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PDBsum entry 1bq2

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Methyltransferase PDB id
1bq2
Jmol
Contents
Protein chain
264 a.a. *
Ligands
PO4
Waters ×186
* Residue conservation analysis
PDB id:
1bq2
Name: Methyltransferase
Title: E. Coli thymidylate synthase mutant n177a
Structure: Thymidylate synthase. Chain: a. Synonym: ts, thymidylate synthetase. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Cell_line: chi-2913. Gene: thya. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: chi-2913.
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.20Å     R-factor:   0.172     R-free:   0.217
Authors: C.L.Reyes,C.R.Sage,E.E.Rutenber,J.S.Finer-Moore,R.M.Stroud
Key ref:
C.L.Reyes et al. (1998). Inactivity of N229A thymidylate synthase due to water-mediated effects: isolating a late stage in methyl transfer. J Mol Biol, 284, 699-712. PubMed id: 9826509 DOI: 10.1006/jmbi.1998.2205
Date:
20-Aug-98     Release date:   27-Apr-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A884  (TYSY_ECOLI) -  Thymidylate synthase
Seq:
Struc:
264 a.a.
264 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.1.1.45  - Thymidylate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Folate Coenzymes
      Reaction: 5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
5,10-methylenetetrahydrofolate
+ dUMP
= dihydrofolate
+ dTMP
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     methylation   5 terms 
  Biochemical function     transferase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1998.2205 J Mol Biol 284:699-712 (1998)
PubMed id: 9826509  
 
 
Inactivity of N229A thymidylate synthase due to water-mediated effects: isolating a late stage in methyl transfer.
C.L.Reyes, C.R.Sage, E.E.Rutenber, R.M.Nissen, J.S.Finer-Moore, R.M.Stroud.
 
  ABSTRACT  
 
Mutation of thymidylate synthase N229(177) to alanine results in an essentially inactive enzyme, yet it leads to formation of a stable ternary complex. The kinetics of N229(177)A show that kcat for Escherichia coli is reduced by 200-fold while the Km for dUMP is increased 200-fold and the Km for folate increased by tenfold versus the wild-type enzyme. The crystal structures of N229(177)A in complex with dUMP and CB3717, and in complex with dUMP alone are determined at 2.4 A, and 2.5 A resolution. These structures identify the covalently bound ternary complex and show how N229(177)A traps an intermediate, and so becomes inactive in a later step of the reaction. Since the smaller alanine side-chain at N229(177)A does not directly sterically impair binding of ligands, the structures implicate, and place quantitative limits on the involvement of the structured water network in the active site of thymidylate synthase in both catalysis and in determining the binding affinity for dUMP (in contrast, the N229(177)V mutation in Lactobacillus casei has minimal effect on activity).
 
  Selected figure(s)  
 
Figure 4.
Figure 4. A representation of the hydrogen-bond network interacting with dUMP in the active site of monomer 1 of (a) wild-type and (b) N229(177)A TS.
Figure 5.
Figure 5. A stereo representation of the superimposition of the active sites of monomer 1 of wild-type E. coli TS (blue) and N229(177)A TS (green).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 284, 699-712) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16768437 Z.Newby, T.T.Lee, R.J.Morse, Y.Liu, L.Liu, P.Venkatraman, D.V.Santi, J.S.Finer-Moore, and R.M.Stroud (2006).
The role of protein dynamics in thymidylate synthase catalysis: variants of conserved 2'-deoxyuridine 5'-monophosphate (dUMP)-binding Tyr-261.
  Biochemistry, 45, 7415-7428.
PDB codes: 2g86 2g89 2g8a 2g8d 2g8m 2g8o 2g8x
10679381 G.A.Petsko, and D.Ringe (2000).
Observation of unstable species in enzyme-catalyzed transformations using protein crystallography.
  Curr Opin Chem Biol, 4, 89-94.  
10858298 R.Contestabile, S.Angelaccio, F.Bossa, H.T.Wright, N.Scarsdale, G.Kazanina, and V.Schirch (2000).
Role of tyrosine 65 in the mechanism of serine hydroxymethyltransferase.
  Biochemistry, 39, 7492-7500.
PDB code: 1eqb
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.