599        610                              643   649              


Chain B from PDB  Type:PROTEIN  Length:103
 aligned with CEIA_ECOLX | P06716 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:103
                                   291       301       311       321       331       341       351       361       371       381   
           CEIA_ECOLX   282 KNTPDGKTIVSPEKFPGRSSTNHSIVVSGDPRFAGTIKITTSAVIDNRANLNYLLSHSGLDYKRNILNDRNPVVTEDVEGDKKIYNAEVAEWDKLRQRLLDAR 384
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2hdiB00 B:282-384 Colicin Ia; domain 2                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.....eeeeeeeeeee.......eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2hdi B 282 KNTPDGKTIVSPEKFPGRSSTNHSIVVSGDPRFAGTIKITTSAVIDNRANLNYLLSHSGLDYKRNILNDRNPVVTEDVEGDKKIYNAEVAEWDKLRQRLLDAR 384
                                   291       301       311       321       331       341       351       361       371       381
   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 2HDI)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HDI)

(-) Gene Ontology  (16, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CIRA_ECOLI | P17315)
molecular function
    GO:0042912    colicin transmembrane transporter activity    Enables the transfer of a colicin from one side of a membrane to the other. Colicins are a group of antibiotics produced by E. coli and related species that are encoded by a group of naturally occurring plasmids, e.g. Col E1.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0015343    siderophore transmembrane transporter activity    Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: siderophore-iron(out) + H+(out) = siderophore-iron(in) + H+(in).
biological process
    GO:0043213    bacteriocin transport    The directed movement of a bacteriocin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Bacteriocins are a group of antibiotics produced by bacteria and are encoded by a group of naturally occurring plasmids, e.g. Col E1. Bacteriocins are toxic to bacteria closely related to the bacteriocin producing strain.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0033212    iron assimilation    A process in which iron is solubilized and transported into a cell.
    GO:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
    GO:0044718    siderophore transmembrane transport    The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, from one side of a membrane to the other, by means of some agent such as a transporter or pore.
    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.

Chain B   (CEIA_ECOLX | P06716)
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
cellular component
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CEIA_ECOLX | P06716: 1cii
        CIRA_ECOLI | P17315: 2hdf

(-) Related Entries Specified in the PDB File

2hdf THE SAME PROTEIN WITHOUT THE R-DOMAIN OF COLICIN IA BOUND