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(-) Description

Title :  ARABIDOPSIS THALIANA MULTIFUCTIONAL PROTEIN, MFP2
 
Authors :  S. Arent, V. E. Pye, C. E. Christensen, A. Norgaard, A. Henriksen
Date :  15 Sep 09  (Deposition) - 12 May 10  (Release) - 04 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Peroxisomes, Beta-Oxidation, Fatty Acid Oxidation, Fatty Acid Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Arent, V. E. Pye, C. E. Christen, A. Norgaard, A. Henriksen
The Multi-Functional Protein In Peroxisomal Beta-Oxidation. Structure And Substrate Specificity Of The Arabidopsis Thaliana Protein, Mfp2
J. Biol. Chem. V. 285 24066 2010
PubMed-ID: 20463021  |  Reference-DOI: 10.1074/JBC.M110.106005
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FATTY ACID MULTIFUNCTIONAL PROTEIN (ATMFP2)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymMFP2

 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 2WTB)

(-) Sites  (0, 0)

(no "Site" information available for 2WTB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:26 -Pro A:27
2Ser A:452 -Pro A:453

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ENOYL_COA_HYDRATASEPS00166 Enoyl-CoA hydratase/isomerase signature.MFP2_ARATH106-126  1A:106-126
23HCDHPS00067 3-hydroxyacyl-CoA dehydrogenase signature.MFP2_ARATH492-516  1A:492-516

(-) Exons   (0, 0)

(no "Exon" information available for 2WTB)

(-) 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:676
 aligned with MFP2_ARATH | Q9ZPI5 from UniProtKB/Swiss-Prot  Length:725

    Alignment length:713
                                    16        26        36        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       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716   
           MFP2_ARATH     7 GKTVMEVGGDGVAVITLINPPVNSLSFDVLYNLKSNYEEALSRNDVKAIVITGAKGRFSGGFDISGFGEMQKGNVKEPKAGYISIDIITDLLEAARKPSVAAIDGLALGGGLELAMACHARISAPAAQLGLPELQLGVIPGFGGTQRLPRLVGLTKALEMILTSKPVKAEEGHSLGLIDAVVPPAELVTTARRWALDIVGRRKPWVSSVSKTDKLPPLGEAREILTFAKAQTLKRAPNMKHPLMCLDAIEVGIVSGPRAGLEKEAEVASQVVKLDTTKGLIHVFFSQRGTAKVPGVTDRGLVPRKIKKVAIIGGGLMGSGIATALILSNYPVILKEVNEKFLEAGIGRVKANLQSRVRKGSMSQEKFEKTMSLLKGSLDYESFRDVDMVIEAVIENISLKQQIFADLEKYCPQHCILASNTSTIDLNKIGERTKSQDRIVGAHFFSPAHIMPLLEIVRTNHTSAQVIVDLLDVGKKIKKTPVVVGNCTGFAVNRMFFPYTQAAMFLVECGADPYLIDRAISKFGMPMGPFRLCDLVGFGVAIATATQFIENFSERTYKSMIIPLMQEDKRAGEATRKGFYLYDDKRKAKPDPELKKYIEKARSISGVKLDPKLANLSEKDIIEMTFFPVVNEACRVFAEGIAVKAADLDIAGIMGMGFPPYRGGIMFWADSIGSKYIYSRLDEWSKAYGEFFKPCAFLAERGSKGVLLSAPVK 719
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------ECH-2wtbA02 A:13-248                                                                                                                                                                                                                        -----------------------------------------------------------------3HCDH_N-2wtbA03 A:314-493                                                                                                                                                           -3HCDH-2wtbA01 A:495-575                                                                               --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eeeee........hhhhhhhhhhhhhhhh.......eeee............------------.....hhhhhhhhhhhhh....eeeee........hhhhhhh.eeee....ee..hhhhh.........hhhhhhh.hhhhhhhhhhh..ee...........ee....hhhhhhhhhhhhhh.......hhhhh........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhh.......hhhhhhhhh....................eeee........hhhhhhh....eee...hhhhhhh...hhhhhhhhh..----..hhhhhh...ee....hhhhh...eeee....hhhhhhhhhhhhhhhh....eeee...................ee..ee........eeeee.....hhhhhhhhhhh......eeeee......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhh..---------------------.......hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.............hhhhhhhh.hhhhhhhhhhhhh........hhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------ENOYL_COA_HYDRATASE  -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3HCDH  PDB: A:492-516    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wtb A   7 GKTVMEVGGDGVAVITLINPPVNSLSFDVLYNLKSNYEEALSRNDVKAIVITGAKGRFSGGFDI------------EPKAGYISIDIITDLLEAARKPSVAAIDGLALGGGLELAMACHARISAPAAQLGLPELQLGVIPGFGGTQRLPRLVGLTKALEMILTSKPVKAEEGHSLGLIDAVVPPAELVTTARRWALDIVGRRKPWVSSVSKTDKLPPLGEAREILTFAKAQTLKRAPNMKHPLMCLDAIEVGIVSGPRAGLEKEAEVASQVVKLDTTKGLIHVFFSQRGTAKVPGVTDRGLVPRKIKKVAIIGGGLMGSGIATALILSNYPVILKEVNEKFLEAGIGRVKANLQSRVR----SQEKFEKTMSLLKGSLDYESFRDVDMVIEAVIENISLKQQIFADLEKYCPQHCILASNTSTIDLNKIGERTKSQDRIVGAHFFSPAHIMPLLEIVRTNHTSAQVIVDLLDVGKKIKKTPVVVGNCTGFAVNRMFFPYTQAAMFLVECGADPYLIDRAISKFGMPMGPFRLCDLVGFGVAIATATQFIENFSERTYKSMIIPLMQEDK---------------------DPELKKYIEKARSISGVKLDPKLANLSEKDIIEMTFFPVVNEACRVFAEGIAVKAADLDIAGIMGMGFPPYRGGIMFWADSIGSKYIYSRLDEWSKAYGEFFKPCAFLAERGSKGVLLSAPVK 719
                                    16        26        36        46        56        66   |     -      | 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       | -  |    376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566        |-         -         -|      606       616       626       636       646       656       666       676       686       696       706       716   
                                                                                          70           83                                                                                                                                                                                                                                                                                      364  369                                                                                                                                                                                                           575                   597                                                                                                                          

   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 2WTB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: 6PGD_C (47)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MFP2_ARATH | Q9ZPI5)
molecular function
    GO:0003857    3-hydroxyacyl-CoA dehydrogenase activity    Catalysis of the reaction: (S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH + H(+).
    GO:0008692    3-hydroxybutyryl-CoA epimerase activity    Catalysis of the reaction: (S)-3-hydroxybutanoyl-CoA = (R)-3-hydroxybutanoyl-CoA.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004165    dodecenoyl-CoA delta-isomerase activity    Catalysis of the reaction: 3-cis-dodecenoyl-CoA = 2-trans-dodecenoyl-CoA.
    GO:0004300    enoyl-CoA hydratase activity    Catalysis of the reaction: (3S)-3-hydroxyacyl-CoA = trans-2-enoyl-CoA + H2O.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0016508    long-chain-enoyl-CoA hydratase activity    Catalysis of the reaction: a long-chain (3S)-3-hydroxyacyl-CoA = a long-chain trans-2-enoyl-CoA + H2O. A long-chain acyl-CoA is an acyl-CoA thioester where the acyl chain contains 13 to 22 carbon atoms.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0006635    fatty acid beta-oxidation    A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0009514    glyoxysome    A specialized form of peroxisome that contains the enzymes of the glyoxylate pathway. The glyoxysome is found in some plant cells, notably the cells of germinating seeds.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.
    GO:0009506    plasmodesma    A fine cytoplasmic channel, found in all higher plants, that connects the cytoplasm of one cell to that of an adjacent cell.

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