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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PERIPLASMIC DOMAIN OF THE ESCHERICHIA COLI YIDC
 
Authors :  M. Paetzel, D. C. Oliver
Date :  10 Dec 07  (Deposition) - 25 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Yidc, Membrane Assembly Facilitator, Chaperone, Periplasmic Domain, Inner Membrane, Transmembrane, Oxaa, Chaperone, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. C. Oliver, M. Paetzel
Crystal Structure Of The Major Periplasmic Domain Of The Bacterial Membrane Protein Assembly Facilitator Yidc.
J. Biol. Chem. V. 283 5208 2008
PubMed-ID: 18093969  |  Reference-DOI: 10.1074/JBC.M708936200

(-) Compounds

Molecule 1 - INNER MEMBRANE PROTEIN OXAA
    Chains: A, B
    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: UNP RESIDUES 26-340
    Gene: OXAA, YIDC
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
    Strain: K-12

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3BLC)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BLC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BLC)

(-) 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:280
 aligned with YIDC_ECOLI | P25714 from UniProtKB/Swiss-Prot  Length:548

    Alignment length:312
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366  
           YIDC_ECOLI    57 QGKLISVKTDVLDLTINTRGGDVEQALLPAYPKELNSTQPFQLLETSPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAYVLAEGQNELQVPMTYTDAAGNTFTKTFVLKRGDYAVNVNYNVQNAGEKPLEISSFGQLKQSITLPPHLDTGSSNFALHTFRGAAYSTPDEKYEKYKFDTIADNENLNISSKGGWVAMLQQYFATAWIPHNDGTNNFYTANLGNGIAAIGYKSQPVLVQPGQTGAMNSTLWVGPEIQDKMAAVAPHLDLTVDYGWLWFISQPLFKLLKWIHSFVGNWGFSIIIITFIVRGI 368
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee....eeeee.....eeeeeeeeee.......eeeeeee....eeeeeeeee......hhhhh..........eee......eeeeeeeee.....eeeeeeeee....eeeeeeeee......eeeeeeeeeeee.......----------..eeeeee.......eehhhhhhh....eeee...eeeeee..eeeeeeee....eeeeeeeee..eeeeeee...eee....eeeeeeeeeeee.hhhhhhhhh....hhhhhhhhhhhh....----------------------..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3blc A  57 QGKLISVKTDVLDLTINTRGGDVEQALLPAYPKELNSTQPFQLLETSPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAYVLAEGQNELQVPmTYTDAAGNTFTKTFVLKRGDYAVNVNYNVQNAGEKPLEISSFGQLKQSITLPPHL----------TFRGAAYSTPDAAYAAYAFDTIADNENLNISSKGGWVAmLQQYFATAWIPHNDGTNNFYTANLGNGIAAIGYKSQPVLVQPGQTGAmNSTLWVGPEIQDKmAAVAPHLDLTVDYGWLWFISQPLL----------------------VPRGS 346
                                    66        76        86        96       106       116       126       136       146    |  156       166       176       186       196       206         -|      226       236       246       256       266       276       286       296      |306       316|      326       336    |    -         -       344  
                                                                                                                        151-MSE                                                206        217                                   255-MSE                                         303-MSE       317-MSE                 341                    342    


Chain B from PDB  Type:PROTEIN  Length:278
 aligned with YIDC_ECOLI | P25714 from UniProtKB/Swiss-Prot  Length:548

    Alignment length:288
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335        
           YIDC_ECOLI    56 GQGKLISVKTDVLDLTINTRGGDVEQALLPAYPKELNSTQPFQLLETSPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAYVLAEGQNELQVPMTYTDAAGNTFTKTFVLKRGDYAVNVNYNVQNAGEKPLEISSFGQLKQSITLPPHLDTGSSNFALHTFRGAAYSTPDEKYEKYKFDTIADNENLNISSKGGWVAMLQQYFATAWIPHNDGTNNFYTANLGNGIAAIGYKSQPVLVQPGQTGAMNSTLWVGPEIQDKMAAVAPHLDLTVDYGWLWFISQPLFKL 343
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee....eeeee.....eeeeeeeeee.......eee..ee....eeeeeeee.......hhhhh..........eee......eeeeeeeee.....eeeeeeeee....eeeeeeeee......eee.eeeeeeee.......----------..eeeeeee..eeeeeehhhhhhh....eeee...eeeeee..eeeeeeee....eeeeeee....eeeeeee...eee....eeeeeeeeeeee.hhhhhhhhh...hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3blc B  56 GQGKLISVKTDVLDLTINTRGGDVEQALLPAYPKELNSTQPFQLLETSPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAYVLAEGQNELQVPmTYTDAAGNTFTKTFVLKRGDYAVNVNYNVQNAGEKPLEISSFGQLKQSITLPPHL----------TFRGAAYSTPDAAYAAYAFDTIADNENLNISSKGGWVAmLQQYFATAWIPHNDGTNNFYTANLGNGIAAIGYKSQPVLVQPGQTGAmNSTLWVGPEIQDKmAAVAPHLDLTVDYGWLWFISQPLLVP 343
                                    65        75        85        95       105       115       125       135       145     | 155       165       175       185       195       205|        - |     225       235       245       255       265       275       285       295       305       315 |     325       335        
                                                                                                                         151-MSE                                                206        217                                   255-MSE                                         303-MSE       317-MSE
   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 3BLC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (YIDC_ECOLI | P25714)
molecular function
    GO:0032977    membrane insertase activity    Mediates the integration of proteins into a membrane from the inner side of the membrane. Membrane insertases are highly conserved and include the bacterial YidC family, the plant chloroplast Alb3 family, and the fungal and animal mitochondrial Oxa1/Cox18 family.
    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:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    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.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, 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: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:0005887    integral component of plasma membrane    The component of the plasma 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

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UniProtKB/Swiss-Prot
        YIDC_ECOLI | P25714: 3bs6 4utq 5m5h 5mg3

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