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PDBsum entry 2roq

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Transferase PDB id
2roq
Jmol
Contents
Protein chain
343 a.a. *
* Residue conservation analysis
PDB id:
2roq
Name: Transferase
Title: Solution structure of the thiolation-thioesterase di-domain of enterobactin synthetase component f
Structure: Enterobactin synthetase component f. Chain: a. Fragment: tte, unp residues 960-1293. Synonym: enterochelin synthase f, serine-activating enzyme, seryl-amp ligase. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: ent. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: D.P.Frueh,H.Arthanari,A.Koglin,D.A.Vosburg,A.E.Bennett, C.T.Walsh,G.Wagner
Key ref:
D.P.Frueh et al. (2008). Dynamic thiolation-thioesterase structure of a non-ribosomal peptide synthetase. Nature, 454, 903-906. PubMed id: 18704088 DOI: 10.1038/nature07162
Date:
05-Apr-08     Release date:   12-Aug-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11454  (ENTF_ECOLI) -  Enterobactin synthase component F
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1293 a.a.
343 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biosynthetic process   1 term 
  Biochemical function     hydrolase activity, acting on ester bonds     1 term  

 

 
DOI no: 10.1038/nature07162 Nature 454:903-906 (2008)
PubMed id: 18704088  
 
 
Dynamic thiolation-thioesterase structure of a non-ribosomal peptide synthetase.
D.P.Frueh, H.Arthanari, A.Koglin, D.A.Vosburg, A.E.Bennett, C.T.Walsh, G.Wagner.
 
  ABSTRACT  
 
Non-ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) produce numerous secondary metabolites with various therapeutic/antibiotic properties. Like fatty acid synthases (FAS), these enzymes are organized in modular assembly lines in which each module, made of conserved domains, incorporates a given monomer unit into the growing chain. Knowledge about domain or module interactions may enable reengineering of this assembly line enzymatic organization and open avenues for the design of new bioactive compounds with improved therapeutic properties. So far, little structural information has been available on how the domains interact and communicate. This may be because of inherent interdomain mobility hindering crystallization, or because crystallized molecules may not represent the active domain orientations. In solution, the large size and internal dynamics of multidomain fragments (>35 kilodaltons) make structure determination by nuclear magnetic resonance a challenge and require advanced technologies. Here we present the solution structure of the apo-thiolation-thioesterase (T-TE) di-domain fragment of the Escherichia coli enterobactin synthetase EntF NRPS subunit. In the holoenzyme, the T domain carries the growing chain tethered to a 4'-phosphopantetheine whereas the TE domain catalyses hydrolysis and cyclization of the iron chelator enterobactin. The T-TE di-domain forms a compact but dynamic structure with a well-defined domain interface; the two active sites are at a suitable distance for substrate transfer from T to TE. We observe extensive interdomain and intradomain motions for well-defined regions and show that these are modulated by interactions with proteins that participate in the biosynthesis. The T-TE interaction described here provides a model for NRPS, PKS and FAS function in general as T-TE-like di-domains typically catalyse the last step in numerous assembly-line chain-termination machineries.
 
  Selected figure(s)  
 
Figure 2.
Figure 2: Structure of the EntF T–TE fragment. a, A ribbon diagram is shown. The T domain (red) is wedged between the core (blue) and the lid (green) of the TE domain. Active sites are shown as yellow spheres. The double-headed arrow emphasizes that the flap formed by the 4[TE] and 5[TE] helices is relatively mobile, opening frequently, which seems to be necessary to accommodate the 4'-PP arm in the processes depicted in Fig. 1. b, Surface representation of the region containing the canyon (grey) which must open to accommodate the 4'-PP arm in the holoprotein. The cyclization bucket^12 is shown in white and grey. In this conformation, Ser48Ala and Ser 180 are buried. c, The domain interface is shown. The side chains of all residues giving rise to interdomain nuclear Overhauser effects (NOEs) are shown.
Figure 4.
Figure 4: Interaction with the C domain. Many resonances experience shifts on addition of the C domain (bottom), indicating a modulation of the environment of the corresponding residues. Those belonging to the T domain form an interaction surface that does not overlap with the T–TE interface (top). Thus, no disruption of the T–TE interaction is observed. The effects on the TE domain may be due to weak, indirect interactions with the C domain, or to a secondary effect due to fluctuations of the dynamics or modifications of the conformations in these regions. Residues with shifts larger than one s.d. from the mean (red line, bottom) are colour coded with a gradation from white to red.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 454, 903-906) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20411119 I.Sainis, D.Fokas, K.Vareli, A.G.Tzakos, V.Kounnis, and E.Briasoulis (2010).
Cyanobacterial cyclopeptides as lead compounds to novel targeted cancer drugs.
  Mar Drugs, 8, 629-657.  
21079635 J.M.Crawford, and C.A.Townsend (2010).
New insights into the formation of fungal aromatic polyketides.
  Nat Rev Microbiol, 8, 879-889.  
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.  
20376388 R.C.Hider, and X.Kong (2010).
Chemistry and biology of siderophores.
  Nat Prod Rep, 27, 637-657.  
21127271 S.Kapur, A.Y.Chen, D.E.Cane, and C.Khosla (2010).
Molecular recognition between ketosynthase and acyl carrier protein domains of the 6-deoxyerythronolide B synthase.
  Proc Natl Acad Sci U S A, 107, 22066-22071.  
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.  
  19610673 A.M.Gulick (2009).
Conformational dynamics in the Acyl-CoA synthetases, adenylation domains of non-ribosomal peptide synthetases, and firefly luciferase.
  ACS Chem Biol, 4, 811-827.  
19189362 B.R.Villiers, and F.Hollfelder (2009).
Mapping the limits of substrate specificity of the adenylation domain of TycA.
  Chembiochem, 10, 671-682.  
19217343 C.Khosla, S.Kapur, and D.E.Cane (2009).
Revisiting the modularity of modular polyketide synthases.
  Curr Opin Chem Biol, 13, 135-143.  
19728110 D.P.Frueh, A.Leed, H.Arthanari, A.Koglin, C.T.Walsh, and G.Wagner (2009).
Time-shared HSQC-NOESY for accurate distance constraints measured at high-field in (15)N-(13)C-ILV methyl labeled proteins.
  J Biomol NMR, 45, 311-318.  
19702261 D.P.Frueh, H.Arthanari, A.Koglin, C.T.Walsh, and G.Wagner (2009).
A double TROSY hNCAnH experiment for efficient assignment of large and challenging proteins.
  J Am Chem Soc, 131, 12880-12881.  
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
19278894 K.Watanabe, H.Oguri, and H.Oikawa (2009).
Diversification of echinomycin molecular structure by way of chemoenzymatic synthesis and heterologous expression of the engineered echinomycin biosynthetic pathway.
  Curr Opin Chem Biol, 13, 189-196.  
19381365 P.Beltran-Alvarez, C.J.Arthur, R.J.Cox, J.Crosby, M.P.Crump, and T.J.Simpson (2009).
Preliminary kinetic analysis of acyl carrier protein-ketoacylsynthase interactions in the actinorhodin minimal polyketide synthase.
  Mol Biosyst, 5, 511-518.  
19201253 P.Bernhardt, and S.E.O'Connor (2009).
Opportunities for enzyme engineering in natural product biosynthesis.
  Curr Opin Chem Biol, 13, 35-42.  
19362634 S.C.Tsai, and B.D.Ames (2009).
Structural enzymology of polyketide synthases.
  Methods Enzymol, 459, 17-47.  
18704072 S.Kapur, and C.Khosla (2008).
Biochemistry: Fit for an enzyme.
  Nature, 454, 832-833.  
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 code is shown on the right.