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(-) Description

Title :  HUMAN MITOCHONDRIAL BETA-KETOACYL ACP SYNTHASE
 
Authors :  C. E. Christensen, B. B. Kragelund, P. Von Wettstein-Knowles, A. Hen
Date :  05 Jul 06  (Deposition) - 06 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mitochondria, Mitochondrion, Lipid Synthesis, Fatty Acid Synthesis, Fatty Acid Biosynthesis, Beta-Ketoacyl Acp Synthase, Transit Peptide, Acyltransferase, Claisen Condensation, Kas, Cerulenin, Transferase, Homo Sapiens (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. E. Christensen, B. B. Kragelund, P. Von Wettstein-Knowles, A. Henriksen
Structure Of The Human Beta-Ketoacyl [Acp] Synthase From The Mitochondrial Type Ii Fatty Acid Synthase.
Protein Sci. V. 16 261 2007
PubMed-ID: 17242430  |  Reference-DOI: 10.1110/PS.062473707
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE
    ChainsA, B
    EC Number2.3.1.41
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE30
    Expression System StrainK12
    Expression System Taxid562
    Expression System VariantM15(PREP4)
    FragmentRESIDUES 38-459
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsSUMIO SUGANO, UNIVERSITY OF TOKYO
    SynonymBETA-KETOACYL SYNTHASE

 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
1NH42Ligand/IonAMMONIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:346 , ALA A:347 , GLU A:394 , THR A:442 , ASN A:443BINDING SITE FOR RESIDUE NH4 A1460
2AC2SOFTWAREASN B:346 , ALA B:347 , GLU B:394 , THR B:442 , ASN B:443BINDING SITE FOR RESIDUE NH4 B1460

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036064F106IOXSM_HUMANUnclassified  ---A/BF106I
2CancerSNPVAR_OXSM_HUMAN_CCDS2643_1_01 *F106IOXSM_HUMANDisease (Breast cancer)  ---A/BF106I
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1B_KETOACYL_SYNTHASEPS00606 Beta-ketoacyl synthases active site.OXSM_HUMAN200-216
 
  2A:200-216
B:200-216

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4aENST000002807014aENSE00000997589chr3:25831571-2583163868OXSM_HUMAN-00--
1.6eENST000002807016eENSE00000997590chr3:25832481-258334881008OXSM_HUMAN1-3263262A:-4-326 (gaps)
B:-1-326 (gaps)
302
298
1.7bENST000002807017bENSE00000997591chr3:25835583-25836025443OXSM_HUMAN326-4591342A:326-459 (gaps)
B:326-459
134
134

(-) 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:420
 aligned with OXSM_HUMAN | Q9NWU1 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:435
                                    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       454     
           OXSM_HUMAN    25 LRSKRKFFGTVPISRLHRRVVITGIGLVTPLGVGTHLVWDRLIGGESGIVSLVGEEYKSIPCSVAAYVPRGSDEGQFNEQNFVSKSDIKSMSSPTIMAIGAAELAMKDSGWHPQSEADQVATGVAIGMGMIPLEVVSETALNFQTKGYNKVSPFFVPKILVNMAAGQVSIRYKLKGPNHAVSTACTTGAHAVGDSFRFIAHGDADVMVAGGTDSCISPLSLAGFSRARALSTNSDPKLACRPFHPKRDGFVMGEGAAVLVLEEYEHAVQRRARIYAEVLGYGLSGDAGHITAPDPEGEGALRCMAAALKDAGVQPEEISYINAHATSTPLGDAAENKAIKHLFKDHAYALAVSSTKGATGHLLGAAGAVEAAFTTLACYYQKLPPTLNLDCSEPEFDLNYVPLKAQEWKTEKRFIGLTNSFGFGGTNATLCIAGL 459
               SCOP domains d2iw         ya1 A:-4-296 automated matches                                                                                                                                                                                                                                     d2iwya2 A:297-459    automated matches                                                                                                                              SCOP domains
               CATH domains 2iwy         A01 A:-4-303  [code=3.40.47.10, no name defined]                                                                                                                                                                                                                          2iwyA02 A:3   04-459  [code=3.40.47.10, no name defined]                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...e---------eee...eeeeeeeeee..eehhhhhhhhhhh....eee..hhhhhhh...eee...........hhhhh.........hhhhhhhhhhhhhhhhhhh....hhhhhhheeeeeee...hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhh..........................eeeeeeeeehhhhhhh.....eeeeeeeeee.....---...hhhhhhhhhhhhhhhh.hhhhh.eee.....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:-4-326 (gaps) UniProt: 1-326 [INCOMPLETE]                                                                                                                                                                                                                                                   ------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7b  PDB: A:326-459 (gaps) UniProt: 326-459                                                                                      Transcript 1 (2)
                 2iwy A  -4 IEGR---------SRLHRRVVITGIGLVTPLGVGTHLVWDRLIGGESGIVSLVGEEYKSIPCSVAAYVPRGSDEGQFNEQNFVSKSDIKSMSSPTIMAIGAAELAMKDSGWHPQSEADQVATGVAIGMGMIPLEVVSETALNFQTKGYNKVSPFFVPKILVNMAAGQVSIRYKLKGPNHAVSTACTTGAHAVGDSFRFIAHGDADVMVAGGTDSCISPLSLAGFSRARALSTNSDPKLACRPFHPKRDGFVMGEGAAVLVLEEYEHAVQRRARIYAEVLGYGLSGDAGHI---DPEGEGALRCMAAALKDAGVQPEEISYINAHATSTPLGDAAENKAIKHLFKDHAYALAVSSTKGATGHLLGAAGAVEAAFTTLACYYQKLPPTLNLDCSEPEFDLNYVPLKAQEW---KRFIGLTNSFGFGGTNATLCIAGL 459
                               |     -   |    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       | - |     444       454     
                              -1        38                                                                                                                                                                                                                                                                                 314 318                                                                                                               432 436                       

Chain B from PDB  Type:PROTEIN  Length:423
 aligned with OXSM_HUMAN | Q9NWU1 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:431
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458 
           OXSM_HUMAN    29 RKFFGTVPISRLHRRVVITGIGLVTPLGVGTHLVWDRLIGGESGIVSLVGEEYKSIPCSVAAYVPRGSDEGQFNEQNFVSKSDIKSMSSPTIMAIGAAELAMKDSGWHPQSEADQVATGVAIGMGMIPLEVVSETALNFQTKGYNKVSPFFVPKILVNMAAGQVSIRYKLKGPNHAVSTACTTGAHAVGDSFRFIAHGDADVMVAGGTDSCISPLSLAGFSRARALSTNSDPKLACRPFHPKRDGFVMGEGAAVLVLEEYEHAVQRRARIYAEVLGYGLSGDAGHITAPDPEGEGALRCMAAALKDAGVQPEEISYINAHATSTPLGDAAENKAIKHLFKDHAYALAVSSTKGATGHLLGAAGAVEAAFTTLACYYQKLPPTLNLDCSEPEFDLNYVPLKAQEWKTEKRFIGLTNSFGFGGTNATLCIAGL 459
               SCOP domains d        2iwyb1 B:-1-296 automated matches                                                                                                                                                                                                                                  d2iwyb2 B:297-459 automated matches                                                                                                                                 SCOP domains
               CATH domains 2        iwyB01 B:-1-303  [code=3.40.47.10, no name defined]                                                                                                                                                                                                                       2iwyB02 B:304-459  [code=3.40.47.10, no name defined]                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------eeee..eeeeeeeeee..eehhhhhhhhhhh....eee..hhhhh.....eee...........hhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhheeeeeee...hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhh...........................eeeeeeeeehhhhhhh.....eeeeeeeeee...........hhhhhhhhhhhhhhhh.hhhhh.eee.....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: B:-1-326 (gaps) UniProt: 1-326 [INCOMPLETE]                                                                                                                                                                                                                                               ------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7b  PDB: B:326-459 UniProt: 326-459                                                                                             Transcript 1 (2)
                 2iwy B  -1 R--------SRLHRRVVITGIGLVTPLGVGTHLVWDRLIGGESGIVSLVGEEYKSIPCSVAAYVPRGSDEGQFNEQNFVSKSDIKSMSSPTIMAIGAAELAMKDSGWHPQSEADQVATGVAIGMGMIPLEVVSETALNFQTKGYNKVSPFFVPKILVNMAAGQVSIRYKLKGPNHAVSTACTTGAHAVGDSFRFIAHGDADVMVAGGTDSCISPLSLAGFSRARALSTNSDPKLACRPFHPKRDGFVMGEGAAVLVLEEYEHAVQRRARIYAEVLGYGLSGDAGHITAPDPEGEGALRCMAAALKDAGVQPEEISYINAHATSTPLGDAAENKAIKHLFKDHAYALAVSSTKGATGHLLGAAGAVEAAFTTLACYYQKLPPTLNLDCSEPEFDLNYVPLKAQEWKTEKRFIGLTNSFGFGGTNATLCIAGL 459
                            |       38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458 
                           -1       38                                                                                                                                                                                                                                                                                                                                                                                                                                     

   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 2IWY)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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 | Q9NWU12c9h 2iwz

(-) Related Entries Specified in the PDB File

2c9h STRUCTURE OF MITOCHONDRIAL BETA-KETOACYL SYNTHASE
2iwz HUMAN MITOCHONDRIAL BETA-KETOACYL ACP SYNTHASE COMPLEXED WITH HEXANOIC ACID
2ix4 ARABIDOPSIS THALIANA MITOCHONDRIAL BETA-KETOACYL ACP SYNTHASE HEXANOIC ACID COMPLEX