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PDBsum entry 2fr0

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Oxidoreductase PDB id
2fr0
Jmol
Contents
Protein chain
468 a.a. *
Ligands
NDP
Waters ×180
* Residue conservation analysis
PDB id:
2fr0
Name: Oxidoreductase
Title: The first ketoreductase of the erythromycin synthase (crystal form 1)
Structure: Erythromycin synthase, eryai. Chain: a. Fragment: residues 1444-1925. Engineered: yes
Source: Saccharopolyspora erythraea. Organism_taxid: 1836. Gene: eryai. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.81Å     R-factor:   0.235     R-free:   0.263
Authors: A.T.Keatinge-Clay,R.M.Stroud
Key ref:
A.T.Keatinge-Clay and R.M.Stroud (2006). The structure of a ketoreductase determines the organization of the beta-carbon processing enzymes of modular polyketide synthases. Structure, 14, 737-748. PubMed id: 16564177 DOI: 10.1016/j.str.2006.01.009
Date:
18-Jan-06     Release date:   04-Apr-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q03131  (ERYA1_SACER) -  Erythronolide synthase, modules 1 and 2
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
3491 a.a.
468 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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
Bound ligand (Het Group name = NDP)
corresponds exactly
= 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

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2006.01.009 Structure 14:737-748 (2006)
PubMed id: 16564177  
 
 
The structure of a ketoreductase determines the organization of the beta-carbon processing enzymes of modular polyketide synthases.
A.T.Keatinge-Clay, R.M.Stroud.
 
  ABSTRACT  
 
The structure of the ketoreductase (KR) from the first module of the erythromycin synthase with NADPH bound was solved to 1.79 A resolution. The 51 kDa domain has two subdomains, each similar to a short-chain dehydrogenase/reductase (SDR) monomer. One subdomain has a truncated Rossmann fold and serves a purely structural role stabilizing the other subdomain, which catalyzes the reduction of the beta-carbonyl of a polyketide and possibly the epimerization of an alpha-substituent. The structure enabled us to define the domain boundaries of KR, the dehydratase (DH), and the enoylreductase (ER). It also constrains the three-dimensional organization of these domains within a module, revealing that KR does not make dimeric contacts across the 2-fold axis of the module. The quaternary structure elucidates how substrates are shuttled between the active sites of polyketide synthases (PKSs), as well as related fatty acid synthases (FASs), and suggests how domains can be swapped to make hybrid synthases that produce novel polyketides.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The Erythromycin Synthase Domain Structure
(A) Domains with predicted or known structure are colored, while regions that have no hypothesized structure are white. The structure of the T2 trypsinolysis fragment presented here allowed for the adjustment of domain boundaries, as indicated by the arrow. LDD, loading didomain.
(B) The synthase produces 6-deoxyerythronolide B (6-dEB), a precursor of erythromycin. Figure 1. The Erythromycin Synthase Domain Structure(A) Domains with predicted or known structure are colored, while regions that have no hypothesized structure are white. The structure of the T2 trypsinolysis fragment presented here allowed for the adjustment of domain boundaries, as indicated by the arrow. LDD, loading didomain.(B) The synthase produces 6-deoxyerythronolide B (6-dEB), a precursor of erythromycin.
Figure 7.
Figure 7. Epimerization
(A) Hypothesized mechanism of epimerization. The diketide formed by the first KS enters the active site of the first KR. The mobile Y1813 acts as a base, acquiring the acidic hydrogen of the diketide to form an enolate. The enolate oxygen accepts the proton back from Y1813, and the enolized diketide is released from the KR. An uncatalyzed tautomerization back to the keto form results in a mixture of the original diketide and the epimerized diketide. The original diketide can be accepted until it is epimerized.
(B) A stereodiagram of the KR active site displays the 2F[o] − F[c] electron density maps contoured at 1.5σ. P1815 breaks the helix that contains the catalytic tyrosine in related SDR enzymes, allowing it greater mobility. The temperature factors for Y1813 and neighboring residues are comparatively high.
(C) The sequence surrounding the catalytic tyrosine from each KR of the erythromycin synthase. The first and third modules catalyze epimerization. Residues that may allow the tyrosine sufficient freedom to catalyze epimerization are underlined. Figure 7. Epimerization(A) Hypothesized mechanism of epimerization. The diketide formed by the first KS enters the active site of the first KR. The mobile Y1813 acts as a base, acquiring the acidic hydrogen of the diketide to form an enolate. The enolate oxygen accepts the proton back from Y1813, and the enolized diketide is released from the KR. An uncatalyzed tautomerization back to the keto form results in a mixture of the original diketide and the epimerized diketide. The original diketide can be accepted until it is epimerized.(B) A stereodiagram of the KR active site displays the 2F[o] − F[c] electron density maps contoured at 1.5σ. P1815 breaks the helix that contains the catalytic tyrosine in related SDR enzymes, allowing it greater mobility. The temperature factors for Y1813 and neighboring residues are comparatively high.(C) The sequence surrounding the catalytic tyrosine from each KR of the erythromycin synthase. The first and third modules catalyze epimerization. Residues that may allow the tyrosine sufficient freedom to catalyze epimerization are underlined.
 
  The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 737-748) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21340070 D.H.Kwan, M.Tosin, N.Schläger, F.Schulz, and P.F.Leadlay (2011).
Insights into the stereospecificity of ketoreduction in a modular polyketide synthase.
  Org Biomol Chem, 9, 2053-2056.  
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
20396881 H.Neumann, and P.Neumann-Staubitz (2010).
Synthetic biology approaches in drug discovery and pharmaceutical biotechnology.
  Appl Microbiol Biotechnol, 87, 75-86.  
20696392 J.Zheng, C.A.Taylor, S.K.Piasecki, and A.T.Keatinge-Clay (2010).
Structural and functional analysis of A-type ketoreductases from the amphotericin modular polyketide synthase.
  Structure, 18, 913-922.
PDB codes: 3mjc 3mje 3mjs 3mjt 3mjv
20095633 M.R.Seyedsayamdost, J.R.Chandler, J.A.Blodgett, P.S.Lima, B.A.Duerkop, K.Oinuma, E.P.Greenberg, and J.Clardy (2010).
Quorum-sensing-regulated bactobolin production by Burkholderia thailandensis E264.
  Org Lett, 12, 716-719.  
20444870 S.Anand, M.V.Prasad, G.Yadav, N.Kumar, J.Shehara, M.Z.Ansari, and D.Mohanty (2010).
SBSPKS: structure based sequence analysis of polyketide synthases.
  Nucleic Acids Res, 38, W487-W496.  
20336235 Z.X.Liang (2010).
Complexity and simplicity in the biosynthesis of enediyne natural products.
  Nat Prod Rep, 27, 499-528.  
19636447 A.Koglin, and C.T.Walsh (2009).
Structural insights into nonribosomal peptide enzymatic assembly lines.
  Nat Prod Rep, 26, 987.  
19217343 C.Khosla, S.Kapur, and D.E.Cane (2009).
Revisiting the modularity of modular polyketide synthases.
  Curr Opin Chem Biol, 13, 135-143.  
19151726 E.J.Brignole, S.Smith, and F.J.Asturias (2009).
Conformational flexibility of metazoan fatty acid synthase enables catalysis.
  Nat Struct Mol Biol, 16, 190-197.  
19362634 S.C.Tsai, and B.D.Ames (2009).
Structural enzymology of polyketide synthases.
  Methods Enzymol, 459, 17-47.  
18772425 J.L.Smith, and D.H.Sherman (2008).
Biochemistry. An enzyme assembly line.
  Science, 321, 1304-1305.  
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.  
19011750 K.L.Kavanagh, H.Jörnvall, B.Persson, and U.Oppermann (2008).
Medium- and short-chain dehydrogenase/reductase gene and protein families : the SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes.
  Cell Mol Life Sci, 65, 3895-3906.  
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.  
18937219 L.Kellenberger, I.S.Galloway, G.Sauter, G.Böhm, U.Hanefeld, J.Cortés, J.Staunton, and P.F.Leadlay (2008).
A polylinker approach to reductive loop swaps in modular polyketide synthases.
  Chembiochem, 9, 2740-2749.  
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.  
18948193 M.Leibundgut, T.Maier, S.Jenni, and N.Ban (2008).
The multienzyme architecture of eukaryotic fatty acid synthases.
  Curr Opin Struct Biol, 18, 714-725.  
18693734 R.Castonguay, C.R.Valenzano, A.Y.Chen, A.Keatinge-Clay, C.Khosla, and D.E.Cane (2008).
Stereospecificity of ketoreductase domains 1 and 2 of the tylactone modular polyketide synthase.
  J Am Chem Soc, 130, 11598-11599.  
18772430 T.Maier, M.Leibundgut, and N.Ban (2008).
The crystal structure of a mammalian fatty acid synthase.
  Science, 321, 1315-1322.
PDB codes: 2vz8 2vz9
17133646 A.Starcevic, M.Jaspars, J.Cullum, D.Hranueli, and P.F.Long (2007).
Predicting the nature and timing of epimerisation on a modular polyketide synthase.
  Chembiochem, 8, 28-31.  
17719489 A.T.Keatinge-Clay (2007).
A tylosin ketoreductase reveals how chirality is determined in polyketides.
  Chem Biol, 14, 898-908.
PDB code: 2z5l
17656315 A.Y.Chen, D.E.Cane, and C.Khosla (2007).
Structure-based dissociation of a type I polyketide synthase module.
  Chem Biol, 14, 784-792.  
17317575 B.Frank, J.Knauber, H.Steinmetz, M.Scharfe, H.Blöcker, S.Beyer, and R.Müller (2007).
Spiroketal polyketide formation in Sorangium: identification and analysis of the biosynthetic gene cluster for the highly cytotoxic spirangienes.
  Chem Biol, 14, 221-233.  
17419733 C.D.Richter, D.A.Stanmore, R.N.Miguel, M.C.Moncrieffe, L.Tran, S.Brewerton, F.Meersman, R.W.Broadhurst, and K.J.Weissman (2007).
Autonomous folding of interdomain regions of a modular polyketide synthase.
  FEBS J, 274, 2196-2209.  
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.  
17553731 H.G.Menzella, and C.D.Reeves (2007).
Combinatorial biosynthesis for drug development.
  Curr Opin Microbiol, 10, 238-245.  
17317568 H.G.Menzella, J.R.Carney, and D.V.Santi (2007).
Rational design and assembly of synthetic trimodular polyketide synthases.
  Chem Biol, 14, 143-151.  
17719493 J.D.Kittendorf, B.J.Beck, T.J.Buchholz, W.Seufert, and D.H.Sherman (2007).
Interrogating the molecular basis for multiple macrolactone ring formation by the pikromycin polyketide synthase.
  Chem Biol, 14, 944-954.  
17935970 R.S.Gokhale, R.Sankaranarayanan, and D.Mohanty (2007).
Versatility of polyketide synthases in generating metabolic diversity.
  Curr Opin Struct Biol, 17, 736-743.  
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.  
18096506 S.Pasta, A.Witkowski, A.K.Joshi, and S.Smith (2007).
Catalytic residues are shared between two pseudosubunits of the dehydratase domain of the animal fatty acid synthase.
  Chem Biol, 14, 1377-1385.  
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.  
17893358 V.Y.Alekseyev, C.W.Liu, D.E.Cane, J.D.Puglisi, and C.Khosla (2007).
Solution structure and proposed domain domain recognition interface of an acyl carrier protein domain from a modular polyketide synthase.
  Protein Sci, 16, 2093-2107.
PDB codes: 2ju1 2ju2
17046237 J.D.Kittendorf, and D.H.Sherman (2006).
Developing tools for engineering hybrid polyketide synthetic pathways.
  Curr Opin Biotechnol, 17, 597-605.  
16710331 J.J.Kohler (2006).
A century at the chemistry-biology interface.
  Nat Chem Biol, 2, 288-292.  
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
17031885 S.Bali, and K.J.Weissman (2006).
Ketoreduction in mycolactone biosynthesis: insight into substrate specificity and stereocontrol from studies of discrete ketoreductase domains in vitro.
  Chembiochem, 7, 1935-1942.  
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.