Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 156.45 kDa 
• Atom Count: 10246 
• Modelled Residue Count: 1301 
• Deposited Residue Count: 1394 
• Unique protein chains: 1

2VXO

Human GMP synthetase in complex with XMP

• PDB DOI: 10.2210/pdb2VXO/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-07-08 Released: 2008-08-12 
• Deposition Author(s): Welin, M., Lehtio, L., Andersson, J., Arrowsmith, C.H., Berglund, H., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nyman, T., Olesen, K., Persson, C., Sagemark, J., Schueler, H., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Wisniewska, M., Wikstrom, M., Nordlund, P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.256 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 

Literature

Substrate Specificity and Oligomerization of Human Gmp Synthetase

Welin, M., Lehtio, L., Johansson, A., Flodin, S., Nyman, T., Tresaugues, L., Hammarstrom, M., Graslund, S., Nordlund, P.

(2013) J Mol Biol 425: 4323

• PubMed: 23816837 
• DOI: 10.1016/j.jmb.2013.06.032
• Primary Citation of Related Structures:  
  2VXO


• PubMed Abstract: 
  

Guanine monophosphate (GMP) synthetase is a bifunctional two-domain enzyme. The N-terminal glutaminase domain generates ammonia from glutamine and the C-terminal synthetase domain aminates xanthine monophosphate (XMP) to form GMP. Mammalian GMP synthetases (GMPSs) contain a 130-residue-long insert in the synthetase domain in comparison to bacterial proteins. We report here the structure of a eukaryotic GMPS. Substrate XMP was bound in the crystal structure of the human GMPS enzyme. XMP is bound to the synthetase domain and covered by a LID motif. The enzyme forms a dimer in the crystal structure with subunit orientations entirely different from the bacterial counterparts. The inserted sub-domain is shown to be involved in substrate binding and dimerization. Furthermore, the structural basis for XMP recognition is revealed as well as a potential allosteric site. Enzymes in the nucleotide metabolism typically display an increased activity in proliferating cells due to the increased need for nucleotides. Many drugs used as immunosuppressants and for treatment of cancer and viral diseases are indeed nucleobase- and nucleoside-based compounds, which are acting on or are activated by enzymes in this pathway. The information obtained from the crystal structure of human GMPS might therefore aid in understanding interactions of nucleoside-based drugs with GMPS and in structure-based design of GMPS-specific inhibitors.

---

Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GMP SYNTHASE [GLUTAMINE-HYDROLYZING]	A, B	697	Homo sapiens	Mutation(s): 0  Gene Names: GMPS EC: 6.3.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P49915 (Homo sapiens) Explore P49915  Go to UniProtKB:  P49915
PHAROS:  P49915

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XMP	C [auth A], G [auth B]	XANTHOSINE-5'-MONOPHOSPHATE C10 H14 N4 O9 P DCTLYFZHFGENCW-UUOKFMHZSA-O
SO4	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.256 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.52	α = 90
b = 123.42	β = 90
c = 127.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-07-08 
• Released Date: 2008-08-12 
Deposition Author(s): Welin, M., Lehtio, L., Andersson, J., Arrowsmith, C.H., Berglund, H., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nyman, T., Olesen, K., Persson, C., Sagemark, J., Schueler, H., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Wisniewska, M., Wikstrom, M., Nordlund, P.

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2013-11-13
  Changes: Database references
• Version 1.3: 2019-10-16
  Changes: Data collection, Experimental preparation, Other