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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI BAMD
 
Authors :  C. Dong, H. Hou, X. Yang, Y. Dong, Y. Shen
Date :  28 Dec 10  (Deposition) - 28 Dec 11  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Lipoprotein, Bamd, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Dong, H. F. Hou, X. Yang, Y. Q. Shen, Y. H. Dong
Structure Of Escherichia Coli Bamd And Its Functional Implications In Outer Membrane Protein Assembly
Acta Crystallogr. , Sect. D V. 68 95 2012
PubMed-ID: 22281737  |  Reference-DOI: 10.1107/S0907444911051031

(-) Compounds

Molecule 1 - UPF0169 LIPOPROTEIN YFIO
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YFIO
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: OUTER MEMBRANE PROTEIN ASSEMBLY COMPLEX SUBUNIT YFIO

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1IOD7Ligand/IonIODIDE ION
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1IOD7Ligand/IonIODIDE ION
Biological Unit 2 (1, 14)
No.NameCountTypeFull Name
1IOD14Ligand/IonIODIDE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:64BINDING SITE FOR RESIDUE IOD A 224
2AC2SOFTWAREARG A:130BINDING SITE FOR RESIDUE IOD A 225
3AC3SOFTWAREASN A:8 , ILE A:13 , THR A:16BINDING SITE FOR RESIDUE IOD A 226
4AC4SOFTWAREGLU A:3 , ASN A:38 , ARG A:39BINDING SITE FOR RESIDUE IOD A 227
5AC5SOFTWARETYR A:45BINDING SITE FOR RESIDUE IOD A 228
6AC6SOFTWAREPRO A:44BINDING SITE FOR RESIDUE IOD A 229

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q5M)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:0 -Ser A:1

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q5M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q5M)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q5M)

(-) 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:210
 aligned with BAMD_ECOLI | P0AC02 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:222
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
           BAMD_ECOLI    22 GSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSS 243
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.------------..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3q5m A   0 ASKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDS------------RDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSS 221
                                     9        19        29        39        49        59        69        79        89        99|        -   |   119       129       139       149       159       169       179       189       199       209       219  
                                                                                                                              100          113
   Legend:   → Mismatch (orange background)
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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 3Q5M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q5M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3Q5M)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (BAMD_ECOLI | P0AC02)
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:0043165    Gram-negative-bacterium-type cell outer membrane assembly    The assembly of an outer membrane of the type formed in Gram-negative bacteria. This membrane is enriched in polysaccharide and protein, and the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0051205    protein insertion into membrane    The process that results in the incorporation of a protein into a biological membrane. Incorporation in this context means having some part or covalently attached group that is inserted into the the hydrophobic region of one or both bilayers.
cellular component
    GO:1990063    Bam protein complex    Protein complex which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. In E. coli it is composed of BamABCDE, of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE. BamA interacts directly with BamB and the BamCDE subcomplex.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BAMD_ECOLI | P0AC02: 2yhc 3tgo 5ayw 5d0o 5d0q 5ekq 5ljo

(-) Related Entries Specified in the PDB File

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