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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III FROM AQUIFEX AEOLICUS VF5
 
Authors :  T. S. Kumarevel, S. Kuramitsu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  08 Feb 07  (Deposition) - 14 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  3-Oxoacyl-[Acyl-Carrier-Protein] Synthase Iii, Fabh, Aquifex Aeolicus Vf5, Aq_1099, Lipid Metabolism, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. S. Kumarevel, S. Kuramitsu, S. Yokoyama
Crystal Structure Of 3-Oxoacyl-[Acyl-Carrier-Protein] Synthase Iii From Aquifex Aeolicus Vf5
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 3
    Chains: A, B
    EC Number: 2.3.1.41
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Strain: BL21 (DE3) CODONPLUS-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AQ_1099
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: 3-OXOACYL- [ACYL-CARRIER-PROTEIN] SYNTHASE III, BETA- KETOACYL-ACP SYNTHASE III, KAS III

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2EBD)

(-) Sites  (0, 0)

(no "Site" information available for 2EBD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:86 -Pro A:87
2Phe B:86 -Pro B:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EBD)

(-) Exons   (0, 0)

(no "Exon" information available for 2EBD)

(-) 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:309
 aligned with FABH_AQUAE | O67185 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:309
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300         
           FABH_AQUAE     1 MGTKIIGTGVYLPKNVLTNFDLEKIVDTSDEWITTRTGIKERRIAKEETITYMATQAAKEALREANLSPEELDLIILATLTPQKRFPSTACLVQAQLKAKGVYAFDISAACSGFIYALDIADSFIKSGKAKNVLVIGAEKLSEAVDWEDRSTCVLFGDGAGAVVVTRSEDKSDILATRMYAEGSLEELLHADNCGYIRMKGRELFKVAVRSMEEVCREVLEKAGVKPEEVSLVIPHQANVRIINALAEKLNIPKEKVFVNIQKYGNTSAASIPIALHEAIKEGKVKRGDLILMTAMGGGLTWGAVLLRY 309
               SCOP domains d2ebda1 A:1-172 automated matches                                                                                                                                           d2ebda2 A:173-309 automated matches                                                                                                       SCOP domains
               CATH domains 2ebdA01 A:1-169  [code=3.40.47.10, no name defined]                                                                                                                      -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...eeeehhhhhh....hhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhh.hhhhh.eeeee.........hhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhh.............eeeeeeeeee.....eeeeeeeee.hhhhh.eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeee...hhhhhhhhhhhh..hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ebd A   1 MGTKIIGTGVYLPKNVLTNFDLEKIVDTSDEWITTRTGIKERRIAKEETITYMATQAAKEALREANLSPEELDLIILATLTPQKRFPSTACLVQAQLKAKGVYAFDISAACSGFIYALDIADSFIKSGKAKNVLVIGAEKLSEAVDWEDRSTCVLFGDGAGAVVVTRSEDKSDILATRMYAEGSLEELLHADNCGYIRMKGRELFKVAVRSMEEVCREVLEKAGVKPEEVSLVIPHQANVRIINALAEKLNIPKEKVFVNIQKYGNTSAASIPIALHEAIKEGKVKRGDLILMTAMGGGLTWGAVLLRY 309
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300         


Chain B from PDB  Type:PROTEIN  Length:308
 aligned with FABH_AQUAE | O67185 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:308
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301        
           FABH_AQUAE     2 GTKIIGTGVYLPKNVLTNFDLEKIVDTSDEWITTRTGIKERRIAKEETITYMATQAAKEALREANLSPEELDLIILATLTPQKRFPSTACLVQAQLKAKGVYAFDISAACSGFIYALDIADSFIKSGKAKNVLVIGAEKLSEAVDWEDRSTCVLFGDGAGAVVVTRSEDKSDILATRMYAEGSLEELLHADNCGYIRMKGRELFKVAVRSMEEVCREVLEKAGVKPEEVSLVIPHQANVRIINALAEKLNIPKEKVFVNIQKYGNTSAASIPIALHEAIKEGKVKRGDLILMTAMGGGLTWGAVLLRY 309
               SCOP domains d2ebdb1 B:2-172 automated matches                                                                                                                                          d2ebdb2 B:173-309 automated matches                                                                                                       SCOP domains
               CATH domains 2ebdB01 B:2-169  [code=3.40.47.10, no name defined]                                                                                                                     -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee...eeeehhhhhh....hhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhh.hhhhh.eeeee.........hhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhh.............eeeeeeeeee.....eeeeeeee.hhhhhh.eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeee...hhhhhhhhhhhhh.hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeeehhheeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ebd B   2 GTKIIGTGVYLPKNVLTNFDLEKIVDTSDEWITTRTGIKERRIAKEETITYMATQAAKEALREANLSPEELDLIILATLTPQKRFPSTACLVQAQLKAKGVYAFDISAACSGFIYALDIADSFIKSGKAKNVLVIGAEKLSEAVDWEDRSTCVLFGDGAGAVVVTRSEDKSDILATRMYAEGSLEELLHADNCGYIRMKGRELFKVAVRSMEEVCREVLEKAGVKPEEVSLVIPHQANVRIINALAEKLNIPKEKVFVNIQKYGNTSAASIPIALHEAIKEGKVKRGDLILMTAMGGGLTWGAVLLRY 309
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FABH_AQUAE | O67185)
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:0033818    beta-ketoacyl-acyl-carrier-protein synthase III activity    Catalysis of the reaction: acetyl-CoA + malonyl-[acyl-carrier protein] = acetoacyl-[acyl-carrier protein] + CoA + CO2.
    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).
biological process
    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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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