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(-) Description

Title :  STRUCTURE OF MITOCHONDRIAL BETA-KETOACYL SYNTHASE
 
Authors :  G. Bunkoczi, X. Wu, C. Smee, O. Gileadi, C. Arrowsmith, A. Edwards, M. Su J. Weigelt, F. Von Delft, U. Oppermann
Date :  12 Dec 05  (Deposition) - 13 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Fatty Acid Synthesis, Mitochondria, Ketoacyl Synthase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Bunkoczi, X. Wu, C. Smee, O. Gileadi, C. Arrowsmith, A. Edwards, M. Sundstrom, J. Weigelt, F. Von Delft, U. Oppermann
Structure Of Mitochondrial Beta-Ketoacyl Synthase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MITOCHONDRIAL BETA-KETOACYL SYNTHASE
    ChainsA
    EC Number2.3.1.41
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cell LineDE3-R3
    Expression System PlasmidPNIC-BSA4
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CSD1Mod. Amino Acid3-SULFINOALANINE
2NI1Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CSD2Mod. Amino Acid3-SULFINOALANINE
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:26 , HIS A:210 , HOH A:2003 , HOH A:2127BINDING SITE FOR RESIDUE NI A1445

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C9H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C9H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036064F106IOXSM_HUMANUnclassified  ---AF91I
2CancerSNPVAR_OXSM_HUMAN_CCDS2643_1_01 *F106IOXSM_HUMANDisease (Breast cancer)  ---AF91I
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036064F106IOXSM_HUMANUnclassified  ---AF91I
2CancerSNPVAR_OXSM_HUMAN_CCDS2643_1_01 *F106IOXSM_HUMANDisease (Breast cancer)  ---AF91I
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1B_KETOACYL_SYNTHASEPS00606 Beta-ketoacyl synthases active site.OXSM_HUMAN200-216  1A:185-201
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1B_KETOACYL_SYNTHASEPS00606 Beta-ketoacyl synthases active site.OXSM_HUMAN200-216  2A:185-201

(-) Exons   (2, 2)

Asymmetric Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4aENST000002807014aENSE00000997589chr3:25831571-2583163868OXSM_HUMAN-00--
1.6eENST000002807016eENSE00000997590chr3:25832481-258334881008OXSM_HUMAN1-3263261A:18-311 (gaps)297
1.7bENST000002807017bENSE00000997591chr3:25835583-25836025443OXSM_HUMAN326-4591341A:311-444134

(-) 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:427
 aligned with OXSM_HUMAN | Q9NWU1 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:430
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459
           OXSM_HUMAN    30 KFFGTVPISRLHRRVVITGIGLVTPLGVGTHLVWDRLIGGESGIVSLVGEEYKSIPCSVAAYVPRGSDEGQFNEQNFVSKSDIKSMSSPTIMAIGAAELAMKDSGWHPQSEADQVATGVAIGMGMIPLEVVSETALNFQTKGYNKVSPFFVPKILVNMAAGQVSIRYKLKGPNHAVSTACTTGAHAVGDSFRFIAHGDADVMVAGGTDSCISPLSLAGFSRARALSTNSDPKLACRPFHPKRDGFVMGEGAAVLVLEEYEHAVQRRARIYAEVLGYGLSGDAGHITAPDPEGEGALRCMAAALKDAGVQPEEISYINAHATSTPLGDAAENKAIKHLFKDHAYALAVSSTKGATGHLLGAAGAVEAAFTTLACYYQKLPPTLNLDCSEPEFDLNYVPLKAQEWKTEKRFIGLTNSFGFGGTNATLCIAGL 459
               SCOP domains d2c9ha   1 A:18-281 automated matches                                                                                                                                                                                                                                      d2c9ha2 A:282-444 automated matches                                                                                                                                 SCOP domains
               CATH domains 2c9hA0   1 A:18-288  [code=3.40.47.10, no name defined]                                                                                                                                                                                                                           2c9hA02 A:289-444  [code=3.40.47.10, no name defined]                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......---.....eeeeeeeeee..eehhhhhhhhhhh....eee..hhhhh.....eee...........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhheeeeeee...hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhh...........................eeeeeeeeehhhhhhhh....eeeeeeeeee...........hhhhhhhhhhhhhhhh.hhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhh.eee.hhhhhh.hhhhhhhhhhhhhhhhhhhhee......................ee.......eeeeeeee...eeeeeeee.. Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------------------------------------I----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------I----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------B_KETOACYL_SYNTHA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6e  PDB: A:18-311 (gaps) UniProt: 1-326 [INCOMPLETE]                                                                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7b  PDB: A:311-444 UniProt: 326-459                                                                                             Transcript 1 (2)
                 2c9h A  18 LYFQSM---RLHRRVVITGIGLVTPLGVGTHLVWDRLIGGESGIVSLVGEEYKSIPCSVAAYVPRGSDEGQFNEQNFVSKSDIKSMSSPTIMAIGAAELAMKDSGWHPQSEADQVATGVAIGMGMIPLEVVSETALNFQTKGYNKVSPFFVPKILVNMAAGQVSIRYKLKGPNHAVSTAcTTGAHAVGDSFRFIAHGDADVMVAGGTDSCISPLSLAGFSRARALSTNSDPKLACRPFHPKRDGFVMGEGAAVLVLEEYEHAVQRRARIYAEVLGYGLSGDAGHITAPDPEGEGALRCMAAALKDAGVQPEEISYINAHATSTPLGDAAENKAIKHLFKDHAYALAVSSTKGATGHLLGAAGAVEAAFTTLACYYQKLPPTLNLDCSEPEFDLNYVPLKAQEWKTEKRFIGLTNSFGFGGTNATLCIAGL 444
                                 |  24        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       424       434       444
                                23  24                                                                                                                                                                       194-CSD                                                                                                                                                                                                                                                      

   Legend:   → Mismatch (orange background)
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  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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C9H)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (OXSM_HUMAN | Q9NWU1)
molecular function
    GO:0004315    3-oxoacyl-[acyl-carrier-protein] synthase activity    Catalysis of the reaction: acyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = 3-oxoacyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein].
    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:0006637    acyl-CoA metabolic process    The chemical reactions and pathways involving acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with an acyl group.
    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: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:0051792    medium-chain fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of any fatty acid with a chain length of between C6 and C12.
    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:0051790    short-chain fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of fatty acids with a chain length of less than C6.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        OXSM_HUMAN | Q9NWU12iwy 2iwz

(-) Related Entries Specified in the PDB File

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