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(-) Description

Title :  CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA OPDO
 
Authors :  D. S. Touw, J. Vijayaraghavan, B. Vandenberg
Date :  03 Dec 10  (Deposition) - 21 Dec 11  (Release) - 21 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym./Biol. Unit :  A
Keywords :  Transport Protein, Outer Membrane, Oprd (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. S. Touw, J. Vijayaraghavan, B. Vandenberg
Crystal Structure Of Pseudomonas Aeruginosa Opdo
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CIS-ACONITATE PORIN OPDH
    Atcc: 47085
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PB22
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: MATURE PROTEIN, RESIDUES 26-427
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1
    Synonym: OPDO

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2Y0L)

(-) Sites  (0, 0)

(no "Site" information available for 2Y0L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y0L)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ile A:230 -Gly A:231
2Ala A:252 -Gly A:253
3Glu A:349 -Gly A:350

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y0L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y0L)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y0L)

(-) 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:362
 aligned with Q9I5H4_PSEAE | Q9I5H4 from UniProtKB/TrEMBL  Length:427

    Alignment length:391
                                    46        56        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       376       386       396       406       416       426 
         Q9I5H4_PSEAE    37 AGFLEDSKASLETRNFYMNRDFRDGPGQSKREEWAQGFILNLQSGYTQGTVGFGLDAMGMLGVKLDSGRGRSGTGLLPKDSDGRAPDTYSKLGLTAKVKVSQSELKVGTLIPKLPSVQPNNGRIFPQIFEGALLTSKEIKDLGFTAGRLEKTKIRDSSDSEDLALNDKNGRFAGVSADHFDLGGLDYKLTDQLTASYHYSNLQDVYRQHFVGLLHSWPIGPGELTSDLRFARSTDSGSAKAGGIDNKSLNGMFTYSLGNHAFGAAWQRMNGDDAFPYLEGSNPYLVNFVQVNDFAGPKERSWQLRYDYDFVGLGIPGLTFMTRYVKGDNVELAGQSGEGREWERNTELQYVFQSGALKNLGIRWRNATFRSNFTRDIDENRLIVSYTLPIW 427
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeeeee.------.eeeeeeeeeee.........eeeeeeeeeeeeeeeee------------------.eeeeeeeeeeeeee..eeeeeeee.......ee........eeeeeeeee.....eeeeeeeeeeee.----........hhhhh........eeeeeeee.....eeeeeeeeee...eeeeeeeeeeeee....eeeeeeeeeeeee.........eeeeeeeeeeeee..eeeeeeeeeee..........ee.................eeeeeeeeee.hhhh...eeeeeeeeeee.......-....eeeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y0l A  12 AGFLEDSKASLETRNFYMNRDFR------KREEWAQGFILNLQSGYTQGTVGFGLDAMGMLGVKLDS------------------PDTYSKLGLTAKVKVSQSELKVGTLIPKLPSVQPNNGRIFPQIFEGALLTSKEIKDLGFTAGRLEKTKI----DSEDLALNDKNGRFAGVSADHFDLGGLDYKLTDQLTASYHYSNLQDVYRQHFVGLLHSWPIGPGELTSDLRFARSTDSGSAKAGGIDNKSLNGMFTYSLGNHAFGAAWQRMNGDDAFPYLEGSNPYLVNFVQVNDFAGPKERSWQLRYDYDFVGLGIPGLTFMTRYVKGDNVELAGQ-GEGREWERNTELQYVFQSGALKNLGIRWRNATFRSNFTRDIDENRLIVSYTLPIW 402
                                    21        31  |     41        51        61        71      |  -         -     | 101       111       121       131       141       151       161   |   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341    | |351       361       371       381       391       401 
                                                 34     41                                   78                 97                                                                 165  170                                                                                                                                                                             346 |                                                      
                                                                                                                                                                                                                                                                                                                                                                          348
   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 2Y0L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y0L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y0L)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9I5H4_PSEAE | Q9I5H4)
molecular function
    GO:0015288    porin activity    Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. 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: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: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.

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  Cis Peptide Bonds
    Ala A:252 - Gly A:253   [ RasMol ]  
    Glu A:349 - Gly A:350   [ RasMol ]  
    Ile A:230 - Gly A:231   [ RasMol ]  
 

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