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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MACROCYCLE-FORMING THIOESTERASE DOMAIN OF ERYTHROMYCIN POLYKETIDE SYNTHASE (DEBS TE)
 
Authors :  S. -C. Tsai, L. J. W. Miercke, J. Krucinski, R. Gokhale, J. C. -H. Chen, P. G. Foster, D. E. Cane, C. Khosla, R. M. Stroud
Date :  19 Nov 01  (Deposition) - 09 Jan 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Polyketide Synthase, 6-Deoxyerythronolide Synthase, Modular Polyketide Synthase, Thioesterase, 6-Deb, Te, Debs, Alpha, Beta-Hydrolase, Macrocycle, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Tsai, L. J. Miercke, J. Krucinski, R. Gokhale, J. C. Chen, P. G. Foster, D. E. Cane, C. Khosla, R. M. Stroud
Crystal Structure Of The Macrocycle-Forming Thioesterase Domain Of The Erythromycin Polyketide Synthase: Versatility From A Unique Substrate Channel.
Proc. Natl. Acad. Sci. Usa V. 98 14808 2001
PubMed-ID: 11752428  |  Reference-DOI: 10.1073/PNAS.011399198
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ERYTHRONOLIDE SYNTHASE
    Chains: A, B, C
    EC Number: 2.3.1.94
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET21C
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: TERMINAL THIOESTERASE DOMAIN, MODULE 6 (RESIDUES 2893-3172)
    Organism Scientific: SACCHAROPOLYSPORA ERYTHRAEA
    Organism Taxid: 1836
    Synonym: 6-DEOXYERYTHRONOLIDE B SYNTHASE III

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1KEZ)

(-) Sites  (0, 0)

(no "Site" information available for 1KEZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KEZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KEZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KEZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KEZ)

(-) Exons   (0, 0)

(no "Exon" information available for 1KEZ)

(-) 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:267
 aligned with ERYA3_SACER | Q03133 from UniProtKB/Swiss-Prot  Length:3172

    Alignment length:267
                                  2913      2923      2933      2943      2953      2963      2973      2983      2993      3003      3013      3023      3033      3043      3053      3063      3073      3083      3093      3103      3113      3123      3133      3143      3153      3163       
         ERYA3_SACER   2904 SSALRDGYRQAGVSGRVRSYLDLLAGLSDFREHFDGSDGFSLDLVDMADGPGEVTVICCAGTAAISGPHEFTRLAGALRGIAPVRAVPQPGYEEGEPLPSSMAAVAAVQADAVIRTQGDKPFVVAGHSAGALMAYALATELLDRGHPPRGVVLIDVYPPGHQDAMNAWLEELTATLFDRETVRMDDTRLTALGAYDRLTGQWRPRETGLPTLLVSAGEPMGPWPDDSWKPTWPFEHDTVAVPGDHFTMVQEHADAIARHIDAWLGGG 3170
               SCOP domains d1keza_ A: Erythromycin polyketide synthase                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1kezA00 A:15-281  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee......eeeee.......hhhhhhhhhhhh.....eeee..........ee.hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh........eeeeeeee..................eeeeeeee..hhhhhhhhhhhhhhhhhhh.. Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------ee----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1kez A   15 SSALRDGYRQAGVSGRVRSYLDLLAGLSDFREHFDGSDGFSLDLVDMADGPGEVTVICCAGTAAISGPHEFTRLAGALRGIAPVRAVPQPGYEEGEPLPSSMAAVAAVQADAVIRTQGDKPFVVAGHSAGALMAYALATELLDRGHPPRGVVLIDVYPPGHQDAMNAWLEELTATLFDRETVRMDDTRLTALGAYDRLTGQWRPRETGLPTLLVSAGEPMGPWPDDSWKPTWPFEHDTVAVPGDHFTMVQEHADAIARHIDAWLGGG  281
                                    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       


Chain B from PDB  Type:PROTEIN  Length:267
 aligned with ERYA3_SACER | Q03133 from UniProtKB/Swiss-Prot  Length:3172

    Alignment length:267
                                  2913      2923      2933      2943      2953      2963      2973      2983      2993      3003      3013      3023      3033      3043      3053      3063      3073      3083      3093      3103      3113      3123      3133      3143      3153      3163       
         ERYA3_SACER   2904 SSALRDGYRQAGVSGRVRSYLDLLAGLSDFREHFDGSDGFSLDLVDMADGPGEVTVICCAGTAAISGPHEFTRLAGALRGIAPVRAVPQPGYEEGEPLPSSMAAVAAVQADAVIRTQGDKPFVVAGHSAGALMAYALATELLDRGHPPRGVVLIDVYPPGHQDAMNAWLEELTATLFDRETVRMDDTRLTALGAYDRLTGQWRPRETGLPTLLVSAGEPMGPWPDDSWKPTWPFEHDTVAVPGDHFTMVQEHADAIARHIDAWLGGG 3170
               SCOP domains d1kezb_ B: Erythromycin polyketide synthase                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1kezB00 B:15-281  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee......eeeee.......hhhhhhhhhhhh.....eeee..........ee.hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh.......eeee.......hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh........eeeeeeee..................eeeeeeee..hhhhhhhhhhhhhhhhhhh.. Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------ee----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1kez B   15 SSALRDGYRQAGVSGRVRSYLDLLAGLSDFREHFDGSDGFSLDLVDMADGPGEVTVICCAGTAAISGPHEFTRLAGALRGIAPVRAVPQPGYEEGEPLPSSMAAVAAVQADAVIRTQGDKPFVVAGHSAGALMAYALATELLDRGHPPRGVVLIDVYPPGHQDAMNAWLEELTATLFDRETVRMDDTRLTALGAYDRLTGQWRPRETGLPTLLVSAGEPMGPWPDDSWKPTWPFEHDTVAVPGDHFTMVQEHADAIARHIDAWLGGG  281
                                    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       


Chain C from PDB  Type:PROTEIN  Length:267
 aligned with ERYA3_SACER | Q03133 from UniProtKB/Swiss-Prot  Length:3172

    Alignment length:267
                                  2913      2923      2933      2943      2953      2963      2973      2983      2993      3003      3013      3023      3033      3043      3053      3063      3073      3083      3093      3103      3113      3123      3133      3143      3153      3163       
         ERYA3_SACER   2904 SSALRDGYRQAGVSGRVRSYLDLLAGLSDFREHFDGSDGFSLDLVDMADGPGEVTVICCAGTAAISGPHEFTRLAGALRGIAPVRAVPQPGYEEGEPLPSSMAAVAAVQADAVIRTQGDKPFVVAGHSAGALMAYALATELLDRGHPPRGVVLIDVYPPGHQDAMNAWLEELTATLFDRETVRMDDTRLTALGAYDRLTGQWRPRETGLPTLLVSAGEPMGPWPDDSWKPTWPFEHDTVAVPGDHFTMVQEHADAIARHIDAWLGGG 3170
               SCOP domains d1kezc_ C: Erythromycin polyketide synthase                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1kezC00 C:15-281  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee......eeeee.......hhhhhhhhhhhh.....eeee..........ee.hhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhh.......eeee.......hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh........eeeeee....................eeeee.....hhhhhhhhhhhhhhhhhh... Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------ee----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1kez C   15 SSALRDGYRQAGVSGRVRSYLDLLAGLSDFREHFDGSDGFSLDLVDMADGPGEVTVICCAGTAAISGPHEFTRLAGALRGIAPVRAVPQPGYEEGEPLPSSMAAVAAVQADAVIRTQGDKPFVVAGHSAGALMAYALATELLDRGHPPRGVVLIDVYPPGHQDAMNAWLEELTATLFDRETVRMDDTRLTALGAYDRLTGQWRPRETGLPTLLVSAGEPMGPWPDDSWKPTWPFEHDTVAVPGDHFTMVQEHADAIARHIDAWLGGG  281
                                    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
   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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1KEZ)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (ERYA3_SACER | Q03133)
molecular function
    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:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    GO:0047879    erythronolide synthase activity    Catalysis of the reaction: 6 malonyl-CoA + propionyl-CoA = 7 CoA + 6-deoxyerythronolide B.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0031177    phosphopantetheine binding    Interacting selectively and non-covalently with phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate).
    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:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0033068    macrolide biosynthetic process    The chemical reactions and pathways leading to the formation of macrolides, any of a large group of polyketide compounds that contain a large lactone ring with few or no double bonds and no nitrogen atoms, linked glycosidically to one or more sugar groups. The macrolides include the carbomycins, the erythromycins, oleandomycin, oligomycins, and the spiramycins, and act as antibiotics, mainly against Gram-positive bacteria.
    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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 Related Entries

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        ERYA3_SACER | Q03133: 1mo2 1pzr 2hg4 5d3k 5d3z

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