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PDBsum entry 1kez

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protein Protein-protein interface(s) links
Transferase PDB id
1kez
Jmol
Contents
Protein chains
267 a.a. *
Waters ×393
* Residue conservation analysis
PDB id:
1kez
Name: Transferase
Title: Crystal structure of the macrocycle-forming thioesterase domain of erythromycin polyketide synthase (debs te)
Structure: Erythronolide synthase. Chain: a, b, c. Fragment: terminal thioesterase domain, module 6 (residues 2893-3172). Synonym: 6-deoxyerythronolide b synthase iii. Engineered: yes
Source: Saccharopolyspora erythraea. Organism_taxid: 1836. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Not given
Resolution:
2.80Å     R-factor:   0.254     R-free:   0.279
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
Key ref:
S.C.Tsai et al. (2001). Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: versatility from a unique substrate channel. Proc Natl Acad Sci U S A, 98, 14808-14813. PubMed id: 11752428 DOI: 10.1073/pnas.011399198
Date:
19-Nov-01     Release date:   09-Jan-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q03133  (ERYA3_SACER) -  Erythronolide synthase, modules 5 and 6
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
3172 a.a.
267 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.1.94  - 6-deoxyerythronolide-B synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Propanoyl-CoA + 6 (2S)-methylmalonyl-CoA + 6 NADPH = 6-deoxyerythronolide B + 7 CoA + 6 CO2 + H2O + 6 NADP+
Propanoyl-CoA
+ 6 × (2S)-methylmalonyl-CoA
+ 6 × NADPH
= 6-deoxyerythronolide B
+ 7 × CoA
+ 6 × CO(2)
+ H(2)O
+ 6 × NADP(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biosynthetic process   1 term 
  Biochemical function     hydrolase activity, acting on ester bonds     1 term  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.011399198 Proc Natl Acad Sci U S A 98:14808-14813 (2001)
PubMed id: 11752428  
 
 
Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: versatility from a unique substrate channel.
S.C.Tsai, L.J.Miercke, J.Krucinski, R.Gokhale, J.C.Chen, P.G.Foster, D.E.Cane, C.Khosla, R.M.Stroud.
 
  ABSTRACT  
 
As the first structural elucidation of a modular polyketide synthase (PKS) domain, the crystal structure of the macrocycle-forming thioesterase (TE) domain from the 6-deoxyerythronolide B synthase (DEBS) was solved by a combination of multiple isomorphous replacement and multiwavelength anomalous dispersion and refined to an R factor of 24.1% to 2.8-A resolution. Its overall tertiary architecture belongs to the alpha/beta-hydrolase family, with two unusual features unprecedented in this family: a hydrophobic leucine-rich dimer interface and a substrate channel that passes through the entire protein. The active site triad, comprised of Asp-169, His-259, and Ser-142, is located in the middle of the substrate channel, suggesting the passage of the substrate through the protein. Modeling indicates that the active site can accommodate and orient the 6-deoxyerythronolide B precursor uniquely, while at the same time shielding the active site from external water and catalyzing cyclization by macrolactone formation. The geometry and organization of functional groups explain the observed substrate specificity of this TE and offer strategies for engineering macrocycle biosynthesis. Docking of a homology model of the upstream acyl carrier protein (ACP6) against the TE suggests that the 2-fold axis of the TE dimer may also be the axis of symmetry that determines the arrangement of domains in the entire DEBS. Sequence conservation suggests that all TEs from modular polyketide synthases have a similar fold, dimer 2-fold axis, and substrate channel geometry.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The modular architecture of DEBS, its intermediates, and its final product as the 14-membered ring of 6-dEB. AT, acyltransferase; ACP, acyl carrier protein; KS, ketosynthase; KR, ketoreductase; DH, dehydratase; ER, enoylreductase; TE, thioesterase.
Figure 5.
Fig. 5. The proposed mechanism of the chain termination reaction catalyzed by DEBS TE. (A) ACP6, which binds to the TE on the N-side via the arginine groove, and a covalent linkage at the N terminus, presents the full-length polyketide as a phosphopentathienyl-bound acyl chain. (B) The functional groups C-1==O, C-3---OH, C-5---OH, C-9==O, C-11---OH, and C13---OH on the polyketide chain anchor the polyketide chain in the active site by forming seven hydrogen bonds with the protein. Upon nucleophilic attack of Ser-142, a covalently bound intermediate is formed. (c) Subsequent attack on C-1==O by C13---OH, which is anchored near C-1==O by the hydrogen-bonding scheme and whose nucleophilicity is enhanced by His-259, results in the formation of the macrolactone. Product can then be released out of the C-side exit.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20152156 D.L.Akey, J.R.Razelun, J.Tehranisa, D.H.Sherman, W.H.Gerwick, and J.L.Smith (2010).
Crystal structures of dehydratase domains from the curacin polyketide biosynthetic pathway.
  Structure, 18, 94.
PDB codes: 3kg6 3kg7 3kg8 3kg9
20358042 H.Zhou, Y.Li, and Y.Tang (2010).
Cyclization of aromatic polyketides from bacteria and fungi.
  Nat Prod Rep, 27, 839-868.  
20432424 K.Buntin, K.J.Weissman, and R.Müller (2010).
An unusual thioesterase promotes isochromanone ring formation in ajudazol biosynthesis.
  Chembiochem, 11, 1137-1146.  
20111804 L.Du, and L.Lou (2010).
PKS and NRPS release mechanisms.
  Nat Prod Rep, 27, 255-278.  
20659683 L.Tran, R.W.Broadhurst, M.Tosin, A.Cavalli, and K.J.Weissman (2010).
Insights into protein-protein and enzyme-substrate interactions in modular polyketide synthases.
  Chem Biol, 17, 705-716.  
20332208 T.P.Korman, J.M.Crawford, J.W.Labonte, A.G.Newman, J.Wong, C.A.Townsend, and S.C.Tsai (2010).
Structure and function of an iterative polyketide synthase thioesterase domain catalyzing Claisen cyclization in aflatoxin biosynthesis.
  Proc Natl Acad Sci U S A, 107, 6246-6251.
PDB code: 3ils
19636447 A.Koglin, and C.T.Walsh (2009).
Structural insights into nonribosomal peptide enzymatic assembly lines.
  Nat Prod Rep, 26, 987.  
19103602 H.B.Claxton, D.L.Akey, M.K.Silver, S.J.Admiraal, and J.L.Smith (2009).
Structure and functional analysis of RifR, the type II thioesterase from the rifamycin biosynthetic pathway.
  J Biol Chem, 284, 5021-5029.
PDB codes: 3fla 3flb
19810731 J.D.Mortison, J.D.Kittendorf, and D.H.Sherman (2009).
Synthesis and biochemical analysis of complex chain-elongation intermediates for interrogation of molecular specificity in the erythromycin and pikromycin polyketide synthases.
  J Am Chem Soc, 131, 15784-15793.  
19388008 M.K.Kharel, P.Pahari, H.Lian, and J.Rohr (2009).
GilR, an unusual lactone-forming enzyme involved in gilvocarcin biosynthesis.
  Chembiochem, 10, 1305-1308.  
19530704 M.Wang, H.Zhou, M.Wirz, Y.Tang, and C.N.Boddy (2009).
A thioesterase from an iterative fungal polyketide synthase shows macrocyclization and cross coupling activity and may play a role in controlling iterative cycling through product offloading.
  Biochemistry, 48, 6288-6290.  
19362634 S.C.Tsai, and B.D.Ames (2009).
Structural enzymology of polyketide synthases.
  Methods Enzymol, 459, 17-47.  
19900898 S.M.Ma, J.W.Li, J.W.Choi, H.Zhou, K.K.Lee, V.A.Moorthie, X.Xie, J.T.Kealey, N.A.Da Silva, J.C.Vederas, and Y.Tang (2009).
Complete reconstitution of a highly reducing iterative polyketide synthase.
  Science, 326, 589-592.  
19549600 T.Awakawa, K.Yokota, N.Funa, F.Doi, N.Mori, H.Watanabe, and S.Horinouchi (2009).
Physically discrete beta-lactamase-type thioesterase catalyzes product release in atrochrysone synthesis by iterative type I polyketide synthase.
  Chem Biol, 16, 613-623.  
18493665 J.L.Meier, T.Barrows-Yano, T.L.Foley, C.L.Wike, and M.D.Burkart (2008).
The unusual macrocycle forming thioesterase of mycolactone.
  Mol Biosyst, 4, 663-671.  
18357594 K.J.Weissman, and R.Müller (2008).
Protein-protein interactions in multienzyme megasynthetases.
  Chembiochem, 9, 826-848.  
19016299 K.J.Weissman (2008).
Taking a closer look at fatty acid biosynthesis.
  Chembiochem, 9, 2929-2931.  
19021139 L.Betancor, M.J.Fernández, K.J.Weissman, and P.F.Leadlay (2008).
Improved catalytic activity of a purified multienzyme from a modular polyketide synthase after coexpression with Streptomyces chaperonins in Escherichia coli.
  Chembiochem, 9, 2962-2966.  
18348128 L.Tran, M.Tosin, J.B.Spencer, P.F.Leadlay, and K.J.Weissman (2008).
Covalent linkage mediates communication between ACP and TE domains in modular polyketide synthases.
  Chembiochem, 9, 905-915.  
18972512 S.C.Wenzel, H.B.Bode, I.Kochems, and R.Müller (2008).
A type I/type III polyketide synthase hybrid biosynthetic pathway for the structurally unique ansa compound kendomycin.
  Chembiochem, 9, 2711-2721.  
18285472 S.Eys, D.Schwartz, W.Wohlleben, and E.Schinko (2008).
Three thioesterases are involved in the biosynthesis of phosphinothricin tripeptide in Streptomyces viridochromogenes Tü494.
  Antimicrob Agents Chemother, 52, 1686-1696.  
18482697 T.Liu, X.Lin, X.Zhou, Z.Deng, and D.E.Cane (2008).
Mechanism of thioesterase-catalyzed chain release in the biosynthesis of the polyether antibiotic nanchangmycin.
  Chem Biol, 15, 449-458.  
18836004 Y.Zhou, Q.Meng, D.You, J.Li, S.Chen, D.Ding, X.Zhou, H.Zhou, L.Bai, and Z.Deng (2008).
Selective removal of aberrant extender units by a type II thioesterase for efficient FR-008/candicidin biosynthesis in Streptomyces sp. strain FR-008.
  Appl Environ Microbiol, 74, 7235-7242.  
17653358 A.C.Mercer, and M.D.Burkart (2007).
The ubiquitous carrier protein--a window to metabolite biosynthesis.
  Nat Prod Rep, 24, 750-773.  
17328673 C.Khosla, Y.Tang, A.Y.Chen, N.A.Schnarr, and D.E.Cane (2007).
Structure and mechanism of the 6-deoxyerythronolide B synthase.
  Annu Rev Biochem, 76, 195-221.  
17653357 F.Kopp, and M.A.Marahiel (2007).
Macrocyclization strategies in polyketide and nonribosomal peptide biosynthesis.
  Nat Prod Rep, 24, 735-749.  
17704771 N.Kadi, D.Oves-Costales, F.Barona-Gomez, and G.L.Challis (2007).
A new family of ATP-dependent oligomerization-macrocyclization biocatalysts.
  Nat Chem Biol, 3, 652-656.  
17466016 S.M.Ma, and Y.Tang (2007).
Biochemical characterization of the minimal polyketide synthase domains in the lovastatin nonaketide synthase LovB.
  FEBS J, 274, 2854-2864.  
17898897 S.Smith, and S.C.Tsai (2007).
The type I fatty acid and polyketide synthases: a tale of two megasynthases.
  Nat Prod Rep, 24, 1041-1072.  
16572230 A.M.Hill (2006).
The biosynthesis, molecular genetics and enzymology of the polyketide-derived metabolites.
  Nat Prod Rep, 23, 256-320.  
16897798 B.M.Harvey, H.Hong, M.A.Jones, Z.A.Hughes-Thomas, R.M.Goss, M.L.Heathcote, V.M.Bolanos-Garcia, W.Kroutil, J.Staunton, P.F.Leadlay, and J.B.Spencer (2006).
Evidence that a novel thioesterase is responsible for polyketide chain release during biosynthesis of the polyether ionophore monensin.
  Chembiochem, 7, 1435-1442.  
16969372 D.L.Akey, J.D.Kittendorf, J.W.Giraldes, R.A.Fecik, D.H.Sherman, and J.L.Smith (2006).
Structural basis for macrolactonization by the pikromycin thioesterase.
  Nat Chem Biol, 2, 537-542.
PDB codes: 2hfj 2hfk
17046237 J.D.Kittendorf, and D.H.Sherman (2006).
Developing tools for engineering hybrid polyketide synthetic pathways.
  Curr Opin Biotechnol, 17, 597-605.  
16969373 J.W.Giraldes, D.L.Akey, J.D.Kittendorf, D.H.Sherman, J.L.Smith, and R.A.Fecik (2006).
Structural and mechanistic insights into polyketide macrolactonization from polyketide-based affinity labels.
  Nat Chem Biol, 2, 531-536.
PDB codes: 2h7x 2h7y
16815901 L.M.Hicks, C.J.Balibar, C.T.Walsh, N.L.Kelleher, and N.J.Hillson (2006).
Probing intra- versus interchain kinetic preferences of L-Thr acylation on dimeric VibF with mass spectrometry.
  Biophys J, 91, 2609-2619.  
16983382 S.E.O'Connor (2006).
Cyclization of natural products.
  Nat Chem Biol, 2, 511-512.  
16322741 K.J.Weissman, and P.F.Leadlay (2005).
Combinatorial biosynthesis of reduced polyketides.
  Nat Rev Microbiol, 3, 925-936.  
15507492 B.Chakravarty, Z.Gu, S.S.Chirala, S.J.Wakil, and F.A.Quiocho (2004).
Human fatty acid synthase: structure and substrate selectivity of the thioesterase domain.
  Proc Natl Acad Sci U S A, 101, 15567-15572.
PDB code: 1xkt
15112993 G.L.Tang, Y.Q.Cheng, and B.Shen (2004).
Leinamycin biosynthesis revealing unprecedented architectural complexity for a hybrid polyketide synthase and nonribosomal peptide synthetase.
  Chem Biol, 11, 33-45.  
15066179 U.Linne, D.Schwarzer, G.N.Schroeder, and M.A.Marahiel (2004).
Mutational analysis of a type II thioesterase associated with nonribosomal peptide synthesis.
  Eur J Biochem, 271, 1536-1545.  
  12889743 C.D.Reeves (2003).
The enzymology of combinatorial biosynthesis.
  Crit Rev Biotechnol, 23, 95.  
12514126 G.Sciara, S.G.Kendrew, A.E.Miele, N.G.Marsh, L.Federici, F.Malatesta, G.Schimperna, C.Savino, and B.Vallone (2003).
The structure of ActVA-Orf6, a novel type of monooxygenase involved in actinorhodin biosynthesis.
  EMBO J, 22, 205-215.
PDB codes: 1lq9 1n5q 1n5s 1n5t 1n5v
12470730 N.L.Pohl (2002).
Nonnatural substrates for polyketide synthases and their associated modifying enzymes.
  Curr Opin Chem Biol, 6, 773-778.  
12323374 S.A.Sieber, U.Linne, N.J.Hillson, E.Roche, C.T.Walsh, and M.A.Marahiel (2002).
Evidence for a monomeric structure of nonribosomal Peptide synthetases.
  Chem Biol, 9, 997.  
12323367 S.Smith (2002).
Modular NRPSs are monomeric.
  Chem Biol, 9, 955-956.  
12055621 T.A.Keating, C.G.Marshall, C.T.Walsh, and A.E.Keating (2002).
The structure of VibH represents nonribosomal peptide synthetase condensation, cyclization and epimerization domains.
  Nat Struct Biol, 9, 522-526.
PDB code: 1l5a
12220180 Z.Zhuang, F.Song, W.Zhang, K.Taylor, A.Archambault, D.Dunaway-Mariano, J.Dong, and P.R.Carey (2002).
Kinetic, Raman, NMR, and site-directed mutagenesis studies of the Pseudomonas sp. strain CBS3 4-hydroxybenzoyl-CoA thioesterase active site.
  Biochemistry, 41, 11152-11160.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.