5X8C

AMPPCP and TMP bound crystal structure of thymidylate kinase from thermus thermophilus HB8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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This is version 1.2 of the entry. See complete history


Literature

Structural and functional roles of dynamically correlated residues in thymidylate kinase.

Chaudhary, S.K.Jeyakanthan, J.Sekar, K.

(2018) Acta Crystallogr D Struct Biol 74: 341-354

  • DOI: 10.1107/S2059798318002267
  • Primary Citation of Related Structures:  
    5XT8, 5X8J, 5X8K, 5X8B, 5X8A, 5X8D, 5X8C, 5X86, 5X8V, 5X99, 5X98, 5XAK, 5XAL

  • PubMed Abstract: 
  • Thymidylate kinase is an important enzyme in DNA synthesis. It catalyzes the conversion of thymidine monophosphate to thymidine diphosphate, with ATP as the preferred phosphoryl donor, in the presence of Mg 2+ . In this study, the dynamics of the active site and the communication paths between the substrates, ATP and TMP, are reported for thymidylate kinase from Thermus thermophilus ...

    Thymidylate kinase is an important enzyme in DNA synthesis. It catalyzes the conversion of thymidine monophosphate to thymidine diphosphate, with ATP as the preferred phosphoryl donor, in the presence of Mg 2+ . In this study, the dynamics of the active site and the communication paths between the substrates, ATP and TMP, are reported for thymidylate kinase from Thermus thermophilus. Conformational changes upon ligand binding and the path for communication between the substrates and the protein are important in understanding the catalytic mechanism of the enzyme. High-resolution X-ray crystal structures of thymidylate kinase in apo and ligand-bound states were solved. This is the first report of structures of binary and ternary complexes of thymidylate kinase with its natural substrates ATP and ATP-TMP, respectively. Distinct conformations of the active-site residues, the P-loop and the LID region observed in the apo and ligand-bound structures revealed that their concerted motion is required for the binding and proper positioning of the substrate TMP. Structural analyses provide an insight into the mode of substrate binding at the active site. The residues involved in communication between the substrates were identified through network analysis using molecular-dynamics simulations. The residues identified showed high sequence conservation across species. Biochemical analyses show that mutations of these residues either resulted in a loss of activity or affected the thermal stability of the protein. Further, molecular-dynamics analyses of mutants suggest that the proper positioning of TMP is important for catalysis. These data also provide an insight into the phosphoryl-transfer mechanism.


    Organizational Affiliation

    Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thymidylate kinaseA, B198Thermus thermophilus HB8Mutation(s): 0 
Gene Names: tmkTTHA1607
EC: 2.7.4.9
UniProt
Find proteins for Q5SHX3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHX3 
Go to UniProtKB:  Q5SHX3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACP (Subject of Investigation/LOI)
Query on ACP

Download Ideal Coordinates CCD File 
K [auth A]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
TMP (Subject of Investigation/LOI)
Query on TMP

Download Ideal Coordinates CCD File 
C [auth A], L [auth B]THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], S [auth B], T [auth B], U [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , M [auth B] , N [auth B] , O [auth B] , 
D [auth A],  E [auth A],  F [auth A],  G [auth A],  H [auth A],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth B],  R [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.1α = 90
b = 47.53β = 90
c = 152.28γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-21
    Changes: Data collection, Database references