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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OUTER MEMBRANE PROTEIN OPRD FROM PSEUDOMONAS AERUGINOSA
 
Authors :  S. Biswas, B. Van Den Berg
Date :  22 Dec 06  (Deposition) - 16 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Outer Membrane Protein, Beta-Barrel, Amino Acid Transport, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Biswas, M. M. Mohammad, D. R. Patel, L. Movileanu, B. Van Den Berg
Structural Insight Into Oprd Substrate Specificity.
Nat. Struct. Mol. Biol. V. 14 1108 2007
PubMed-ID: 17952093  |  Reference-DOI: 10.1038/NSMB1304

(-) Compounds

Molecule 1 - PORIN D
    Chains: A, B
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PB22
    Expression System Strain: C43
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: OPRD
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1
    Synonym: OUTER MEMBRANE PROTEIN D2, IMIPENEM/BASIC AMINO ACID- SPECIFIC OUTER MEMBRANE PORE

 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  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1C8E8Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1C8E6Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1C8E2Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:109 , THR A:111 , LEU A:142 , GLU A:146 , TYR B:27 , TRP B:42 , PHE B:388 , VAL B:413BINDING SITE FOR RESIDUE C8E B 429
2AC2SOFTWAREPHE A:231BINDING SITE FOR RESIDUE C8E A 429
3AC3SOFTWAREILE A:14 , GLU A:15 , TYR A:50 , ALA A:65 , GLU A:363 , LEU A:420 , LEU B:256BINDING SITE FOR RESIDUE C8E A 430
4AC4SOFTWARETYR B:260 , PHE B:267 , LEU B:269 , ARG B:319 , VAL B:336BINDING SITE FOR RESIDUE C8E B 430
5AC5SOFTWAREVAL A:329 , TYR A:376 , PHE A:409 , TYR B:191 , LEU B:201BINDING SITE FOR RESIDUE C8E A 431
6AC6SOFTWARETYR A:320 , VAL A:336 , TRP A:394 , C8E A:433 , THR B:111 , GLU B:146BINDING SITE FOR RESIDUE C8E A 432
7AC7SOFTWAREPHE A:267 , THR A:268 , ALA A:318 , ARG A:319 , THR A:370 , C8E A:432 , C8E A:434BINDING SITE FOR RESIDUE C8E A 433
8AC8SOFTWARETYR A:338 , C8E A:433 , ILE B:14BINDING SITE FOR RESIDUE C8E A 434

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala B:122 -Pro B:123

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ODJ)

(-) 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:382
 aligned with PORD_PSEAE | P32722 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:426
                                                                                                                                                                                                                                                                                                                                                                                                                                                             443      
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443      
           PORD_PSEAE    24 DAFVSDQAEAKGFIEDSSLDLLLRNYYFNRDGKSGSGDRVDWTQGFLTTYESGFTQGTVGFGVDAFGYLGLKLDGTSDKTGTGNLPVMNDGKPRDDYSRAGGAVKVRISKTMLKWGEMQPTAPVFAAGGSRLFPQTATGFQLQSSEFEGLDLEAGHFTEGKEPTTVKSRGELYATYAGETAKSADFIGGRYAITDNLSASLYGAELEDIYRQYYLNSNYTIPLASDQSLGFDFNIYRTNDEGKAKAGDISNTTWSLAAAYTLDAHTFTLAYQKVHGDQPFDYIGFGRNGSGAGGDSIFLANSVQYSDFNGPGEKSWQARYDLNLASYGVPGLTFMVRYINGKDIDGTKMSDNNVGYKNYGYGEDGKHHETNLEAKYVVQSGPAKDLSFRIRQAWHRANADQGEGDQNEFRLIVDYPLSIL------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ---------------2odjA01 A:16-419 P     orin                                                                                                                                                                                                                                                                                                                                                                                         ------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................eeeeeeeeeeeeee..-----.eeeeeeeeeeee.......eeeeeeeeeeeeeeee..-------------------..eeeeeeeeeee..eeeeeeee..................eeeeeeee.....eeeeeeee..-----------.eee.....ee..eeeeeeee.....eeeeeeeeee...eeeeeeeeeeeeeee..eeeeeeeeeeeee..........ee..eeeeeeeee..eeeeeeeee.........ee..---------..................eeeeeeeee.........eeeeeeeeeeeee....................eeeeeeeeeeeee.........eeeeeeeeeee.........eeeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2odj A   1 GmFVSDQAEAKGFIEDSSLDLLLRNYYFNRDGK-----RVDWTQGFLTTYESGFTQGTVGFGVDAFGYLGLKLDGT-------------------DYSRAGGAVKVRISKTmLKWGEmQPTAPVFAAGGSRLFPQTATGFQLQSSEFEGLDLEAGHFTE-----------ELYATYAGETAKSADFIGGRYAITDNLSASLYGAELEDIYRQYYLNSNYTIPLASDQSLGFDFNIYRTNDEGKAKAGDISNTTWSLAAAYTLDAHTFTLAYQKVHGDQPFDYIGFG---------SIFLANSVQYSDFNGPGEKSWQARYDLNLASYGVPGLTFmVRYINGKDIDGTKmSDNNVGYKNYGYGEDGKHHETNLEAKYVVQSGPAKDLSFRIRQAWHRANADQGEGDQNEFRLIVDYPLSILHHHHHH 426
                             |      10        20        30  |     40        50        60        70     |   -         -     | 100       110 |     120       130       140       150        |-         -|      180       190       200       210       220       230       240       250       260       270       280     |   -     | 300       310       320       330    |  340       350       360       370       380       390       400       410       420      
                             |                             33    39                                   76                  96             112-MSE |                                      159         171                                                                                                                286       296                                    335-MSE       349-MSE                                                                         
                             2-MSE                                                                                                             118-MSE                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:388
 aligned with PORD_PSEAE | P32722 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:428
                                                                                                                                                                                                                                                                                                                                                                                                                                                             443        
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443        
           PORD_PSEAE    24 DAFVSDQAEAKGFIEDSSLDLLLRNYYFNRDGKSGSGDRVDWTQGFLTTYESGFTQGTVGFGVDAFGYLGLKLDGTSDKTGTGNLPVMNDGKPRDDYSRAGGAVKVRISKTMLKWGEMQPTAPVFAAGGSRLFPQTATGFQLQSSEFEGLDLEAGHFTEGKEPTTVKSRGELYATYAGETAKSADFIGGRYAITDNLSASLYGAELEDIYRQYYLNSNYTIPLASDQSLGFDFNIYRTNDEGKAKAGDISNTTWSLAAAYTLDAHTFTLAYQKVHGDQPFDYIGFGRNGSGAGGDSIFLANSVQYSDFNGPGEKSWQARYDLNLASYGVPGLTFMVRYINGKDIDGTKMSDNNVGYKNYGYGEDGKHHETNLEAKYVVQSGPAKDLSFRIRQAWHRANADQGEGDQNEFRLIVDYPLSIL--------   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------2odjB01 B:16-419 P    orin                                                                                                                                                                                                                                                                                                                                                                                          --------- CATH domains
           Pfam domains (1) ----------OprD-2odjB01 B:11-419                                                                                                                                                                                                                                                                                                                                                                                                    --------- Pfam domains (1)
           Pfam domains (2) ----------OprD-2odjB02 B:11-419                                                                                                                                                                                                                                                                                                                                                                                                    --------- Pfam domains (2)
         Sec.struct. author .................eeeeeeeeeeeeee..----.eeeeeeeeeeeee........eeeeeeeeeeeeeeeee-------------------.eeeeeeeeeeee..eeeeeeee..................eeeeeeee.....eeeeeeeee.-----------.eee....ee..eeeeeeeee.....eeeeeeeeee...eeeeeeeeeeeeeee..eeeeeeeeeeeee.-........eeeeeeeeeeeee..eeeeeeeeeeee......eee..-----.....................eeeeeeeeee........eeeeeeeeeeeee........hhhhhh......eeeeeeeeeeeee.........eeeeeeeeeee.hhhh....eeeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2odj B   1 GmFVSDQAEAKGFIEDSSLDLLLRNYYFNRDGK----DRVDWTQGFLTTYESGFTQGTVGFGVDAFGYLGLKLDGT-------------------DYSRAGGAVKVRISKTmLKWGEmQPTAPVFAAGGSRLFPQTATGFQLQSSEFEGLDLEAGHFTE-----------ELYATYAGETAKSADFIGGRYAITDNLSASLYGAELEDIYRQYYLNSNYTIPLASDQSLGFDFNIYRTND-GKAKAGDISNTTWSLAAAYTLDAHTFTLAYQKVHGDQPFDYIGFGR-----GGDSIFLANSVQYSDFNGPGEKSWQARYDLNLASYGVPGLTFmVRYINGKDIDGTKmSDNNVGYKNYGYGEDGKHHETNLEAKYVVQSGPAKDLSFRIRQAWHRANADQGEGDQNEFRLIVDYPLSILHHHHHHHH 428
                             |      10        20        30  |    |40        50        60        70     |   -         -     | 100       110 |     120       130       140       150        |-         -|      180       190       200       210       220       230       240 |     250       260       270       280      |  -  |    300       310       320       330    |  340       350       360       370       380       390       400       410       420        
                             2-MSE                         33   38                                    76                  96             112-MSE |                                      159         171                                                                  240 |                                          287   293                                       335-MSE       349-MSE                                                                           
                                                                                                                                               118-MSE                                                                                                                     242
   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 2ODJ)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: MBB (97)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PORD_PSEAE | P32722)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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.
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0015802    basic amino acid transport    The directed movement of basic amino acids, amino acids with a pH above 7, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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:0045203    integral component of cell outer membrane    The component of the cell outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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.
    GO:0046930    pore complex    Any small opening in a membrane that allows the passage of gases and/or liquids.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PORD_PSEAE | P32722: 3sy7 4foz

(-) Related Entries Specified in the PDB File

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