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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III FROM BURKHOLDERIA XENOVORANS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  23 Jan 12  (Deposition) - 08 Feb 12  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Ssgcid, Seattle Structural Genomics Center For Infectious Disease, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, L. A. Gallagher, R. Patrapuvich, M. C. Clifton, A. S. Gardberg, T. E. Edwards, B. Armour, D. W. Begley, S. H. Dieterich, D. M. Dranow, J. Abendroth, J. W. Fairman, D. Fox, B. L. Staker, I. Phan, A. Gillespie, R. Choi, S. Nakazawa-Hewitt, M. T. Nguyen, A. Napuli, L. Barrett, G. W. Buchko, R. Stacy, P. J. Myler, L. J. Stewart, C. Manoil W. C. Van Voorhis
Combining Functional And Structural Genomics To Sample The Essential Burkholderia Structome.
Plos One V. 8 53851 2013
PubMed-ID: 23382856  |  Reference-DOI: 10.1371/JOURNAL.PONE.0053851

(-) Compounds

Molecule 1 - 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 3
    Chains: A, B, C, D
    EC Number: 2.3.1.180
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: FABH, BXENO_A3336, BXE_A1072
    Organism Scientific: BURKHOLDERIA XENOVORANS
    Organism Taxid: 266265
    Strain: LB400
    Synonym: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III, BETA- KETOACYL-ACP SYNTHASE III

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CSO4Mod. Amino AcidS-HYDROXYCYSTEINE
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
2EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA B:189 , LEU B:190 , GLU B:238 , LYS B:242BINDING SITE FOR RESIDUE EDO B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DFE)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Phe A:97 -Pro A:98
2Gly A:319 -Phe A:320
3Phe B:97 -Pro B:98
4Gly B:319 -Phe B:320
5Phe C:97 -Pro C:98
6Gly C:319 -Phe C:320
7Phe D:97 -Pro D:98
8Gly D:319 -Phe D:320

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DFE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DFE)

(-) Exons   (0, 0)

(no "Exon" information available for 4DFE)

(-) 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:322
 aligned with Q13VL5_PARXL | Q13VL5 from UniProtKB/TrEMBL  Length:329

    Alignment length:325
                                    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     
         Q13VL5_PARXL     5 TIYSRVLGTGSYLPPNRVTNQDLAKRLAEQGIETSDEWIVARTGIHARYFAEPDVTTSDLAFIASQRAIEAADIDPQSIDLIIVATSTPDFVFPSTACLLQNKLGIRNHGAAFDVQAVCSGFAYAVATADSFIRSGQHRTALVIGAETFSRILDFKDRTTCVLFGDGAGAVILQASDEPGVLASALHADGSHSNILCTPGNVNGGVVSGSAFLHMDGQAVFKLAVNVLEKVAVEALEKANLSAEQIDWLIPHQANIRIMQSTCRKLGLPQERMIVTVGEHGNTSAASIPLALDVAVRDGRIKRGQNVLIEGVGGGFTWGASVIRY 329
               SCOP domains d4dfea1 A:5-185 automated ma   tches                                                                                                                                                 d4dfea2 A:186-329 automated matches                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee...eeeehhhhhhhhh---...hhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhh.hhhhh.eeeee.........hhhhhhhhhh......eeeeeehhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhhh............eeeeeeeeeee....eeeeeeee.hhhhh.ee..eeee..eeee....eehhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhh..hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dfe A   5 TIYSRVLGTGSYLPPNRVTNQDLAKRLA---IETSDEWIVARTGIHARYFAEPDVTTSDLAFIASQRAIEAADIDPQSIDLIIVATSTPDFVFPSTACLLQNKLGIRNHGAAFDVQAVcSGFAYAVATADSFIRSGQHRTALVIGAETFSRILDFKDRTTCVLFGDGAGAVILQASDEPGVLASALHADGSHSNILCTPGNVNGGVVSGSAFLHMDGQAVFKLAVNVLEKVAVEALEKANLSAEQIDWLIPHQANIRIMQSTCRKLGLPQERMIVTVGEHGNTSAASIPLALDVAVRDGRIKRGQNVLIEGVGGGFTWGASVIRY 329
                                    14        24       | - |      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     
                                                      32  36                                                                                    123-CSO                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:324
 aligned with Q13VL5_PARXL | Q13VL5 from UniProtKB/TrEMBL  Length:329

    Alignment length:325
                                    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     
         Q13VL5_PARXL     5 TIYSRVLGTGSYLPPNRVTNQDLAKRLAEQGIETSDEWIVARTGIHARYFAEPDVTTSDLAFIASQRAIEAADIDPQSIDLIIVATSTPDFVFPSTACLLQNKLGIRNHGAAFDVQAVCSGFAYAVATADSFIRSGQHRTALVIGAETFSRILDFKDRTTCVLFGDGAGAVILQASDEPGVLASALHADGSHSNILCTPGNVNGGVVSGSAFLHMDGQAVFKLAVNVLEKVAVEALEKANLSAEQIDWLIPHQANIRIMQSTCRKLGLPQERMIVTVGEHGNTSAASIPLALDVAVRDGRIKRGQNVLIEGVGGGFTWGASVIRY 329
               SCOP domains d4dfeb1 B:5-185 automated matc hes                                                                                                                                                   d4dfeb2 B:186-329 automated matches                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee...eeeehhhhhhhhhh.-...hhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhh.hhhhh.eeeee.........hhhhhhhhhh......eeeeeehhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhhh............eeeeeeeeeee....eeeeeeee.hhhhh.ee..eeee..eeee....eehhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhh..hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dfe B   5 TIYSRVLGTGSYLPPNRVTNQDLAKRLAEQ-IETSDEWIVARTGIHARYFAEPDVTTSDLAFIASQRAIEAADIDPQSIDLIIVATSTPDFVFPSTACLLQNKLGIRNHGAAFDVQAVcSGFAYAVATADSFIRSGQHRTALVIGAETFSRILDFKDRTTCVLFGDGAGAVILQASDEPGVLASALHADGSHSNILCTPGNVNGGVVSGSAFLHMDGQAVFKLAVNVLEKVAVEALEKANLSAEQIDWLIPHQANIRIMQSTCRKLGLPQERMIVTVGEHGNTSAASIPLALDVAVRDGRIKRGQNVLIEGVGGGFTWGASVIRY 329
                                    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     
                                                        34 |                                                                                    123-CSO                                                                                                                                                                                                          
                                                          36                                                                                                                                                                                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:322
 aligned with Q13VL5_PARXL | Q13VL5 from UniProtKB/TrEMBL  Length:329

    Alignment length:325
                                    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     
         Q13VL5_PARXL     5 TIYSRVLGTGSYLPPNRVTNQDLAKRLAEQGIETSDEWIVARTGIHARYFAEPDVTTSDLAFIASQRAIEAADIDPQSIDLIIVATSTPDFVFPSTACLLQNKLGIRNHGAAFDVQAVCSGFAYAVATADSFIRSGQHRTALVIGAETFSRILDFKDRTTCVLFGDGAGAVILQASDEPGVLASALHADGSHSNILCTPGNVNGGVVSGSAFLHMDGQAVFKLAVNVLEKVAVEALEKANLSAEQIDWLIPHQANIRIMQSTCRKLGLPQERMIVTVGEHGNTSAASIPLALDVAVRDGRIKRGQNVLIEGVGGGFTWGASVIRY 329
               SCOP domains d4dfec1 C:5-185 automated ma   tches                                                                                                                                                 d4dfec2 C:186-329 automated matches                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee...eeeehhhhhhhhh---...hhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhh.hhhhh.eeeee.........hhhhhhhhhh......eeeeeehhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhhh............eeeeeeeeeee....eeeeeeee.hhhhh.ee..eeee..eeee....eehhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhh..hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dfe C   5 TIYSRVLGTGSYLPPNRVTNQDLAKRLA---IETSDEWIVARTGIHARYFAEPDVTTSDLAFIASQRAIEAADIDPQSIDLIIVATSTPDFVFPSTACLLQNKLGIRNHGAAFDVQAVcSGFAYAVATADSFIRSGQHRTALVIGAETFSRILDFKDRTTCVLFGDGAGAVILQASDEPGVLASALHADGSHSNILCTPGNVNGGVVSGSAFLHMDGQAVFKLAVNVLEKVAVEALEKANLSAEQIDWLIPHQANIRIMQSTCRKLGLPQERMIVTVGEHGNTSAASIPLALDVAVRDGRIKRGQNVLIEGVGGGFTWGASVIRY 329
                                    14        24       | - |      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     
                                                      32  36                                                                                    123-CSO                                                                                                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:323
 aligned with Q13VL5_PARXL | Q13VL5 from UniProtKB/TrEMBL  Length:329

    Alignment length:325
                                    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     
         Q13VL5_PARXL     5 TIYSRVLGTGSYLPPNRVTNQDLAKRLAEQGIETSDEWIVARTGIHARYFAEPDVTTSDLAFIASQRAIEAADIDPQSIDLIIVATSTPDFVFPSTACLLQNKLGIRNHGAAFDVQAVCSGFAYAVATADSFIRSGQHRTALVIGAETFSRILDFKDRTTCVLFGDGAGAVILQASDEPGVLASALHADGSHSNILCTPGNVNGGVVSGSAFLHMDGQAVFKLAVNVLEKVAVEALEKANLSAEQIDWLIPHQANIRIMQSTCRKLGLPQERMIVTVGEHGNTSAASIPLALDVAVRDGRIKRGQNVLIEGVGGGFTWGASVIRY 329
               SCOP domains d4dfed1 D:5-185 automated matc  hes                                                                                                                                                  d4dfed2 D:186-329 automated matches                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee...eeeehhhhhhhhhh.--..hhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhh.hhhhh.eeeee.........hhhhhhhhhh......eeeeeehhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhhh............eeeeeeeeeee....eeeeeeee.hhhhh.ee..eeee..eeee....eehhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhh..hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dfe D   5 TIYSRVLGTGSYLPPNRVTNQDLAKRLAEQ--ETSDEWIVARTGIHARYFAEPDVTTSDLAFIASQRAIEAADIDPQSIDLIIVATSTPDFVFPSTACLLQNKLGIRNHGAAFDVQAVcSGFAYAVATADSFIRSGQHRTALVIGAETFSRILDFKDRTTCVLFGDGAGAVILQASDEPGVLASALHADGSHSNILCTPGNVNGGVVSGSAFLHMDGQAVFKLAVNVLEKVAVEALEKANLSAEQIDWLIPHQANIRIMQSTCRKLGLPQERMIVTVGEHGNTSAASIPLALDVAVRDGRIKRGQNVLIEGVGGGFTWGASVIRY 329
                                    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     
                                                        34 37                                                                                   123-CSO
   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, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Fold: Thiolase-like (231)
(-)
Superfamily: Thiolase-like (231)
(-)
Family: automated matches (108)
(-)
Protein domain: automated matches (108)
(-)
Burkholderia xenovorans [TaxId: 266265] (2)
1ad4dfea1A:5-185
1bd4dfea2A:186-329
1cd4dfeb1B:5-185
1dd4dfeb2B:186-329
1ed4dfec1C:5-185
1fd4dfec2C:186-329
1gd4dfed1D:5-185
1hd4dfed2D:186-329

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DFE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DFE)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q13VL5_PARXL | Q13VL5)
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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  4dfe
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  2.3.1.180
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 Related Entries

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