1JMI

CONTRIBUTIONS OF ORIENTATION AND HYDROGEN BONDING TO CATALYSIS IN ASN-229 MUTANTS OF THYMIDYLATE SYNTHASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Contributions of orientation and hydrogen bonding to catalysis in Asn229 mutants of thymidylate synthase.

Finer-Moore, J.S.Liu, L.Birdsall, D.L.Brem, R.Apfeld, J.Santi, D.V.Stroud, R.M.

(1998) J.Mol.Biol. 276: 113-129

  • DOI: 10.1006/jmbi.1997.1495
  • Primary Citation of Related Structures:  1JMF, 1JMG, 1JMH, 1TVU, 1TVV, 1TVW

  • PubMed Abstract: 
  • We have determined structures of binary and ternary complexes of five Asn229 variants of thymidylate synthase (TS) and related their structures to the kinetic constants measured previously. Asn229 forms two hydrogen bonds to the pyrimidine ring of th ...

    We have determined structures of binary and ternary complexes of five Asn229 variants of thymidylate synthase (TS) and related their structures to the kinetic constants measured previously. Asn229 forms two hydrogen bonds to the pyrimidine ring of the substrate 2'-deoxyuridine-5'-monophosphate (dUMP). These hydrogen bonds constrain the orientation of dUMP in binary complexes with dUMP, and in ternary complexes with dUMP and the TS cofactor, 5,10-methylene-5,6,7,8-tetrahydrofolate. In N229 mutants, where these hydrogen bonds cannot be made, dUMP binds in a misoriented or more disordered fashion. Most N229 mutants exhibit no activity for the dehalogenation of 5-bromo-dUMP, which requires correct orientation of dUMP against Cys198. Since bound dUMP forms the binding surface against which the pterin ring of cofactor binds, misorientation of dUMP results in higher Km values for cofactor. At the same time, binding of the cofactor aids in ordering and positioning dUMP for catalysis. Hydrophobic mutants, such as N229I, favor an arrangement of solvent molecules and side-chains around the ligands similar to that in a proposed transition state for ternary complex formation in wild-type TS, and kcat values are similar to the wild-type value. Smaller, more hydrophilic mutants favor arrangements of the solvent and side-chains surrounding the ligands that do not resemble the proposed transition state. These changes correspond to decreases in kcat of up to 2000-fold, with only modest increases in Km or Kd. These results are consistent with the proposal that the hydrogen-bonding network between water, dUMP and side-chains in the active-site cavity contributes to catalysis in TS. Asn229 has the unique ability to maintain this critical network, without sterically interfering with dUMP binding.


    Related Citations: 
    • Stereochemistry of a Multistep/Bipartite Methyl Transfer Reaction: Thymidylate Synthase
      Stroud, R.M.,Finer-Moore, J.S.
      (1993) Faseb J. 7: 671
    • Partitioning Roles of Side Chains in Affinity, Orientation, and Catalysis with Structures for Mutant Complexes: Asparagine-229 in Thymidylate Synthase
      Finer-Moore, J.S.,Liu, L.,Schafmeister, C.E.,Birdsall, D.L.,Mau, T.,Santi, D.V.,Stroud, R.M.
      (1996) Biochemistry 35: 5125
    • Refined Structures of Substrate-Bound and Phosphate-Bound Thymidylate Synthase from Lactobacillus Casei
      Finer-Moore, J.,Fauman, E.B.,Foster, P.G.,Perry, K.M.,Santi, D.V.,Stroud, R.M.
      (1993) J.Mol.Biol. 232: 1101
    • Asparagine 229 in Thymidylate Synthase Contributes to, But is not Essential for, Catalysis
      Liu, L.,Santi, D.V.
      (1993) Proc.Natl.Acad.Sci.USA 90: 8604


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE SYNTHASE
A
316Lactobacillus caseiGene Names: thyA
EC: 2.1.1.45
Find proteins for P00469 (Lactobacillus casei)
Go to UniProtKB:  P00469
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UMP
Query on UMP

Download SDF File 
Download CCD File 
A
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DUKi: 2260 nM (99) BINDINGDB
UMPKd: 870 nM BINDINGMOAD
UMPKd: 870 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.182 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 78.200α = 90.00
b = 78.200β = 90.00
c = 240.900γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
R-AXISdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance