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PDBsum entry 1lcb

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Transferase (methyltransferase) PDB id
1lcb
Jmol
Contents
Protein chain
316 a.a. *
Ligands
TMP
DHF
Waters ×117
* Residue conservation analysis
PDB id:
1lcb
Name: Transferase (methyltransferase)
Title: Lactobacillus casei thymidylate synthase ternary complex wit h2folate
Structure: Thymidylate synthase. Chain: a. Synonym: ts, lcts. Ec: 2.1.1.45
Source: Lactobacillus casei. Organism_taxid: 1582
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.204    
Authors: D.L.Birdsall,J.Finer-Moore,R.M.Stroud
Key ref: J.Finer-Moore et al. (1993). Refined structures of substrate-bound and phosphate-bound thymidylate synthase from Lactobacillus casei. J Mol Biol, 232, 1101-1116. PubMed id: 8371269
Date:
22-Jun-95     Release date:   15-Oct-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00469  (TYSY_LACCA) -  Thymidylate synthase
Seq:
Struc:
316 a.a.
316 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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
Bound ligand (Het Group name = DHF)
corresponds exactly
+
dTMP
Bound ligand (Het Group name = TMP)
corresponds exactly
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   4 terms 
  Biochemical function     transferase activity     3 terms  

 

 
    reference    
 
 
J Mol Biol 232:1101-1116 (1993)
PubMed id: 8371269  
 
 
Refined structures of substrate-bound and phosphate-bound thymidylate synthase from Lactobacillus casei.
J.Finer-Moore, E.B.Fauman, P.G.Foster, K.M.Perry, D.V.Santi, R.M.Stroud.
 
  ABSTRACT  
 
Crystal structures of two crystal forms of the complex of Lactobacillus casei (TS) with its substrate dUMP have been solved and refined at 2.55 A resolution. The two crystal forms differ by approximately 5% in the c-axis length. The TS-dUMP complexes are symmetric dimers with dUMP bound equivalently in both active sites. dUMP is non-covalently bound in the same conformation as in ternary complexes of TS with dUMP and cofactor or cofactor analogs. The same hydrogen bonds are made between TS and substrate in the binary and ternary complexes. We have also determined the 2.36 A crystal structure of phosphate-bound L. casei TS. This structure has been refined to an R-factor of 19.3% with highly constrained geometry. Refinement has revealed the locations of all residues in the protein, including the disordered residues 90 to 119, which are part of an insert found only in the L. casei and Staphylococcus aureus transposon Tn4003 TS sequences. The 2.9 A multiple isomorphous replacement (MIR) structure of L. casei TS in a complex with its substrate dUMP has been refined to a crystallographic R-factor of 15.5%. Reducing agents were withheld from crystallization solutions during MIR structure determination to allow heavy-metal labeling of the cysteine residues. Therefore, the active-site cysteine residue in this structure is oxidized and the dUMP is found at half-occupancy in the active site. No significant conformational difference was found between the phosphate-bound and dUMP-bound structures. The TS-dUMP structures were better ordered than the phosphate-bound TS or the oxidized TS-dUMP, particularly Arg23, which is clearly hydrogen-bonded to the phosphate group of dUMP. A large and a small P6(1)22 crystal form are observed for both phosphate-bound and dUMP-bound L. casei TS. The small cell forms of the phosphate-bound and dUMP-bound enzyme are isomorphous, whereas the cell constants of the larger cell form change slightly when dUMP is bound (c = 240 A versus c = 243 A). For both liganded and unliganded enzyme, conversion from the small to the large crystal form sometimes occurs spontaneously, and the crystal packing changes at a single interface. Conversion may be the result of a small change in pH in the mother liquor surrounding the crystal. A single intermolecular contact between symmetry-related Asp287 residues is disrupted on going from the small to the large crystal form.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19955218 D.Cardinale, O.M.Salo-Ahen, G.Guaitoli, S.Ferrari, A.Venturelli, S.Franchini, R.Battini, G.Ponterini, R.C.Wade, and M.P.Costi (2010).
Design and characterization of a mutation outside the active site of human thymidylate synthase that affects ligand binding.
  Protein Eng Des Sel, 23, 81-89.  
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
12754260 C.E.Atreya, E.F.Johnson, J.Williamson, S.Y.Chang, P.H.Liang, and K.S.Anderson (2003).
Probing electrostatic channeling in protozoal bifunctional thymidylate synthase-dihydrofolate reductase using site-directed mutagenesis.
  J Biol Chem, 278, 28901-28911.  
14700626 S.Ferrari, P.M.Costi, and R.C.Wade (2003).
Inhibitor specificity via protein dynamics: insights from the design of antibacterial agents targeted against thymidylate synthase.
  Chem Biol, 10, 1183-1193.  
12192007 E.F.Johnson, W.Hinz, C.E.Atreya, F.Maley, and K.S.Anderson (2002).
Mechanistic characterization of Toxoplasma gondii thymidylate synthase (TS-DHFR)-dihydrofolate reductase. Evidence for a TS intermediate and TS half-sites reactivity.
  J Biol Chem, 277, 43126-43136.  
11727827 B.Gołos, J.M.Dzik, Z.Kazimierczuk, J.Cieśla, Z.Zieliński, J.Jankowska, A.Kraszewski, J.Stawiński, W.Rode, and D.Shugar (2001).
Interaction of thymidylate synthase with the 5'-thiophosphates, 5'-dithiophosphates, 5'-H-phosphonates and 5'-S-thiosulfates of 2'-deoxyuridine, thymidine and 5-fluoro-2'-deoxyuridine.
  Biol Chem, 382, 1439-1445.  
11316879 R.Almog, C.A.Waddling, F.Maley, G.F.Maley, and P.Van Roey (2001).
Crystal structure of a deletion mutant of human thymidylate synthase Delta (7-29) and its ternary complex with Tomudex and dUMP.
  Protein Sci, 10, 988-996.
PDB codes: 1hzw 1i00
11685240 S.Y.Stevens, S.Sanker, C.Kent, and E.R.Zuiderweg (2001).
Delineation of the allosteric mechanism of a cytidylyltransferase exhibiting negative cooperativity.
  Nat Struct Biol, 8, 947-952.  
10841779 J.Phan, E.Mahdavian, M.C.Nivens, W.Minor, S.Berger, H.T.Spencer, R.B.Dunlap, and L.Lebioda (2000).
Catalytic cysteine of thymidylate synthase is activated upon substrate binding.
  Biochemistry, 39, 6969-6978.
PDB codes: 1ev5 1ev8 1evf 1evg
10653645 R.J.Morse, S.Kawase, D.V.Santi, J.Finer-Moore, and R.M.Stroud (2000).
Energetic contributions of four arginines to phosphate-binding in thymidylate synthase are more than additive and depend on optimization of "effective charge balance".
  Biochemistry, 39, 1011-1020.
PDB codes: 1bo7 1bo8 1bp0 1bp6 1bpj
10336382 B.K.Shoichet, A.R.Leach, and I.D.Kuntz (1999).
Ligand solvation in molecular docking.
  Proteins, 34, 4.  
9894005 R.R.Sotelo-Mundo, J.Ciesla, J.M.Dzik, W.Rode, F.Maley, G.F.Maley, L.W.Hardy, and W.R.Montfort (1999).
Crystal structures of rat thymidylate synthase inhibited by Tomudex, a potent anticancer drug.
  Biochemistry, 38, 1087-1094.
PDB codes: 1rts 2tsr
9931028 T.J.Stout, D.Tondi, M.Rinaldi, D.Barlocco, P.Pecorari, D.V.Santi, I.D.Kuntz, R.M.Stroud, B.K.Shoichet, and M.P.Costi (1999).
Structure-based design of inhibitors specific for bacterial thymidylate synthase.
  Biochemistry, 38, 1607-1617.
PDB codes: 1tsl 1tsm
10024022 V.Prasanna, B.Gopal, M.R.Murthy, D.V.Santi, and P.Balaram (1999).
Effect of amino acid substitutions at the subunit interface on the stability and aggregation properties of a dimeric protein: role of Arg 178 and Arg 218 at the Dimer interface of thymidylate synthase.
  Proteins, 34, 356-368.  
9436180 M.P.Costi (1998).
Thymidylate synthase inhibition: a structure-based rationale for drug design.
  Med Res Rev, 18, 21-42.  
9501173 R.Aurora, and G.D.Rose (1998).
Seeking an ancient enzyme in Methanococcus jannaschii using ORF, a program based on predicted secondary structure comparisons.
  Proc Natl Acad Sci U S A, 95, 2818-2823.  
9687366 T.J.Stout, C.R.Sage, and R.M.Stroud (1998).
The additivity of substrate fragments in enzyme-ligand binding.
  Structure, 6, 839-848.
PDB codes: 1an5 1aob 1bdu 1bid 1ddu 1tdu 1tjs 1trg
9565579 Y.Tong, X.Liu-Chen, E.A.Ercikan-Abali, G.M.Capiaux, S.C.Zhao, D.Banerjee, and J.R.Bertino (1998).
Isolation and characterization of thymitaq (AG337) and 5-fluoro-2-deoxyuridylate-resistant mutants of human thymidylate synthase from ethyl methanesulfonate-exposed human sarcoma HT1080 cells.
  J Biol Chem, 273, 11611-11618.  
9813027 Y.Tong, X.Liu-Chen, E.A.Ercikan-Abali, S.C.Zhao, D.Banerjee, F.Maley, and J.R.Bertino (1998).
Probing the folate-binding site of human thymidylate synthase by site-directed mutagenesis. Generation of mutants that confer resistance to raltitrexed, Thymitaq, and BW1843U89.
  J Biol Chem, 273, 31209-31214.  
9109668 D.C.Hyatt, F.Maley, and W.R.Montfort (1997).
Use of strain in a stereospecific catalytic mechanism: crystal structures of Escherichia coli thymidylate synthase bound to FdUMP and methylenetetrahydrofolate.
  Biochemistry, 36, 4585-4594.
PDB codes: 1tls 1tsn
9100016 H.T.Spencer, J.E.Villafranca, and J.R.Appleman (1997).
Kinetic scheme for thymidylate synthase from Escherichia coli: determination from measurements of ligand binding, primary and secondary isotope effects, and pre-steady-state catalysis.
  Biochemistry, 36, 4212-4222.  
9048572 W.Huang, and D.V.Santi (1997).
Active site general catalysts are not necessary for some proton transfer reactions of thymidylate synthase.
  Biochemistry, 36, 1869-1873.  
9535167 W.R.Montfort, and A.Weichsel (1997).
Thymidylate synthase: structure, inhibition, and strained conformations during catalysis.
  Pharmacol Ther, 76, 29-43.  
8888067 B.L.Stoddard (1996).
Intermediate trapping and laue X-ray diffraction: potential for enzyme mechanism, dynamics, and inhibitor screening.
  Pharmacol Ther, 70, 215-256.  
8994964 D.G.Vassylyev, and K.Morikawa (1996).
Precluding uracil from DNA.
  Structure, 4, 1381-1385.  
8611496 J.S.Finer-Moore, L.Liu, C.E.Schafmeister, D.L.Birdsall, T.Mau, D.V.Santi, and R.M.Stroud (1996).
Partitioning roles of side chains in affinity, orientation, and catalysis with structures for mutant complexes: asparagine-229 in thymidylate synthase.
  Biochemistry, 35, 5125-5136.
PDB codes: 1nja 1njb 1njc 1njd 1nje
8672425 P.M.Costi, L.Liu, J.S.Finer-Moore, R.M.Stroud, and D.V.Santi (1996).
Asparagine 229 mutants of thymidylate synthase catalyze the methylation of 3-methyl-2'-deoxyuridine 5'-monophosphate.
  Biochemistry, 35, 3944-3949.  
8679542 R.S.Gokhale, S.Agarwalla, D.V.Santi, and P.Balaram (1996).
Covalent reinforcement of a fragile region in the dimeric enzyme thymidylate synthase stabilizes the protein against chaotrope-induced unfolding.
  Biochemistry, 35, 7150-7158.  
8805515 T.J.Stout, and R.M.Stroud (1996).
The complex of the anti-cancer therapeutic, BW1843U89, with thymidylate synthase at 2.0 A resolution: implications for a new mode of inhibition.
  Structure, 4, 67-77.
PDB code: 1syn
7724588 A.Weichsel, W.R.Montfort, J.Cieśla, and F.Maley (1995).
Promotion of purine nucleotide binding to thymidylate synthase by a potent folate analogue inhibitor, 1843U89.
  Proc Natl Acad Sci U S A, 92, 3493-3497.
PDB code: 1tlc
7556218 L.García-Fuentes, P.Reche, O.López-Mayorga, D.V.Santi, D.González-Pacanowska, and C.Barón (1995).
Thermodynamic analysis of the binding of 5-fluoro-2'-deoxyuridine 5'-monophosphate to thymidylate synthase over a range of temperatures.
  Eur J Biochem, 232, 641-645.  
7656037 D.R.Knighton, C.C.Kan, E.Howland, C.A.Janson, Z.Hostomska, K.M.Welsh, and D.A.Matthews (1994).
Structure of and kinetic channelling in bifunctional dihydrofolate reductase-thymidylate synthase.
  Nat Struct Biol, 1, 186-194.  
7812717 L.W.Hardy, D.F.Pacitti, and E.Nalivaika (1994).
Use of a purified heterodimer to test negative cooperativity as the basis of substrate inactivation of Escherichia coli thymidylate synthase (Asn177-->Asp).
  Structure, 2, 833-838.  
7656026 R.M.Stroud (1994).
An electrostatic highway.
  Nat Struct Biol, 1, 131-134.  
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.