5TT6

T4 RNA Ligase 1 (K99M)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NAD(+)-dependent polynucleotide ligases.

Unciuleac, M.C.Goldgur, Y.Shuman, S.

(2017) Proc Natl Acad Sci U S A 114: 2592-2597

  • DOI: 10.1073/pnas.1619220114
  • Primary Citation of Related Structures:  
    5TT5, 5TT6

  • PubMed Abstract: 
  • Polynucleotide ligases comprise a ubiquitous superfamily of nucleic acid repair enzymes that join 3'-OH and 5'-PO 4 DNA or RNA ends. Ligases react with ATP or NAD + and a divalent cation cofactor to form a covalent enzyme-(lysine-Nζ)-adenylate intermediate ...

    Polynucleotide ligases comprise a ubiquitous superfamily of nucleic acid repair enzymes that join 3'-OH and 5'-PO 4 DNA or RNA ends. Ligases react with ATP or NAD + and a divalent cation cofactor to form a covalent enzyme-(lysine-Nζ)-adenylate intermediate. Here, we report crystal structures of the founding members of the ATP-dependent RNA ligase family (T4 RNA ligase 1; Rnl1) and the NAD + -dependent DNA ligase family ( Escherichia coli LigA), captured as their respective Michaelis complexes, which illuminate distinctive catalytic mechanisms of the lysine adenylylation reaction. The 2.2-Å Rnl1•ATP•(Mg 2+ ) 2 structure highlights a two-metal mechanism, whereby: a ligase-bound "catalytic" Mg 2+ (H 2 O) 5 coordination complex lowers the p K a of the lysine nucleophile and stabilizes the transition state of the ATP α phosphate; a second octahedral Mg 2+ coordination complex bridges the β and γ phosphates; and protein elements unique to Rnl1 engage the γ phosphate and associated metal complex and orient the pyrophosphate leaving group for in-line catalysis. By contrast, the 1.55-Å LigA•NAD + •Mg 2+ structure reveals a one-metal mechanism in which a ligase-bound Mg 2+ (H 2 O) 5 complex lowers the lysine p K a and engages the NAD + α phosphate, but the β phosphate and the nicotinamide nucleoside of the nicotinamide mononucleotide (NMN) leaving group are oriented solely via atomic interactions with protein elements that are unique to the LigA clade. The two-metal versus one-metal dichotomy demarcates a branchpoint in ligase evolution and favors LigA as an antibacterial drug target.


    Organizational Affiliation

    Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065; s-shuman@ski.mskcc.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
T4 RNA ligase 1A394Escherichia virus T4Mutation(s): 1 
Gene Names: 63
EC: 6.5.1.3
UniProt
Find proteins for P00971 (Enterobacteria phage T4)
Explore P00971 
Go to UniProtKB:  P00971
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00971
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
D [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.293α = 90
b = 39.96β = 116.36
c = 108.268γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Database references