Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 96.66 kDa 
• Atom Count: 6964 
• Residue Count: 838 
• Unique protein chains: 1

6YB9

Human octameric PAICS in complex with SAICAR, AMP-PNP, and magnesium

• DOI: 10.2210/pdb6YB9/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-16 Released: 2020-07-08 
• Deposition Author(s): Skerlova, J., Unterlass, J., Gottmann, M., Homan, E., Helleday, T., Jemth, A.S., Stenmark, P.
• Funding Organization(s): Swedish Research Council, European Research Council (ERC), Ministry of Education (MoE, Czech Republic)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.229 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 

Literature

Crystal structures of human PAICS reveal substrate and product binding of an emerging cancer target.

Skerlova, J., Unterlass, J., Gottmann, M., Marttila, P., Homan, E., Helleday, T., Jemth, A.S., Stenmark, P.

(2020) J Biol Chem 295: 11656-11668

• PubMed: 32571877 
• DOI: 10.1074/jbc.RA120.013695
• Primary Citation of Related Structures:  
  6YB8, 6YB9


• PubMed Abstract: 
  

The bifunctional human enzyme phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthetase (PAICS) catalyzes two essential steps in the de novo purine biosynthesis pathway. PAICS is overexpressed in many cancers and could be a promising target for the development of cancer therapeutics. Here, using gene knockdowns and clonogenic survival and cell viability assays, we demonstrate that PAICS is required for growth and survival of prostate cancer cells. PAICS catalyzes the carboxylation of aminoimidazole ribonucleotide (AIR) and the subsequent conversion of carboxyaminoimidazole ribonucleotide (CAIR) and l-aspartate to N -succinylcarboxamide-5-aminoimidazole ribonucleotide (SAICAR). Of note, we present the first structures of human octameric PAICS in complexes with native ligands. In particular, we report the structure of PAICS with CAIR bound in the active sites of both domains and SAICAR bound in one of the SAICAR synthetase domains. Moreover, we report the PAICS structure with SAICAR and an ATP analog occupying the SAICAR synthetase active site. These structures provide insight into substrate and product binding and the architecture of the active sites, disclosing important structural information for rational design of PAICS inhibitors as potential anticancer drugs.

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Organizational Affiliation: 

Department of Experimental Medical Science, Lund University, Lund, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multifunctional protein ADE2	A, B	425	Homo sapiens	Mutation(s): 0  Gene Names: PAICS, ADE2, AIRC, PAIS EC: 6.3.2.6 (PDB Primary Data), 4.1.1.21 (PDB Primary Data)
Find proteins for P22234 (Homo sapiens) Explore P22234  Go to UniProtKB:  P22234
NIH Common Fund Data Resources
PHAROS:  P22234 GTEx:  ENSG00000128050

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	A, B	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
OK8	A, B	(2~{S})-2-[[5-azanyl-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]imidazol-4-yl]car bonylamino]butanedioic acid C13 H19 N4 O12 P NAQGHJTUZRHGAC-ZZZDFHIKSA-N
EDO	A, B	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.229 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.263	α = 90
b = 154.019	β = 90
c = 223.624	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-03-16 
• Released Date: 2020-07-08 
Deposition Author(s): Skerlova, J., Unterlass, J., Gottmann, M., Homan, E., Helleday, T., Jemth, A.S., Stenmark, P.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--
European Research Council (ERC)	European Union	695376
Ministry of Education (MoE, Czech Republic)	Czech Republic	CZ.02.2.69/0.0/0.0/16_027/0008477

Revision History 

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2020-09-02
  Changes: Database references, Derived calculations