6JT8 | pdb_00006jt8

Crystal structure of 450-451_deletion mutant of FGAM Synthetase

• PDB DOI: https://doi.org/10.2210/pdb6JT8/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-04-10 Released: 2020-03-04 
• Deposition Author(s): Sharma, N., Ahalawat, N., Sandhu, P., Mondal, J., Anand, R.
• Funding Organization(s): Department of Science & Technology (India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.159 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.125 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.127 (Depositor) 

Starting Model: experimental

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

• PubMed: 32284973 
• DOI: https://doi.org/10.1126/sciadv.aay7919
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
Center for Interdisciplinary Science, Tata Institute of Fundamental Research, Hyderabad 500107, India.
Department of Biochemistry, Stellenbosch University, Stellenbosch 7602, South Africa.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 146.93 kDa 
• Atom Count: 11,874 
• Modeled Residue Count: 1,288 
• Deposited Residue Count: 1,301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylformylglycinamidine synthase	A	1,301	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: purL, C2273_06610, DD95_10355 EC: 6.3.5.3
UniProt
Find proteins for P74881 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P74881  Go to UniProtKB:  P74881

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	M [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4	AA [auth A], BA [auth A], CA [auth A], DA [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [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]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	EA [auth A], FA [auth A], GA [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]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	WA [auth A], XA [auth A], YA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CYG	A	L-PEPTIDE LINKING	C8 H14 N2 O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.159 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.125 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.127 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.151	α = 90
b = 147.151	β = 90
c = 141.346	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): Sharma, N., Ahalawat, N., Sandhu, P., Mondal, J., Anand, R.

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Funding Organization	Location	Grant Number
Department of Science & Technology (India)	India	DST/INT/SOUTH AFRICA/P-04/2014

Revision History  

• 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