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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LONG-CHAIN FATTY ACID TRANSPORTER FADL MUTANT DELTA S3 KINK
 
Authors :  E. M. Hearn, D. R. Patel, B. W. Lepore, M. Indic, B. Van Den Berg
Date :  10 Sep 07  (Deposition) - 23 Sep 08  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Barrel, Outer Membrane Protein, Lipid Transport, Phage Recognition, Transmembrane, Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. M. Hearn, D. R. Patel, B. W. Lepore, M. Indic, B. Van Den Berg
Transmembrane Passage Of Hydrophobic Compounds Through A Protein Channel Wall
Nature V. 458 367 2009
PubMed-ID: 19182779  |  Reference-DOI: 10.1038/NATURE07678
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LONG-CHAIN FATTY ACID TRANSPORT PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD22
    Expression System Strain: C43(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FADL, TTR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: OUTER MEMBRANE FADL PROTEIN, OUTER MEMBRANE FLP 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2R88)

(-) Sites  (0, 0)

(no "Site" information available for 2R88)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R88)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R88)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R88)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R88)

(-) Exons   (0, 0)

(no "Exon" information available for 2R88)

(-) 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:365
 aligned with FADL_ECOLI | P10384 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:419
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437         
           FADL_ECOLI    28 FQLNEFSSSGLGRAYSGEGAIADDAGNVSRNPALITMFDRPTFSAGAVYIDPDVNISGTSPSGRSLKADNIAPTAWVPNMHFVAPINDQFGWGASITSNYGLATEFNDTYAGGSVGGTTDLETMNLNLSGAYRLNNAWSFGLGFNAVYARAKIERFAGDLGQLVAGQIMQSPAGQTQQGQALAATANGIDSNTKIAHLNGNQWGFGWNAGILYELDKNNRYALTYRSEVKIDFKGNYSSDLNRAFNNYGLPIPTATGGATQSGYLTLNLPEMWEVSGYNRVDPQWAIHYSLAYTSWSQFQQLKATSTSGDTLFQKHEGFKDAYRIALGTTYYYDDNWTFRTGIAFDDSPVPAQNRSISIPDQDRFWLSAGTTYAFNKDASVDVGVSYMHGQSVKINEGPYQFESEGKAWLFGTNFNYAF 446
               SCOP domains d2r88a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2r88A00 A:3-420 Outer membrane protein transport protein (OMPP1/FadL/TodX)                                                                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh...........hhhhhhhhhhhhhhh...eeeeeeeeeeeeeeeee................eeeeeeeeeee....eeeeeeeeee-eeeee......hhhhh.eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeee.hhhhhhhhhhhh.......hhhhhhhhhhh....eeeeeeeeeeeeeeeeeeeeeeee..eeeeeeee.........------------------------------.....eeeeeeeee.....eeeeeeeeeee.-----------------------...eeeeeeeee.....eeeeeeeeeee................eeeeeeeeeee....eeeeeeeeeeee..eee......eeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r88 A   3 FQLNEFSSSGLGRAYSGEGAIADDAGNVSRNPALITMFDRPTFSAGAVYIDPDVNISGTSPSGRSLKADNIAPTAWVPNMHFVAPINDQFGWGASITAN-DLATEFNDTYAGGSVGGTTDLETMNLNLSGAYRLNNAWSFGLGFNAVYARAKIERFAGDLGQLVAGQIMQSPAGQTQQGQALAATANGIDSNTKTAHLNGNQWGFGWNAGILYELDKNNRYALTYRSEVKIDFKG------------------------------TLNLPEMWEVSGYNRVDPQWAIHYSLAYTSW-----------------------KDAYRIALGTTYYYDDNWTFRTGIAFDDSPVPAQNRSISIPDQDRFWLSAGTTYAFNKDASVDVGVSYMHGQSVKINEGPYQFESEGKAWLFGTNFNYAF 420
                                    12        22        32        42        52        62        72        82        92        |-|      111       121       131       141       151       161       171       181       191       201       211       221       231    |    -         -         -     | 271       281       291     |   -         -       321       331       341       351       361       371       381       391       401       411         
                                                                                                                            101 |                                                                                                                                   236                            267                           297                     321                                                                                                   
                                                                                                                              102                                                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:365
 aligned with FADL_ECOLI | P10384 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:419
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437         
           FADL_ECOLI    28 FQLNEFSSSGLGRAYSGEGAIADDAGNVSRNPALITMFDRPTFSAGAVYIDPDVNISGTSPSGRSLKADNIAPTAWVPNMHFVAPINDQFGWGASITSNYGLATEFNDTYAGGSVGGTTDLETMNLNLSGAYRLNNAWSFGLGFNAVYARAKIERFAGDLGQLVAGQIMQSPAGQTQQGQALAATANGIDSNTKIAHLNGNQWGFGWNAGILYELDKNNRYALTYRSEVKIDFKGNYSSDLNRAFNNYGLPIPTATGGATQSGYLTLNLPEMWEVSGYNRVDPQWAIHYSLAYTSWSQFQQLKATSTSGDTLFQKHEGFKDAYRIALGTTYYYDDNWTFRTGIAFDDSPVPAQNRSISIPDQDRFWLSAGTTYAFNKDASVDVGVSYMHGQSVKINEGPYQFESEGKAWLFGTNFNYAF 446
               SCOP domains d2r88b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2r88B00 B:3-420 Outer membrane protein transport protein (OMPP1/FadL/TodX)                                                                                                                                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) Toluene_X-2r88B01 B:3-420                                                                                                                                                                                                                                                                                                                                                                                                           Pfam domains (1)
           Pfam domains (2) Toluene_X-2r88B02 B:3-420                                                                                                                                                                                                                                                                                                                                                                                                           Pfam domains (2)
         Sec.struct. author ......hhhhhh...........hhhhhhhhhhhhhhh...eeeeeeeeeeeeeeeee................eeeeeeeeeee....eeeeeeeeee-eeeee......hhhhh.eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeee.hhhhhhhhhhhh.......hhhhhhhhhhh....eeeeeeeeeeeeeeeeeeeeee....eeeeeeee.........------------------------------.....eeeeeeeee.....eeeeeeeeeee.-----------------------...eeeeeeeee.....eeeeeeeeeee................eeeeeeeeeee....eeeeeeeeeeee..eee......eeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r88 B   3 FQLNEFSSSGLGRAYSGEGAIADDAGNVSRNPALITMFDRPTFSAGAVYIDPDVNISGTSPSGRSLKADNIAPTAWVPNMHFVAPINDQFGWGASITAN-DLATEFNDTYAGGSVGGTTDLETMNLNLSGAYRLNNAWSFGLGFNAVYARAKIERFAGDLGQLVAGQIMQSPAGQTQQGQALAATANGIDSNTKTAHLNGNQWGFGWNAGILYELDKNNRYALTYRSEVKIDFKG------------------------------TLNLPEMWEVSGYNRVDPQWAIHYSLAYTSW-----------------------KDAYRIALGTTYYYDDNWTFRTGIAFDDSPVPAQNRSISIPDQDRFWLSAGTTYAFNKDASVDVGVSYMHGQSVKINEGPYQFESEGKAWLFGTNFNYAF 420
                                    12        22        32        42        52        62        72        82        92        |-|      111       121       131       141       151       161       171       181       191       201       211       221       231    |    -         -         -     | 271       281       291     |   -         -       321       331       341       351       361       371       381       391       401       411         
                                                                                                                            101 |                                                                                                                                   236                            267                           297                     321                                                                                                   
                                                                                                                              102
   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  (1, 2)

Asymmetric Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: MBB (97)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FADL_ECOLI | P10384)
molecular function
    GO:0022834    ligand-gated channel activity    Enables the transmembrane transfer of a solute by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.
    GO:0015483    long-chain fatty acid transporting porin activity    Enables the transfer of long-chain fatty acids from one side of the membrane to the other. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22. This transporter is a porin and so enables the energy independent passage of substances, sized less than 1000 Da, across a membrane. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
biological process
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0015909    long-chain fatty acid transport    The directed movement of long-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22.
    GO:0015718    monocarboxylic acid transport    The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FADL_ECOLI | P10384: 1t16 1t1l 2r4l 2r4n 2r4o 2r4p 2r89 2r8a 3dwn 3pf1 3pgr 3pgs 3pgu

(-) Related Entries Specified in the PDB File

1t16 CRYSTAL STRUCTURE OF THE BACTERIAL FATTY ACID TRANSPORTER FADL (WILD-TYPE, MONOCLINIC SPACE GROUP P21)
1t1l CRYSTAL STRUCTURE OF THE BACTERIAL FATTY ACID TRANSPORTER FADL (WILD-TYPE, HEXAGONAL SPACE GROUP P3121)
2r4l FADL MUTANT P34A
2r4m FADL MUTANT A77E/S100R
2r4n FADL MUTANT N33A
2r4o FADL MUTANT DELTA NPA
2r4p FADL MUTANT G212E
2r89 FADL MUTANT DELTA N3
2r8a FADL MUTANT DELTA N8
3dwn FADL MUTANT A77E/S100R
3dwo FADL HOMOLOGUE IN PSEUDOMONAS AERUGINOSA