2QK4 | pdb_00002qk4

Human glycinamide ribonucleotide synthetase

• PDB DOI: https://doi.org/10.2210/pdb2QK4/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-07-10 Released: 2007-07-24 
• Deposition Author(s): Lehtio, L., Welin, M., Arrowsmith, C.H., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Herman, M.D., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg-Schiavone, L., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Moche, M., Nyman, T., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Tresaugues, L., van den Berg, S., Weigelt, J., Nordlund, P., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.221 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Structural studies of tri-functional human GART.

Welin, M., Grossmann, J.G., Flodin, S., Nyman, T., Stenmark, P., Tresaugues, L., Kotenyova, T., Johansson, I., Nordlund, P., Lehtio, L.

(2010) Nucleic Acids Res 38: 7308-7319

• PubMed: 20631005 
• DOI: https://doi.org/10.1093/nar/gkq595
• Primary Citation Related Structures: 
  2QK4, 2V9Y


• PubMed Abstract: 
  

  Human purine de novo synthesis pathway contains several multi-functional enzymes, one of which, tri-functional GART, contains three enzymatic activities in a single polypeptide chain. We have solved structures of two domains bearing separate catalytic functions: glycinamide ribonucleotide synthetase and aminoimidazole ribonucleotide synthetase. Structures are compared with those of homologous enzymes from prokaryotes and analyzed in terms of the catalytic mechanism. We also report small angle X-ray scattering models for the full-length protein. These models are consistent with the enzyme forming a dimer through the middle domain. The protein has an approximate seesaw geometry where terminal enzyme units display high mobility owing to flexible linker segments. This resilient seesaw shape may facilitate internal substrate/product transfer or forwarding to other enzymes in the pathway.

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Organizational Affiliation: 
• Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 98.2 kDa 
• Atom Count: 6,471 
• Modeled Residue Count: 844 
• Deposited Residue Count: 904 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trifunctional purine biosynthetic protein adenosine-3	A, B	452	Homo sapiens	Mutation(s): 1  Gene Names: GART, PGFT, PRGS EC: 6.3.4.13 (PDB Primary Data), 2.1.2.2 (UniProt), 6.3.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P22102 (Homo sapiens) Explore P22102  Go to UniProtKB:  P22102
PHAROS:  P22102 GTEx:  ENSG00000159131

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth A], J [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SO4	D [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], K [auth B], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.221 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.28	α = 90
b = 79.81	β = 104.07
c = 113.87	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-24 
Deposition Author(s): Lehtio, L., Welin, M., Arrowsmith, C.H., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Herman, M.D., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg-Schiavone, L., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Moche, M., Nyman, T., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Tresaugues, L., van den Berg, S., Weigelt, J., Nordlund, P., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-07-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description