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(-) Description

Title :  CRYSTAL STRUCTURE OF PEROXISOMAL KAT2 FROM ARABIDOPSIS THALIANA
 
Authors :  V. E. Pye, C. E. Christensen, J. H. Dyer, S. Arent, A. Henriksen
Date :  01 Oct 09  (Deposition) - 12 May 10  (Release) - 04 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cysteine Oxidation, Fatty Acid Metabolism, Oxylipin Biosynthesis, Plant Lipid Metabolism, Fatty Acid Biosynthesis, Acyltransferase, Lipid Metabolism, Transferase, Beta Oxidation, Lipid Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. E. Pye, C. E. Christensen, J. H. Dyer, S. Arent, A. Henriksen
Peroxisomal Plant 3-Ketoacyl-Coa Thiolases Structure And Activity Are Regulated By A Sensitive Redox Switch
J. Biol. Chem. V. 285 24078 2010
PubMed-ID: 20463027  |  Reference-DOI: 10.1074/JBC.M110.106013

(-) Compounds

Molecule 1 - 3-KETOACYL-COA THIOLASE 2, PEROXISOMAL
    Atcc77500
    ChainsA, B
    EC Number2.3.1.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainPET46 EK/LIC
    Expression System Taxid562
    Expression System VariantROSETTAGAMI2(DE3)
    FragmentRESIDUES 36-462
    OrganellePEROXISOME
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymBETA-KETOTHIOLASE 2, ACETYL-COA ACYLTRANSFERASE 2, PEROXISOMAL 3-OXOACYL-COA THIOLASE 2, PEROXISOME DEFECTIVE PROTEIN 1,3-KETOACYL-COA THIOLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric/Biological Unit (1, 9)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:50 , HOH A:2595 , HOH A:2596BINDING SITE FOR RESIDUE EDO A1449
2AC2SOFTWAREPRO A:75 , ALA A:107 , PRO A:108 , GLN A:111 , ARG A:112 , GLU A:115 , THR A:170 , ASN A:171 , HOH A:2597BINDING SITE FOR RESIDUE EDO A1450
3AC3SOFTWAREGLY A:155 , ASP A:158 , HOH A:2255 , HOH A:2454BINDING SITE FOR RESIDUE EDO A1451
4AC4SOFTWAREALA A:217 , SER A:221 , LYS A:224 , GLU A:362 , PHE A:368 , HOH A:2527 , HOH A:2599BINDING SITE FOR RESIDUE EDO A1452
5AC5SOFTWARECYS A:192 , LEU A:194 , MET A:196 , THR A:199 , PRO A:330 , MET A:333 , THR A:428 , HOH A:2600BINDING SITE FOR RESIDUE EDO A1453
6AC6SOFTWAREGLN A:216 , VAL A:219 , LEU A:270 , HOH A:2358 , HOH A:2601 , HOH B:2531BINDING SITE FOR RESIDUE EDO A1454
7AC7SOFTWAREALA B:217 , ASP B:220 , SER B:221 , LYS B:224 , GLU B:362 , PHE B:368 , HOH B:2297 , HOH B:2532BINDING SITE FOR RESIDUE EDO B1449
8AC8SOFTWARELEU B:47 , ARG B:306 , VAL B:316 , VAL B:319 , ARG B:321 , GLY B:439 , ASP B:440 , GLU B:444BINDING SITE FOR RESIDUE EDO B1450
9AC9SOFTWAREPHE A:156 , THR B:322 , PHE B:323 , ALA B:347 , HOH B:2424 , HOH B:2533BINDING SITE FOR RESIDUE EDO B1451

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WU9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WU9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WU9)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOLASE_1PS00098 Thiolases acyl-enzyme intermediate signature.THIK2_ARATH134-152
 
  2A:134-152
B:134-152
2THIOLASE_2PS00737 Thiolases signature 2.THIK2_ARATH383-399
 
  2A:383-399
B:383-399
3THIOLASE_3PS00099 Thiolases active site.THIK2_ARATH420-433
 
  2A:420-433
B:420-433

(-) Exons   (0, 0)

(no "Exon" information available for 2WU9)

(-) 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:403
 aligned with THIK2_ARATH | Q56WD9 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:403
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445   
          THIK2_ARATH    46 SLYGDDVVIVAAHRTPLCKSKRGNFKDTYPDDLLAPVLRALIEKTNLNPSEVGDIVVGTVLAPGSQRASECRMAAFYAGFPETVAVRTVNRQCSSGLQAVADVAAAIKAGFYDIGIGAGLESMTTNPMAWEGSVNPAVKKFAQAQNCLLPMGVTSENVAQRFGVSRQEQDQAAVDSHRKAAAATAAGKFKDEIIPVKTKLVDPKTGDEKPITVSVDDGIRPTTTLASLGKLKPVFKKDGTTTAGNSSQVSDGAGAVLLMKRSVAMQKGLPVLGVFRTFAAVGVDPAIMGIGPAVAIPAAVKAAGLELDDIDLFEINEAFASQFVYCRNKLGLDPEKINVNGGAMAIGHPLGATGARCVATLLHEMKRRGKDCRFGVVSMCIGTGMGAAAVFERGDGVDELRNA 448
               SCOP domains d2wu9a1 A:46-311 automated matches                                                                                                                                                                                                                                        d2wu9a2 A:312-448 automated matches                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eeeeeeee...ee.........hhhhhhhhhhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.........eeeeee......eeeeee..........hhhhhhh...........hhhh....eeeeeeeeeeehhhhhhhh....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhhh.hhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhh....eeeeeeee...eeeeeeeee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------THIOLASE_1         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOLASE_2       --------------------THIOLASE_3    --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wu9 A  46 SLYGDDVVIVAAHRTPLCKSKRGNFKDTYPDDLLAPVLRALIEKTNLNPSEVGDIVVGTVLAPGSQRASECRMAAFYAGFPETVAVRTVNRQCSSGLQAVADVAAAIKAGFYDIGIGAGLESMTTNPMAWEGSVNPAVKKFAQAQNCLLPMGVTSENVAQRFGVSRQEQDQAAVDSHRKAAAATAAGKFKDEIIPVKTKLVDPKTGDEKPITVSVDDGIRPTTTLASLGKLKPVFKKDGTTTAGNSSQVSDGAGAVLLMKRSVAMQKGLPVLGVFRTFAAVGVDPAIMGIGPAVAIPAAVKAAGLELDDIDLFEINEAFASQFVYCRNKLGLDPEKINVNGGAMAIGHPLGATGARCVATLLHEMKRRGKDCRFGVVSMCIGTGMGAAAVFERGDGVDELRNA 448
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445   

Chain B from PDB  Type:PROTEIN  Length:402
 aligned with THIK2_ARATH | Q56WD9 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:402
                                    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  
          THIK2_ARATH    47 LYGDDVVIVAAHRTPLCKSKRGNFKDTYPDDLLAPVLRALIEKTNLNPSEVGDIVVGTVLAPGSQRASECRMAAFYAGFPETVAVRTVNRQCSSGLQAVADVAAAIKAGFYDIGIGAGLESMTTNPMAWEGSVNPAVKKFAQAQNCLLPMGVTSENVAQRFGVSRQEQDQAAVDSHRKAAAATAAGKFKDEIIPVKTKLVDPKTGDEKPITVSVDDGIRPTTTLASLGKLKPVFKKDGTTTAGNSSQVSDGAGAVLLMKRSVAMQKGLPVLGVFRTFAAVGVDPAIMGIGPAVAIPAAVKAAGLELDDIDLFEINEAFASQFVYCRNKLGLDPEKINVNGGAMAIGHPLGATGARCVATLLHEMKRRGKDCRFGVVSMCIGTGMGAAAVFERGDGVDELRNA 448
               SCOP domains d2wu9b1 B:47-311 automated matches                                                                                                                                                                                                                                       d2wu9b2 B:312-448 automated matches                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --Thiolase_N-2wu9B03 B:49-307                                                                                                                                                                                                                                        ------Thiolase_C-2wu9B01 B:314-438                                                                                                 ---------- Pfam domains (1)
           Pfam domains (2) --Thiolase_N-2wu9B04 B:49-307                                                                                                                                                                                                                                        ------Thiolase_C-2wu9B02 B:314-438                                                                                                 ---------- Pfam domains (2)
         Sec.struct. author ............................hhhhhhhhhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.........eeeeee......eeeeee..........hhhhhhh...........hhhh...............hhhhhhhh...............hhhhhhhhhhhhhhhhhhhh..hhhhh........hhhhhhhhhhhh..hhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhh...........................hhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------THIOLASE_1         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOLASE_2       --------------------THIOLASE_3    --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wu9 B  47 LYGDDVVIVAAHRTPLCKSKRGNFKDTYPDDLLAPVLRALIEKTNLNPSEVGDIVVGTVLAPGSQRASECRMAAFYAGFPETVAVRTVNRQCSSGLQAVADVAAAIKAGFYDIGIGAGLESMTTNPMAWEGSVNPAVKKFAQAQNCLLPMGVTSENVAQRFGVSRQEQDQAAVDSHRKAAAATAAGKFKDEIIPVKTKLVDPKTGDEKPITVSVDDGIRPTTTLASLGKLKPVFKKDGTTTAGNSSQVSDGAGAVLLMKRSVAMQKGLPVLGVFRTFAAVGVDPAIMGIGPAVAIPAAVKAAGLELDDIDLFEINEAFASQFVYCRNKLGLDPEKINVNGGAMAIGHPLGATGARCVATLLHEMKRRGKDCRFGVVSMCIGTGMGAAAVFERGDGVDELRNA 448
                                    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  

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WU9)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Thiolase (72)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (THIK2_ARATH | Q56WD9)
molecular function
    GO:0003988    acetyl-CoA C-acyltransferase activity    Catalysis of the reaction: acyl-CoA + acetyl-CoA = CoA + 3-oxoacyl-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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0016747    transferase activity, transferring acyl groups other than amino-acyl groups    Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
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:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    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:0010111    glyoxysome organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the glyoxysome. A glyoxysome is a microbody that contains the enzymes of the glyoxylate pathway.
    GO:0009695    jasmonic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of jasmonic acid, a fatty acid derivative.
    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:0031408    oxylipin biosynthetic process    The chemical reactions and pathways resulting in the formation of any oxylipin, any of a group of biologically active compounds formed by oxidative metabolism of polyunsaturated fatty acids.
    GO:0009789    positive regulation of abscisic acid-activated signaling pathway    Any process that activates or increases the frequency, rate or extent of abscisic acid (ABA) signaling.
    GO:0009611    response to wounding    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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:0005774    vacuolar membrane    The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.

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 Related Entries

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

UniProtKB/Swiss-Prot
        THIK2_ARATH | Q56WD92c7y 2c7z

(-) Related Entries Specified in the PDB File

2c7y PLANT ENZYME
2c7z PLANT ENZYME CRYSTAL FORM II
2wua STRUCTURE OF THE PEROXISOMAL 3-KETOACYL-COA THIOLASE FROM SUNFLOWER