6TNH | pdb_00006tnh

Deoxyguanylosuccinate synthase (DgsS) quaternary structure with AMPPcP, dGMP, Asp, Magnesium at 2.21 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 
    0.228 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6TNH

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes.

Sleiman, D.Garcia, P.S.Lagune, M.Loc'h, J.Haouz, A.Taib, N.Rothlisberger, P.Gribaldo, S.Marliere, P.Kaminski, P.A.

(2021) Science 372: 516-520

  • DOI: https://doi.org/10.1126/science.abe6494
  • Primary Citation Related Structures: 
    6FLF, 6FM0, 6FM1, 6TNH

  • PubMed Abstract: 

    Cells have two purine pathways that synthesize adenine and guanine ribonucleotides from phosphoribose via inosylate. A chemical hybrid between adenine and guanine, 2-aminoadenine (Z), replaces adenine in the DNA of the cyanobacterial virus S-2L. We show that S-2L and Vibrio phage PhiVC8 encode a third purine pathway catalyzed by PurZ, a distant paralog of succinoadenylate synthase (PurA), the enzyme condensing aspartate and inosylate in the adenine pathway. PurZ condenses aspartate with deoxyguanylate into dSMP (N6-succino-2-amino-2'-deoxyadenylate), which undergoes defumarylation and phosphorylation to give dZTP (2-amino-2'-deoxyadenosine-5'-triphosphate), a substrate for the phage DNA polymerase. Crystallography and phylogenetics analyses indicate a close relationship between phage PurZ and archaeal PurA enzymes. Our work elucidates the biocatalytic innovation that remodeled a DNA building block beyond canonical molecular biology.


  • Organizational Affiliation
    • Biology of Gram-Positive Pathogens, Institut Pasteur, CNRS-UMR 2001, Paris, France.

Macromolecule Content 

  • Total Structure Weight: 83.54 kDa 
  • Atom Count: 5,861 
  • Modeled Residue Count: 689 
  • Deposited Residue Count: 726 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Adenylosuccinate synthetase
A, B
363Vibrio phage phiVC8Mutation(s): 0 
Gene Names: phiVC8_p27
EC: 6.3.4.25
UniProt
Find proteins for G3FFN6 (Vibrio phage phiVC8)
Explore G3FFN6 
Go to UniProtKB:  G3FFN6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3FFN6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACP
(Subject of Investigation/LOI)

Query on ACP



Download:Ideal Coordinates CCD File
H [auth A],
L [auth B]
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
DGP
(Subject of Investigation/LOI)

Query on DGP



Download:Ideal Coordinates CCD File
G [auth A],
J [auth B]
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
LTFMZDNNPPEQNG-KVQBGUIXSA-N
ASP
(Subject of Investigation/LOI)

Query on ASP



Download:Ideal Coordinates CCD File
I [auth A]ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG

Query on MG



Download:Ideal Coordinates CCD File
M [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free:  0.228 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.64α = 90
b = 91.64β = 90
c = 189.5γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-06-02
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description