spacer
spacer

PDBsum entry 1w2n

Go to PDB code: 
protein ligands metals links
Oxidoreductase PDB id
1w2n
Jmol
Contents
Protein chain
277 a.a. *
Ligands
PN1
Metals
_FE
Waters ×29
* Residue conservation analysis
PDB id:
1w2n
Name: Oxidoreductase
Title: Deacetoxycephalosporin c synthase (with a n-terminal his- tag) in complex with fe(ii) and ampicillin
Structure: Deacetoxycephalosporin c synthase. Chain: a. Synonym: daocs, expandase. Engineered: yes
Source: Streptomyces clavuligerus. Organism_taxid: 1901. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.70Å     R-factor:   0.249     R-free:   0.287
Authors: L.M.Oster,A.C.Terwisscha Van Scheltinga,K.Valegard,A.Mackenz A.Dubus,J.Hajdu,I.Andersson
Key ref:
L.M.Oster et al. (2004). Conformational flexibility of the C terminus with implications for substrate binding and catalysis revealed in a new crystal form of deacetoxycephalosporin C synthase. J Mol Biol, 343, 157-171. PubMed id: 15381427 DOI: 10.1016/j.jmb.2004.07.049
Date:
07-Jul-04     Release date:   30-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P18548  (CEFE_STRCL) -  Deacetoxycephalosporin C synthase
Seq:
Struc:
311 a.a.
277 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.14.20.1  - Deacetoxycephalosporin-C synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Penicillin N and Deacetoxycephalosporin C Biosynthesis
      Reaction: Penicillin N + 2-oxoglutarate + O2 = deacetoxycephalosporin C + succinate + CO2 + H2O
Penicillin N
Bound ligand (Het Group name = PN1)
matches with 77.78% similarity
+ 2-oxoglutarate
+ O(2)
= deacetoxycephalosporin C
+ succinate
+ CO(2)
+ H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biosynthetic process   3 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2004.07.049 J Mol Biol 343:157-171 (2004)
PubMed id: 15381427  
 
 
Conformational flexibility of the C terminus with implications for substrate binding and catalysis revealed in a new crystal form of deacetoxycephalosporin C synthase.
L.M.Oster, A.C.van Scheltinga, K.Valegård, A.M.Hose, A.Dubus, J.Hajdu, I.Andersson.
 
  ABSTRACT  
 
Deacetoxycephalosporin C synthase (DAOCS) from Streptomyces clavuligerus catalyses the oxidative ring expansion of the penicillin nucleus into the nucleus of cephalosporins. The reaction requires dioxygen and 2-oxoglutarate as co-substrates to create a reactive iron-oxygen intermediate from a ferrous iron in the active site. The active enzyme is monomeric in solution. The structure of DAOCS was determined earlier from merohedrally twinned crystals where the last four C-terminal residues (308-311) of one molecule penetrate the active site of a neighbouring molecule, creating a cyclic trimeric structure in the crystal. Shortening the polypeptide chain from the C terminus by more than four residues diminishes activity. Here, we describe a new crystal form of DAOCS in which trimer formation is broken and the C-terminal arm is free. These crystals show no signs of twinning, and were obtained from DAOCS labelled with an N-terminal His-tag. The modified DAOCS is catalytically active. The free C-terminal arm protrudes into the solvent, and the C-terminal domain (residues 268-299) is rotated by about 16 degrees towards the active site. The last 12 residues (300-311) are disordered. Structures for various enzyme-substrate and enzyme-product complexes in the new crystal form confirm overlapping binding sites for penicillin and 2-oxoglutarate. The results support the notion that 2-oxoglutarate and dioxygen need to react first to produce an oxidizing iron species, followed by reaction with the penicillin substrate. The position of the penicillin nucleus is topologically similar in the two crystal forms, but the penicillin side-chain in the new non-twinned crystals overlaps with the position of residues 304-306 of the C-terminal arm in the twinned crystals. An analysis of the interactions between the C-terminal region and residues in the active site indicates that DAOCS could also accept polypeptide chains as ligands, and these could bind near the iron.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Key steps in the biosynthesis of penicillins and cephalosporins. IPNS creates from the linear tripeptide L-d-(a-aminoadipoyl)-L-cysteinyl-D-valine (ACV) the bicyclic core of the penicillins in a desaturative ring closure with concomitant reduction of dioxygen. This reaction creates isopenicillin N, which is then converted to penicillin N by epimerisation at the side-chain. DAOCS expands the five-membered thiazolidine ring of the penicillin nucleus into the six-membered dihydrothiazine ring of the cephalosporin nucleus. The physiological substrate of DAOCS is penicillin N (side-chain=D-d-(a-aminoadipoyl)-) and the product is deacetoxycephalosporin C (DAOC). DAOCS has broad substrate specificity and can catalyse the ring expansion in penicillins with various side-chains. Here, we used ampicillin (side-chain=R-(2-amino)phenylacetyl-; product: cephalexin) and penicillin G (side-chain=phenylacetyl-; product: phenylacetyl-7-aminodeacetoxycephalosporanic acid) as substrates.
Figure 7.
Figure 7. Binding of peptides and substrate in the active site groove of DAOCS. (a) Surface representation of the form I structure with the iron in green and ampicillin in yellow. The C-terminal arm (residues 300-311) was omitted for clarity. (b) Same as (a), but with the C-terminal arm represented by red sticks. (c) Same as (b) and with the C-terminal arm of an adjacent molecule in the trimer represented by blue sticks. (d) Close-up of the active site in form II crystals, with bound ampicillin in red. Superimposed in blue is the active site of a complex of IPNS with its substrate ACV (coordinates 1bko).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 343, 157-171) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21190060 X.B.Wu, X.Y.Tian, J.J.Ji, W.B.Wu, K.Q.Fan, and K.Q.Yang (2011).
Saturation mutagenesis of Acremonium chrysogenum deacetoxy/deacetylcephalosporin C synthase R308 site confirms its role in controlling substrate specificity.
  Biotechnol Lett, 33, 805-812.  
19625206 P.He, and G.R.Moran (2009).
We two alone will sing: the two-substrate alpha-keto acid-dependent oxygenases.
  Curr Opin Chem Biol, 13, 443-450.  
17431691 V.Purpero, and G.R.Moran (2007).
The diverse and pervasive chemistries of the alpha-keto acid dependent enzymes.
  J Biol Inorg Chem, 12, 587-601.  
15634676 H.Zhou, W.Wang, and Y.Luo (2005).
Contributions of disulfide bonds in a nested pattern to the structure, stability, and biological functions of endostatin.
  J Biol Chem, 280, 11303-11312.  
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.