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(-) Description

Title :  STRUCTURE OF N-TERMINAL DOMAIN OF E. COLI YAET
 
Authors :  S. Kim, J. C. Malinverni, P. Sliz, T. J. Silhavy, S. C. Harrison, D. Kahne
Date :  20 Jun 07  (Deposition) - 04 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Potra Domain, Membrane Protein, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kim, J. C. Malinverni, P. Sliz, T. J. Silhavy, S. C. Harrison, D. Kahne
Structure And Function Of An Essential Component Of The Outer Membrane Protein Assembly Machine.
Science V. 317 961 2007
PubMed-ID: 17702946  |  Reference-DOI: 10.1126/SCIENCE.1143993
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR YAET
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 21-351
    Gene: YAET
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
    Strain: K-12
    Synonym: OMP85

 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
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (0, 0)

(no "Site" information available for 2QDF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 5)

Asymmetric/Biological Unit (1, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1POTRAPS51779 POTRA domain profile.BAMA_ECOLI24-91
92-172
175-263
266-344
347-421		  5A:24-91
A:92-172
A:175-263
A:266-344
A:347-351

(-) Exons   (0, 0)

(no "Exon" information available for 2QDF)

(-) 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:318
 aligned with BAMA_ECOLI | P0A940 from UniProtKB/Swiss-Prot  Length:810

    Alignment length:332
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349  
           BAMA_ECOLI    20 GAEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRK 351
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..eeeee.....hhhhhhhh.......eehhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee..eeeeeeee.....hhhhhhhhhhh............hhhhhhhhhhhhhhhhh....eeeeeeeee...eeeeeeeee.....eeeeeeee.....hhhhhhhhhh..--------------...hhhhhhhhhhhhhhh......eeeeeeeee.....eeeeeeeee.....eeeeeeeeee...hhhhhhhhh.....ee.hhhhhhhhhhhhhhhhhh......eeeeeeeee....eeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----POTRA  PDB: A:24-91 UniProt: 24-91                                  POTRA  PDB: A:92-172 UniProt: 92-172                                             --POTRA  PDB: A:175-263 UniProt: 175-263                                                   --POTRA  PDB: A:266-344 UniProt: 266-344                                         --POTRA PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qdf A  20 MAEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLR--------------QKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRK 351
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199|        -     | 219       229       239       249       259       269       279       289       299       309       319       329       339       349  
                                                                                                                                                                                                              200            215
   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 2QDF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BAMA_ECOLI | P0A940)
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:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0071709    membrane assembly    The aggregation, arrangement and bonding together of a set of components to form a membrane.
    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: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:0019867    outer membrane    The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BAMA_ECOLI | P0A940: 2qcz 2v9h 3efc 3og5 3q6b 4c4v 4n75 4pk1 4xga 5ayw 5d0o 5d0q 5ekq 5ljo

(-) Related Entries Specified in the PDB File

2qcz THE SAME PROTEIN IN A DIFFERENT SPACE GROUP (P212121).