3PKP

Q83S Variant of S. Enterica RmlA with dATP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Expanding the Nucleotide and Sugar 1-Phosphate Promiscuity of Nucleotidyltransferase RmlA via Directed Evolution.

Moretti, R., Chang, A., Peltier-Pain, P., Bingman, C.A., Phillips, G.N., Thorson, J.S.

(2011) J Biol Chem 286: 13235-13243

  • DOI: 10.1074/jbc.M110.206433
  • Primary Citation of Related Structures:  
    3PKP, 3PKQ

  • PubMed Abstract: 

    • Directed evolution is a valuable technique to improve enzyme activity in the absence of a priori structural knowledge, which can be typically enhanced via structure-guided strategies. In this study, a combination of both whole-gene error-prone polymerase chain reaction and site-saturation mutagenesis enabled the rapid identification of mutations that improved RmlA activity toward non-native substrates ...

    Directed evolution is a valuable technique to improve enzyme activity in the absence of a priori structural knowledge, which can be typically enhanced via structure-guided strategies. In this study, a combination of both whole-gene error-prone polymerase chain reaction and site-saturation mutagenesis enabled the rapid identification of mutations that improved RmlA activity toward non-native substrates. These mutations have been shown to improve activities over 10-fold for several targeted substrates, including non-native pyrimidine- and purine-based NTPs as well as non-native D- and L-sugars (both α- and β-isomers). This study highlights the first broadly applicable high throughput sugar-1-phosphate nucleotidyltransferase screen and the first proof of concept for the directed evolution of this enzyme class toward the identification of uniquely permissive RmlA variants.

    Organizational Affiliation: 

    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucose-1-phosphate thymidylyltransferase292Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 1 
Gene Names: rfbA, rmlA, STM2095
EC: 2.7.7.24
UniProt
Find proteins for P26393 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P26393 
Go to UniProtKB:  P26393
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26393
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP
Download Ideal Coordinates CCD File 
AA [auth K],
DA [auth L],
I [auth A],
L [auth B],
O [auth C],
AA [auth K],
DA [auth L],
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth I],
X [auth J]
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
BA [auth K],
CA [auth K],
EA [auth L],
FA [auth L],
J [auth A],
BA [auth K],
CA [auth K],
EA [auth L],
FA [auth L],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
S [auth D],
T [auth D],
V [auth I],
W [auth I],
Y [auth J],
Z [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.879α = 90
b = 134.313β = 90
c = 175.829γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description