6JT7

Crystal structure of 452-453_deletion mutant of FGAM Synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.125 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation.

Sharma, N.Ahalawat, N.Sandhu, P.Strauss, E.Mondal, J.Anand, R.

(2020) Sci Adv 6: eaay7919-eaay7919

  • DOI: https://doi.org/10.1126/sciadv.aay7919
  • Primary Citation of Related Structures:  
    6JT7, 6JT8, 6JT9, 6JTA

  • PubMed Abstract: 

    Transient tunnels that assemble and disassemble to facilitate passage of unstable intermediates in enzymes containing multiple reaction centers are controlled by allosteric cues. Using the 140-kDa purine biosynthetic enzyme PurL as a model system and a combination of biochemical and x-ray crystallographic studies, we show that long-distance communication between ~25-Å distal active sites is initiated by an allosteric switch, residing in a conserved catalytic loop, adjacent to the synthetase active site. Further, combinatory experiments seeded from molecular dynamics simulations help to delineate transient states that bring out the central role of nonfunctional adaptor domains. We show that carefully orchestrated conformational changes, facilitated by interplay of dynamic interactions at the allosteric switch and adaptor-domain interface, control reactivity and concomitant formation of the ammonia tunnel. This study asserts that substrate channeling is modulated by allosteric hotspots that alter protein energy landscape, thereby allowing the protein to adopt transient conformations paramount to function.


  • Organizational Affiliation

    Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoribosylformylglycinamidine synthase1,301Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: purLC2273_06610DD95_10355
EC: 6.3.5.3
UniProt
Find proteins for P74881 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P74881 
Go to UniProtKB:  P74881
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP74881
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
GA [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
HA [auth A]
IA [auth A]
JA [auth A]
KA [auth A]
LA [auth A]
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth A],
PA [auth A],
QA [auth A],
RA [auth A],
SA [auth A],
TA [auth A],
UA [auth A],
VA [auth A],
WA [auth A],
XA [auth A],
YA [auth A],
ZA [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AC [auth A]
BC [auth A]
CC [auth A]
DB [auth A]
DC [auth A]
AC [auth A],
BC [auth A],
CC [auth A],
DB [auth A],
DC [auth A],
EB [auth A],
EC [auth A],
FB [auth A],
GB [auth A],
HB [auth A],
IB [auth A],
JB [auth A],
KB [auth A],
LB [auth A],
MB [auth A],
NB [auth A],
OB [auth A],
PB [auth A],
QB [auth A],
RB [auth A],
SB [auth A],
TB [auth A],
UB [auth A],
VB [auth A],
WB [auth A],
XB [auth A],
YB [auth A],
ZB [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
FA [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A]
B [auth A]
BA [auth A]
C [auth A]
CA [auth A]
AA [auth A],
B [auth A],
BA [auth A],
C [auth A],
CA [auth A],
D [auth A],
DA [auth A],
E [auth A],
EA [auth A],
F [auth A],
FC [auth A],
G [auth A],
GC [auth A],
H [auth A],
HC [auth A],
I [auth A],
IC [auth A],
J [auth A],
JC [auth A],
K [auth A],
KC [auth A],
L [auth A],
LC [auth A],
M [auth A],
MC [auth A],
N [auth A],
NC [auth A],
O [auth A],
OC [auth A],
P [auth A],
PC [auth A],
Q [auth A],
QC [auth A],
R [auth A],
RC [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
SC [auth A],
TC [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth A],
BB [auth A],
CB [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CYG
Query on CYG
A
L-PEPTIDE LINKINGC8 H14 N2 O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.125 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.271α = 90
b = 146.271β = 90
c = 140.989γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Science & Technology (India)IndiaDST/INT/SOUTH AFRICA/P-04/2014

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description