4JA0 | pdb_00004ja0

Crystal structure of the invertebrate bi-functional purine biosynthesis enzyme PAICS at 2.8 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4JA0/pdb

• Classification: PROTEIN BINDING
• Organism(s): Bombyx mori
• Mutation(s): No 


• Deposited: 2013-02-18 Released: 2013-02-27 
• Deposition Author(s): Taschner, M., Basquin, J., Benda, C., Lorentzen, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.263 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the invertebrate bifunctional purine biosynthesis enzyme PAICS at 2.8 angstrom resolution.

Taschner, M., Basquin, J., Benda, C., Lorentzen, E.

(2013) Proteins 81: 1473-1478

• PubMed: 23553965 
• DOI: https://doi.org/10.1002/prot.24296
• Primary Citation Related Structures: 
  4JA0


• PubMed Abstract: 
  

  Two important steps of the de novo purine biosynthesis pathway are catalyzed by the 5-aminoimidazole ribonucleotide carboxylase and the 4-(N-succinylcarboxamide)-5-aminoimidazole ribonucleotide synthetase enzymes. In most eukaryotic organisms, these two activities are present in the bifunctional enzyme complex known as PAICS. We have determined the 2.8-Å resolution crystal structure of the 350-kDa invertebrate PAICS from insect cells (Trichoplusia ni) using single-wavelength anomalous dispersion methods. Comparison of insect PAICS to human and prokaryotic homologs provides insights into substrate binding and reveals a highly conserved enzymatic framework across divergent species.

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Organizational Affiliation: 
• Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, Martinsried, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 191.26 kDa 
• Atom Count: 12,091 
• Modeled Residue Count: 1,570 
• Deposited Residue Count: 1,700 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole carboxylase	A, B, C, D	425	Bombyx mori	Mutation(s): 0
UniProt
Find proteins for Q1HQ66 (Bombyx mori) Explore Q1HQ66  Go to UniProtKB:  Q1HQ66

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth D], T [auth D], U [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.263 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.729	α = 90
b = 219.726	β = 90
c = 60.645	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-27 
Deposition Author(s): Taschner, M., Basquin, J., Benda, C., Lorentzen, E.

Revision History  

• Version 1.0: 2013-02-27
  Type: Initial release
  
• Version 1.1: 2013-04-10
  Changes: Database references
• Version 1.2: 2013-10-23
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description