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(-) Description

Title :  CRYSTAL STRUCTURE OF CERULENIN BOUND XANTHOMONAS CAMPESTRI OLEA (SOAK)
 
Authors :  B. R. Goblirsch, C. M. Wilmot
Date :  16 May 11  (Deposition) - 16 May 12  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Non-Decarboxylative Claisen Condensation Reaction, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. R. Goblirsch, J. A. Frias, L. P. Wackett, C. M. Wilmot
Crystal Structures Of Xanthomonas Campestris Olea Reveal Features That Promote Head-To-Head Condensation Of Two Long-Chain Fatty Acids.
Biochemistry V. 51 4138 2012
PubMed-ID: 22524624  |  Reference-DOI: 10.1021/BI300386M

(-) Compounds

Molecule 1 - 3-OXOACYL-[ACP] SYNTHASE III
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FABH, XCC0212
    Organism Scientific: XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS
    Organism Taxid: 340

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CER2Ligand/Ion(2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:142 , CYS A:143 , CYS A:239 , LEU A:253 , HIS A:285 , VAL A:287 , HIS A:291 , ASN A:315 , ILE A:345 , GLY A:346 , SER A:347 , HOH A:539 , HOH A:540 , HOH A:581 , GLU B:117 , HOH B:486BINDING SITE FOR RESIDUE CER A 1
2AC2SOFTWARELYS A:297 , SER A:298 , HOH A:590BINDING SITE FOR RESIDUE PEG A 359
3AC3SOFTWAREGLU A:117 , HOH B:551BINDING SITE FOR RESIDUE PEG A 360
4AC4SOFTWAREHOH A:3 , GLU A:117 , ALA B:142 , CYS B:143 , LEU B:253 , ILE B:258 , HIS B:285 , VAL B:287 , ASN B:315 , GLY B:346 , SER B:347 , HOH B:485BINDING SITE FOR RESIDUE CER B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S20)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:117 -Pro A:118
2Gly A:348 -Leu A:349
3Glu B:117 -Pro B:118
4Gly B:348 -Leu B:349

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S20)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S20)

(-) Exons   (0, 0)

(no "Exon" information available for 3S20)

(-) 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:344
 aligned with Q8PDX2_XANCP | Q8PDX2 from UniProtKB/TrEMBL  Length:338

    Alignment length:344
                                  1                                                                                                                                                                                                                                                                                                                                                 
                                  |  4        14        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    
         Q8PDX2_XANCP     - ------MLFQNVSIAGLAHIDAPHTLTSKEINERLQPTYDRLGIKTDVLGDVAGIHARRLWDQDVQASDAATQAARKALIDANIGIEKIGLLINTSVSRDYLEPSTASIVSGNLGVSDHCMTFDVANACLAFINGMDIAARMLERGEIDYALVVDGETANLVYEKTLERMTSPDVTEEEFRNELAALTLGCGAAAMVMARSELVPDAPRYKGGVTRSATEWNKLCRGNLDRMVTDTRLLLIEGIKLAQKTFVAAKQVLGWAVEELDQFVIHQVSRPHTAAFVKSFGIDPAKVMTIFGEHGNIGPASVPIVLSKLKELGRLKKGDRIALLGIGSGLNCSMAEVVW 338
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeee..eeeehhhhhhhhhhhhhhhh.............eeee.....hhhhhhhhhhhhhhhhhh.hhh.eeeeee..........hhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeeeeeeee.hhh....eeeeeeeee.hhhh..eee....eeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhh..hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s20 A  15 VPRGSHMLFQNVSIAGLAHIDAPHTLTSKEINERLQPTYDRLGIKTDVLGDVAGIHARRLWDQDVQASDAATQAARKALIDANIGIEKIGLLINTSVSRDYLEPSTASIVSGNLGVSDHCMTFDVANACLAFINGMDIAARMLERGEIDYALVVDGETANLVYEKTLERMTSPDVTEEEFRNELAALTLGCGAAAMVMARSELVPDAPRYKGGVTRSATEWNKLCRGNLDRMVTDTRLLLIEGIKLAQKTFVAAKQVLGWAVEELDQFVIHQVSRPHTAAFVKSFGIDPAKVMTIFGEHGNIGPASVPIVLSKLKELGRLKKGDRIALLGIGSGLNCSMAEVVW 358
                                    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    


Chain B from PDB  Type:PROTEIN  Length:326
 aligned with Q8PDX2_XANCP | Q8PDX2 from UniProtKB/TrEMBL  Length:338

    Alignment length:338
                                    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       310       320       330        
         Q8PDX2_XANCP     1 MLFQNVSIAGLAHIDAPHTLTSKEINERLQPTYDRLGIKTDVLGDVAGIHARRLWDQDVQASDAATQAARKALIDANIGIEKIGLLINTSVSRDYLEPSTASIVSGNLGVSDHCMTFDVANACLAFINGMDIAARMLERGEIDYALVVDGETANLVYEKTLERMTSPDVTEEEFRNELAALTLGCGAAAMVMARSELVPDAPRYKGGVTRSATEWNKLCRGNLDRMVTDTRLLLIEGIKLAQKTFVAAKQVLGWAVEELDQFVIHQVSRPHTAAFVKSFGIDPAKVMTIFGEHGNIGPASVPIVLSKLKELGRLKKGDRIALLGIGSGLNCSMAEVVW 338
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee..eeeehhhhhhhhhhhhhh...............eeee.....hhhhhhhhhhhhhhhhhh.hhh.eeeeee..........hhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhh......hhhhhhhhhh....eeeeeeeee.hhh....eeeeeeeee.hhhh.------------hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeee...hhhhhhhhhhhhh.hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s20 B  21 MLFQNVSIAGLAHIDAPHTLTSKEINERLQPTYDRLGIKTDVLGDVAGIHARRLWDQDVQASDAATQAARKALIDANIGIEKIGLLINTSVSRDYLEPSTASIVSGNLGVSDHCMTFDVANACLAFINGMDIAARMLERGEIDYALVVDGETANLVYEKTLERMTSPDVTEEEFRNELAALTLGCGAAAMVMARSELVPDAPRYKGGVTRSATEWNK------------TRLLLIEGIKLAQKTFVAAKQVLGWAVEELDQFVIHQVSRPHTAAFVKSFGIDPAKVMTIFGEHGNIGPASVPIVLSKLKELGRLKKGDRIALLGIGSGLNCSMAEVVW 358
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      |  -       250       260       270       280       290       300       310       320       330       340       350        
                                                                                                                                                                                                                                                  237          250
   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  (0, 0)

(no "SCOP Domain" information available for 3S20)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S20)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S20)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8PDX2_XANCP | Q8PDX2)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
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: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.

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  Cis Peptide Bonds
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 Related Entries

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UniProtKB/TrEMBL
        Q8PDX2_XANCP | Q8PDX2: 3row 3s1z 3s21 3s23 4kti 4ktm 4ku2 4ku3 4ku5

(-) Related Entries Specified in the PDB File

3row 3s1z 3s21 3s23