Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 36.93 kDa 
• Atom Count: 2672 
• Modelled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

1NJA

THYMIDYLATE SYNTHASE, MUTATION, N229C WITH 2'-DEOXYCYTIDINE 5'-MONOPHOSPHATE (DCMP)

• PDB DOI: 10.2210/pdb1NJA/pdb

• Classification: TRANSFERASE (METHYLTRANSFERASE)
• Organism(s): Lacticaseibacillus casei
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1996-01-23 Released: 1996-07-11 
• Deposition Author(s): Finer-Moore, J., Stroud, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.180 
• R-Value Observed: 0.180 

Literature

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: 5125-5136

• PubMed: 8611496 
• DOI: 10.1021/bi952751x
• Primary Citation of Related Structures:  
  1NJA, 1NJB, 1NJC, 1NJD, 1NJE


• PubMed Abstract: 
  

Thymidylate synthase (TS) methylates only dUMP, not dCMP. The crystal structure of TS.dCMP shows sCMP 4-NH2 excluded from the space between Asn-229 and His-199 by the hydrogen bonding and steric properties and Asn-229. Consequently, 6-C of dCMP is over 4 A from the active site sulfhydryl. The Asn-229 side chain is prevented from flipping 180 degrees to and orientation the could hydrogen bond to dCMP by a hydrogen bond network between conserved residues. Thus, the specific binding of dUMP by TS results from occlusion of competing substrates by steric and electronic effects of residues in the active site cavity. When Asn-229 is replaced by a cysteine, the Cys-229 S gamma rotates out of the active site, and the mutant enzyme binds both dCMP and dUMP tightly but does not methylate dCMP. Thus simply admitting dCMP into the dUMP binding site of TS is not sufficient for methylation of dCMP. Structures of nucleotide complexes of TS N229D provide a reasonable explanation for the preferential methylation of dCMP instead of dUMP by this mutant. In TS N229D.dCMP, Asp-229 forms hydrogen bonds to 3-N and 40NH2 of dCMP. Neither the Asp-229 carboxyl moiety nor ordered water appears to hydrogen bond to 4-O of dUMP. Hydrogen bonds to 4-O (or 4-NH2) have been proposed to stabilize reaction intermediates. If their absence in TS N229D.dUMP persists in the ternary complex, it could explain the 10(4)-fold decrease in kcat/Km for dUMP.

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Related Citations: 

• Stereochemistry of a Multistep/Bipartite Methyl Transfer Reaction: Thymidylate Synthase
  Stroud, R.M., Finer-Moore, J.S.
  (1993) FASEB J 7: 671

• 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

• Exclusion of 2'-Deoxycytidine 5'-Monophosphate by Asparagine 229 of Thymidylate Synthase
  Liu, L., Santi, D.V.
  (1993) Biochemistry 32: 9263

• Mutation of Asparagine 229 to Aspartate in Thymidylate Synthase Converts the Enzyme to a Deoxycytidylate Methylase
  Liu, L., Santi, D.V.
  (1992) Biochemistry 31: 5100

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDYLATE SYNTHASE	A	316	Lacticaseibacillus casei	Mutation(s): 1  Gene Names: N229C MUTANT OF CLONED L. CASE, thyA EC: 2.1.1.45
UniProt
Find proteins for P00469 (Lactobacillus casei) Explore P00469  Go to UniProtKB:  P00469

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCM	B [auth A]	2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O7 P NCMVOABPESMRCP-SHYZEUOFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DCM	Binding MOAD:  1NJA	Kd: 490 (nM) from 1 assay(s)
	PDBBind:  1NJA	Kd: 490 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.180 
• R-Value Observed: 0.180 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.7	α = 90
b = 78.7	β = 90
c = 230.6	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
R-AXIS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-01-23 
• Released Date: 1996-07-11 
Deposition Author(s): Finer-Moore, J., Stroud, R.M.

Revision History  

• Version 1.0: 1996-07-11
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations, Other