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(-) Description

Title :  THE 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE DIMERIC PEROXISOMAL THIOLASE OF SACCHAROMYCES CEREVISIAE
 
Authors :  M. Mathieu, R. K. Wierenga
Date :  15 Mar 97  (Deposition) - 16 Jun 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Thiolase, Fatty Acid Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Mathieu, Y. Modis, J. P. Zeelen, C. K. Engel, R. A. Abagyan, A. Ahlberg, B. Rasmussen, V. S. Lamzin, W. H. Kunau, R. K. Wierenga
The 1. 8 A Crystal Structure Of The Dimeric Peroxisomal 3-Ketoacyl-Coa Thiolase Of Saccharomyces Cerevisiae: Implications For Substrate Binding And Reaction Mechanism.
J. Mol. Biol. V. 273 714 1997
PubMed-ID: 9402066  |  Reference-DOI: 10.1006/JMBI.1997.1331
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-KETOACETYL-COA THIOLASE
    Cellular LocationPEROXISOME
    ChainsA, B
    EC Number2.3.1.16
    OrganellePEROXISOME
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:124 , CYS A:182 , LEU A:183 , ILE A:184 , HOH A:533 , HOH A:615BINDING SITE FOR RESIDUE MRD A 501
2AC2SOFTWAREGLN B:124 , CYS B:182 , LEU B:183 , ILE B:184 , HOH B:534 , HOH B:642BINDING SITE FOR RESIDUE MRD B 502
3AVAUNKNOWNCYS A:125 , HIS A:375 , CYS A:403ACTIVE SITE IN CHAIN A.
4AVBUNKNOWNCYS B:125 , HIS B:375 , CYS B:403ACTIVE SITE IN CHAIN B.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1AFW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1AFW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AFW)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOLASE_1PS00098 Thiolases acyl-enzyme intermediate signature.THIK_YEAST121-139
 
  2A:121-139
B:121-139
2THIOLASE_2PS00737 Thiolases signature 2.THIK_YEAST365-381
 
  2A:365-381
B:365-381
3THIOLASE_3PS00099 Thiolases active site.THIK_YEAST398-411
 
  2A:398-411
B:398-411

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YIL160C1YIL160C.1IX:41444-401911254THIK_YEAST1-4174172A:25-417 (gaps)
B:25-417
393
393

(-) 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:390
 aligned with THIK_YEAST | P27796 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:393
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414   
           THIK_YEAST    25 KNSLLEKRPEDVVIVAANRSAIGKGFKGAFKDVNTDYLLYNFLNEFIGRFPEPLRADLNLIEEVACGNVLNVGAGATEHRAACLASGIPYSTPFVALNRQCSSGLTAVNDIANKIKVGQIDIGLALGVESMTNNYKNVNPLGMISSEELQKNREAKKCLIPMGITNENVAANFKISRKDQDEFAANSYQKAYKAKNEGLFEDEILPIKLPDGSICQSDEGPRPNVTAESLSSIRPAFIKDRGTTTAGNASQVSDGVAGVLLARRSVANQLNLPVLGRYIDFQTVGVPPEIMGVGPAYAIPKVLEATGLQVQDIDIFEINEAFAAQALYCIHKLGIDLNKVNPRGGAIALGHPLGCTGARQVATILRELKKDQIGVVSMCIGTGMGAAAIFIKE 417
               SCOP domains d1afwa1 A:25-293 Thiolase                                                                                                                                                                                                                                                    d1afwa2 A:294-417 Thiolase                                                                                                   SCOP domains
               CATH domains ---1afwA01 A:28-160,A:223-302  [code=3.40.47.10, no name defined]                                                                       -------------1afwA02 A:174-222,A:303-414                      1afwA01 A:28-160,A:223-302  [code=3.40.4   7.10, no name defined]               1afwA02 A:174-222,A:303-414  [code=3.40.47.10, no name defined]                                                 --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeee...............hhhhhhhhhhhhhh...hhhhhhhhh..eeeee....hhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhhhhhhhh....eeeeeeeeehhhhhhh.........hhhhh...hhhhh..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..............................hhhhhh......---............eeeeeeeeeehhhhhh......eeeeeeeeee..hhhhhhhhhhhhhhhhhhh...hhh..eeee....hhhhhhhhhhh...hhh......hhhh......hhhhhhhhhhhh.....eeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------THIOLASE_1         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOLASE_2       ----------------THIOLASE_3    ------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:25-417 (gaps) UniProt: 1-417 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                Transcript 1
                 1afw A  25 KNSLLEKRPEDVVIVAANRSAIGKGFKGAFKDVNTDYLLYNFLNEFIGRFPEPLRADLNLIEEVACGNVLNVGAGATEHRAACLASGIPYSTPFVALNRQCSSGLTAVNDIANKIKVGQIDIGLALGVESMTNNYKNVNPLGMISSEELQKNREAKKCLIPMGITNENVAANFKISRKDQDEFAANSYQKAYKAKNEGLFEDEILPIKLPDGSICQSDEGPRPNVTAESLSSIRPAFI---GTTTAGNASQVSDGVAGVLLARRSVANQLNLPVLGRYIDFQTVGVPPEIMGVGPAYAIPKVLEATGLQVQDIDIFEINEAFAAQALYCIHKLGIDLNKVNPRGGAIALGHPLGCTGARQVATILRELKKDQIGVVSMCIGTGMGAAAIFIKE 417
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       | - |     274       284       294       304       314       324       334       344       354       364       374       384       394       404       414   
                                                                                                                                                                                                                                                                       262 266                                                                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:393
 aligned with THIK_YEAST | P27796 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:393
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414   
           THIK_YEAST    25 KNSLLEKRPEDVVIVAANRSAIGKGFKGAFKDVNTDYLLYNFLNEFIGRFPEPLRADLNLIEEVACGNVLNVGAGATEHRAACLASGIPYSTPFVALNRQCSSGLTAVNDIANKIKVGQIDIGLALGVESMTNNYKNVNPLGMISSEELQKNREAKKCLIPMGITNENVAANFKISRKDQDEFAANSYQKAYKAKNEGLFEDEILPIKLPDGSICQSDEGPRPNVTAESLSSIRPAFIKDRGTTTAGNASQVSDGVAGVLLARRSVANQLNLPVLGRYIDFQTVGVPPEIMGVGPAYAIPKVLEATGLQVQDIDIFEINEAFAAQALYCIHKLGIDLNKVNPRGGAIALGHPLGCTGARQVATILRELKKDQIGVVSMCIGTGMGAAAIFIKE 417
               SCOP domains d1afwb1 B:25-293 Thiolase                                                                                                                                                                                                                                                    d1afwb2 B:294-417 Thiolase                                                                                                   SCOP domains
               CATH domains ---1afwB01 B:28-160,B:223-302  [code=3.40.47.10, no name defined]                                                                       -------------1afwB02 B:174-222,B:303-414                      1afwB01 B:28-160,B:223-302  [code=3.40.47.10, no name defined]                  1afwB02 B:174-222,B:303-414  [code=3.40.47.10, no name defined]                                                 --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeee...............hhhhhhhhhhhhhhh..hhhhh.hhh..eeeee....hhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhhhhhhh.....eeeeeeeeehhhhhhh.........hhhh....hhhhh..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..............................hhhhhh.....................eeeeeeeeeehhhhhhh.....eeeeeeeeee..hhhhhhhhhhhhhhhhhhh...hhh..eeee....hhhhhhhhhhh...hhh......hhhh......hhhhhhhhhhhh.....eeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------THIOLASE_1         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOLASE_2       ----------------THIOLASE_3    ------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:25-417 UniProt: 1-417 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                       Transcript 1
                 1afw B  25 KNSLLEKRPEDVVIVAANRSAIGKGFKGAFKDVNTDYLLYNFLNEFIGRFPEPLRADLNLIEEVACGNVLNVGAGATEHRAACLASGIPYSTPFVALNRQCSSGLTAVNDIANKIKVGQIDIGLALGVESMTNNYKNVNPLGMISSEELQKNREAKKCLIPMGITNENVAANFKISRKDQDEFAANSYQKAYKAKNEGLFEDEILPIKLPDGSICQSDEGPRPNVTAESLSSIRPAFIKDRGTTTAGNASQVSDGVAGVLLARRSVANQLNLPVLGRYIDFQTVGVPPEIMGVGPAYAIPKVLEATGLQVQDIDIFEINEAFAAQALYCIHKLGIDLNKVNPRGGAIALGHPLGCTGARQVATILRELKKDQIGVVSMCIGTGMGAAAIFIKE 417
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414   

   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AFW)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (THIK_YEAST | P27796)
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:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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: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.
cellular component
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005782    peroxisomal matrix    The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        THIK_YEAST | P277961afy 1pxt 3w15

(-) Related Entries Specified in the PDB File

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