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(-) Description

Title :  HIGH RESOLUTION X-RAY STRUCTURE OF OMP32 IN COMPLEX WITH MALATE
 
Authors :  K. Zeth, H. Engelhardt
Date :  22 Dec 05  (Deposition) - 31 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (3x)
Keywords :  Porin, Malate, Outer Membrane Protein, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Zachariae, T. Kluhspies, S. De, H. Engelhardt, K. Zeth
High Resolution Crystal Structures And Molecular Dynamics Studies Reveal Substrate Binding In The Porin Omp32
J. Biol. Chem. V. 281 7413 2006
PubMed-ID: 16434398  |  Reference-DOI: 10.1074/JBC.M510939200

(-) Compounds

Molecule 1 - OUTER MEMBRANE PORIN PROTEIN 32
    Chains: X
    Organism Scientific: DELFTIA ACIDOVORANS
    Organism Taxid: 80866
    Synonym: OMP32

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : X
Biological Unit 1 (3x): X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1BOG1Ligand/IonB-OCTYLGLUCOSIDE
2CA3Ligand/IonCALCIUM ION
3MLT1Ligand/IonMALATE ION
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1BOG3Ligand/IonB-OCTYLGLUCOSIDE
2CA-1Ligand/IonCALCIUM ION
3MLT3Ligand/IonMALATE ION
4SO46Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU X:6 , HOH X:1477 , HOH X:1510BINDING SITE FOR RESIDUE BOG X 1170
2AC2SOFTWARELEU X:29 , ASP X:64 , ASN X:136 , GLU X:158 , GLY X:309 , HOH X:1180BINDING SITE FOR RESIDUE CA X 501
3AC3SOFTWAREGLY X:70 , PHE X:71BINDING SITE FOR RESIDUE CA X 502
4AC4SOFTWAREPHE X:55 , ARG X:76 , THR X:78 , SER X:80BINDING SITE FOR RESIDUE CA X 503
5AC5SOFTWAREGLU X:254 , LYS X:256 , ARG X:329 , HOH X:1356 , HOH X:1383 , HOH X:1451BINDING SITE FOR RESIDUE SO4 X 600
6AC6SOFTWAREARG X:38 , HOH X:1251 , HOH X:1357BINDING SITE FOR RESIDUE SO4 X 601
7AC7SOFTWARETHR X:36 , ARG X:75 , THR X:102 , ARG X:133 , HOH X:1454 , HOH X:1481BINDING SITE FOR RESIDUE MLT X 700

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FGQ)

(-) 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 X from PDB  Type:PROTEIN  Length:330
 aligned with OMP32_DELAC | P24305 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:330
                                    31        41        51        61        71        81        91       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
          OMP32_DELAC    22 SVTLFGIVDTNVAYVNKDAAGDSRYGLGTSGASTSRLGLRGTEDLGGGLKAGFWLEGEIFGDDGNASGFNFKRRSTVSLSGNFGEVRLGRDLVPTSQKLTSYDLFSATGIGPFMGFRNWAAGQGADDNGIRANNLISYYTPNFGGFNAGFGYAFDEKQTIGTADSVGRYIGGYVAYDNGPLSASLGLAQQKTAVGGLATDRDEITLGASYNFGVAKLSGLLQQTKFKRDIGGDIKTNSYMLGASAPVGGVGEVKLQYALYDQKAIDSKAHQITLGYVHNLSKRTALYGNLAFLKNKDASTLGLQAKGVYAGGVQAGESQTGVQVGIRHAF 351
               SCOP domains d2fgqx_ X: automated matches                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2fgqX00 X:3-332 Porin                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee........eeeeee......eeeeeeeeeee..eeeeeeeeee...............eeeeeeee..eeeee..eehhhhhhhhhhh...........................ee..eeeee......eeeeeeee...............eeeeeeeee...eeeeeeeeeeeeee..eeeeeeeeeeeeeee....eeeeeeeeeeeee....eeeeeeeeeeeeeee...eeeeeeeeeeee.hhheeeeeeeeeeeee....eeeeeeeeeeee......................eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2fgq X   3 SVTLFGIVDTNVAYVNKDAAGDSRYGLGTSGASTSRLGLRGTEDLGGGLKAGFWLEGEIFGDDGNASGFNFKRRSTVSLSGNFGEVRLGRDLVPTSQKLTSYDLFSATGIGPFMGFRNWAAGQGADDNGIRANNLISYYTPNFGGFNAGFGYAFDEKQTIGTADSVGRYIGGYVAYDNGPLSASLGLAQQKTAVGGLATDRDEITLGASYNFGVAKLSGLLQQTKFKRDIGGDIKTNSYMLGASAPVGGVGEVKLQYALYDQKAIDSKAHQITLGYVHNLSKRTALYGNLAFLKNKDASTLGLQAKGVYAGGVQAGESQTGVQVGIRHAF 332
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain X   (OMP32_DELAC | P24305)
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: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: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.
    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
        OMP32_DELAC | P24305: 1e54 2fgr

(-) Related Entries Specified in the PDB File

2fgr