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(-) Description

Title :  THE X-RAY STRUCTURE OF THE ESCHERICHIA COLI COLICIN M IMMUNITY PROTEIN DEMONSTRATES THE PRESENCE OF A DISULPHIDE BRIDGE, WHICH IS FUNCTIONALLY ESSENTIAL
 
Authors :  F. Gerard, M. A. Brooks, H. Barreteau, T. Touze, M. Graille, A. Bouhss, D H. V. Tilbeurgh, D. Mengin-Lecreulx
Date :  07 Jun 10  (Deposition) - 17 Nov 10  (Release) - 22 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Antibiotic, Bacterial Cell Wall, Bacteriocin Immunity, Bacterial Immunity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Gerard, M. A. Brooks, H. Barreteau, T. Touze, M. Graille, A. Bouhss, D. Blanot, H. V. Tilbeurgh, D. Mengin-Lecreulx
X-Ray Structure And Site-Directed Mutagenesis Analysis Of The Escherichia Coli Colicin M Immunity Protein.
J. Bacteriol. V. 193 205 2011
PubMed-ID: 21037007  |  Reference-DOI: 10.1128/JB.01119-10

(-) Compounds

Molecule 1 - COLICIN-M IMMUNITY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET2160
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Variant: PLYSS RARE
    Fragment: PERIPLASMIC DOMAIN, RESIDUES 48-141
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: PLASMID PCOLBM-C1139
    Synonym: MICROCIN-M IMMUNITY PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 32)

Asymmetric Unit (3, 32)
No.NameCountTypeFull Name
1CD7Ligand/IonCADMIUM ION
2CL11Ligand/IonCHLORIDE ION
3NA14Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NA-1Ligand/IonSODIUM ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:106 , GLU A:109 , TYR A:111 , ASP B:82 , LYS B:84 , CL B:1118BINDING SITE FOR RESIDUE CD A1116
02AC2SOFTWAREASP A:55 , ASP A:79 , GLU B:113BINDING SITE FOR RESIDUE CD A1117
03AC3SOFTWAREGLU A:113 , ASP B:55 , ASP B:79BINDING SITE FOR RESIDUE CD A1118
04AC4SOFTWAREGLU A:71 , MET A:100 , CL A:1128 , ASP B:96BINDING SITE FOR RESIDUE CD A1119
05AC5SOFTWAREGLU A:93 , GLU B:93BINDING SITE FOR RESIDUE CD A1120
06AC6SOFTWARETRP A:70BINDING SITE FOR RESIDUE CL A1121
07AC7SOFTWAREALA A:30 , CYS A:31 , GLU A:83 , LYS A:84 , GLU A:108 , CL A:1129BINDING SITE FOR RESIDUE NA A1122
08AC8SOFTWARETYR A:105 , CYS A:107 , ASN B:45BINDING SITE FOR RESIDUE NA A1123
09AC9SOFTWAREGLU A:109 , TYR A:111 , ASP B:82BINDING SITE FOR RESIDUE NA A1124
10BC1SOFTWAREILE A:73 , GLU A:74 , LEU A:87BINDING SITE FOR RESIDUE CL A1125
11BC2SOFTWAREASP A:82 , LYS A:84 , LYS B:84 , CD B:1116 , NA B:1126BINDING SITE FOR RESIDUE CL A1126
12BC3SOFTWAREMET A:100 , TYR A:102 , CD A:1119 , ASP B:96BINDING SITE FOR RESIDUE CL A1128
13BC4SOFTWAREGLU A:81 , LYS A:84 , GLU A:108 , NA A:1122BINDING SITE FOR RESIDUE CL A1129
14BC5SOFTWAREARG A:40 , TRP A:70 , GLU A:71 , ILE A:73 , VAL A:88 , PRO A:89BINDING SITE FOR RESIDUE CL A1130
15BC6SOFTWAREGLU A:74 , GLU A:83 , THR A:85 , LEU A:86 , LEU A:87BINDING SITE FOR RESIDUE NA A1131
16BC7SOFTWAREASP A:82 , LYS A:84 , CL A:1126 , HIS B:106 , GLU B:109 , TYR B:111BINDING SITE FOR RESIDUE CD B1116
17BC8SOFTWAREASP A:96 , GLU B:71 , MET B:100 , CL B:1122BINDING SITE FOR RESIDUE CD B1117
18BC9SOFTWARELYS A:84 , HIS A:106 , GLU A:109 , CD A:1116 , ASP B:82 , LYS B:84BINDING SITE FOR RESIDUE CL B1118
19CC1SOFTWARETYR B:114BINDING SITE FOR RESIDUE CL B1119
20CC2SOFTWARELYS B:52 , ASP B:55 , ASP B:79BINDING SITE FOR RESIDUE NA B1120
21CC3SOFTWAREGLU B:93BINDING SITE FOR RESIDUE CL B1121
22CC4SOFTWAREASP A:96 , TYR B:102 , CD B:1117BINDING SITE FOR RESIDUE CL B1122
23CC5SOFTWAREGLU B:83BINDING SITE FOR RESIDUE CL B1123
24CC6SOFTWAREGLU B:108BINDING SITE FOR RESIDUE NA B1125
25CC7SOFTWARECL A:1126 , LYS B:84BINDING SITE FOR RESIDUE NA B1126
26CC8SOFTWAREASP B:57BINDING SITE FOR RESIDUE NA B1127
27CC9SOFTWAREGLN A:33 , TYR B:105 , CYS B:107 , GLY B:110BINDING SITE FOR RESIDUE NA B1128

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:31 -A:107
2B:31 -B:107

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XGL)

(-) 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:91
 aligned with IMMM_ECOLX | P18002 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:91
                                    58        68        78        88        98       108       118       128       138 
           IMMM_ECOLX    49 EDKGPACYQVSDEQARTFVKNDYLQRMKRWDNDVQLLGTEIPKITWEKIERSLTDVEDEKTLLVPFKAEGPDGKRMYYGMYHCEEGYVEYA 139
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....eeee........hhhhh..eeeeeeee....eeeeeeeee....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 2xgl A  25 EDKGPACYQVSDEQARTFVKNDYLQRMKRWDNDVQLLGTEIPKITWEKIERSLTDVEDEKTLLVPFKAEGPDGKRMYYGMYHCEEGYVEYA 115
                                    34        44        54        64        74        84        94       104       114 


Chain B from PDB  Type:PROTEIN  Length:89
 aligned with IMMM_ECOLX | P18002 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:89
                                    60        70        80        90       100       110       120       130         
           IMMM_ECOLX    51 KGPACYQVSDEQARTFVKNDYLQRMKRWDNDVQLLGTEIPKITWEKIERSLTDVEDEKTLLVPFKAEGPDGKRMYYGMYHCEEGYVEYA 139
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) YebF-2xglB01 B:27-115                                                                     Pfam domains (1)
           Pfam domains (2) YebF-2xglB02 B:27-115                                                                     Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....eeee........hhhhh..eeeeeeee....eeeeeeee.hhhh.eeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 2xgl B  27 KGPACYQVSDEQARTFVKNDYLQRMKRWDNDVQLLGTEIPKITWEKIERSLTDVEDEKTLLVPFKAEGPDGKRMYYGMYHCEEGYVEYA 115
                                    36        46        56        66        76        86        96       106
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2XGL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: YebF] (1)
(-)
Family: YebF (1)
(-)
Escherichia coli (1)
1aYebF-2xglB01B:27-115
1bYebF-2xglB02B:27-115

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IMMM_ECOLX | P18002)
biological process
    GO:0030153    bacteriocin immunity    A process that mediates resistance to a bacteriocin: any of a heterogeneous group of polypeptide antibiotics that are secreted by certain bacterial strains and are able to kill cells of other susceptible (frequently related) strains after adsorption at specific receptors on the cell surface. They include the colicins, and their mechanisms of action vary.

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        IMMM_ECOLX | P18002: 4aeq

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