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(-) Description

Title :  STRUCTURE OF THE N-TERMINAL DOMAIN OF BAMC FROM E. COLI
 
Authors :  K. Zeth, R. Albrecht
Date :  27 Apr 11  (Deposition) - 25 May 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Albrecht, K. Zeth
Structural Basis Of Outer Membrane Protein Biogenesis In Bacteria.
J. Biol. Chem. V. 286 27792 2011
PubMed-ID: 21586578  |  Reference-DOI: 10.1074/JBC.M111.238931

(-) Compounds

Molecule 1 - LIPOPROTEIN 34
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: N-TERMINAL DOMAIN, RESIDUES 101-212
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 469008
    Other Details: DOMAIN WAS IDENTIFIED BY LIMITED PROTEOLYSIS
    Strain: K-12
    Synonym: BAMC

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):   CD
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:126 , LEU A:127 , ASP A:128 , ALA C:183 , ARG D:172BINDING SITE FOR RESIDUE SO4 A1188
2AC2SOFTWAREARG A:172 , ALA B:183 , ARG D:126 , LEU D:127 , ASP D:128BINDING SITE FOR RESIDUE SO4 A1189
3AC3SOFTWAREGLN C:101 , ILE C:107 , ARG C:110 , HOH C:2008 , HOH C:2010 , GLN D:101 , ILE D:107 , ARG D:110BINDING SITE FOR RESIDUE SO4 C1188
4AC4SOFTWARETHR A:108 , GLN A:109 , ARG A:136 , LYS B:162 , HOH B:2022BINDING SITE FOR RESIDUE SO4 B1189
5AC5SOFTWAREHOH C:2029 , ARG D:126 , TYR D:133 , GLN D:159BINDING SITE FOR RESIDUE SO4 D1189
6AC6SOFTWAREASN A:125 , ASN D:125BINDING SITE FOR RESIDUE SO4 A1190

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YH6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly B:145 -Tyr B:146
2Gly C:145 -Tyr C:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YH6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YH6)

(-) Exons   (0, 0)

(no "Exon" information available for 2YH6)

(-) 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:108
 aligned with BAMC_ECOLI | P0A903 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:111
                                   110       120       130       140       150       160       170       180       190       200       210 
           BAMC_ECOLI   101 GDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDK 211
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..---.hhhhhhhhhhhhh...eeeeehhh.eeee..eee...hhhh.eeeeeeeeeeee..eeeeeeeeeeeee..eee.hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 2yh6 A  77 GDTASLLVEN---NTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDK 187
                                    86   |    96       106       116       126       136       146       156       166       176       186 
                                    86  90                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:107
 aligned with BAMC_ECOLI | P0A903 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:112
                                   110       120       130       140       150       160       170       180       190       200       210  
           BAMC_ECOLI   101 GDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDKS 212
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...--.hhhhhhhhhhhhh...eeeeehhh.eeee..eee...---..eeeeeeeee......eeeeeeeeeeee..ee..hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2yh6 B  77 GDTASLLVENG--NTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRL---EQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDKS 188
                                    86|  |    96       106       116       126|   |  136       146       156       166       176       186  
                                     87 90                                  127 131                                                         


Chain C from PDB  Type:PROTEIN  Length:109
 aligned with BAMC_ECOLI | P0A903 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:111
                                   110       120       130       140       150       160       170       180       190       200       210 
           BAMC_ECOLI   101 GDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDK 211
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...--.hhhhhhhhhhhhh...eeeeehhh.eeee..eee...hhhh.eeeeeeeeeeee..eeeeeeeeeeeee..ee..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 2yh6 C  77 GDTASLLVENG--NTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDK 187
                                    86|  |    96       106       116       126       136       146       156       166       176       186 
                                     87 90                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:110
 aligned with BAMC_ECOLI | P0A903 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:112
                                   110       120       130       140       150       160       170       180       190       200       210  
           BAMC_ECOLI   101 GDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDKS 212
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...--.hhhhhhhhhhhhh...eeeeehhh.eeee..eee...hhhh.eeeeeeeeeeee..eeeeeeeeeeeee..ee..hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2yh6 D  77 GDTASLLVENG--NTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDKS 188
                                    86|  |    96       106       116       126       136       146       156       166       176       186  
                                     87 90
   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 2YH6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YH6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YH6)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (BAMC_ECOLI | P0A903)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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
        BAMC_ECOLI | P0A903: 2lae 2laf 2yh5 3sns 3tgo 5ayw 5d0o 5d0q 5ekq 5ljo

(-) Related Entries Specified in the PDB File

2yh3 THE STRUCTURE OF BAMB FROM E. COLI
2yh5 STRUCTURE OF THE C-TERMINAL DOMAIN OF BAMC