Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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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: 156447.02 
• Atom Count: 10121 
• Residue Count: 1394 
• Unique protein chains: 1

2VXO

Human GMP synthetase in complex with XMP

• DOI: 10.2210/pdb2VXO/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.256 
• R-Value Work: 0.203 

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


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
GMP SYNTHASE [GLUTAMINE-HYDROLYZING]	A, B	697	Homo sapiens	Mutation(s): 0  Gene Names: GMPS EC: 6.3.5.2
Find proteins for P49915 (Homo sapiens) Go to Gene View: GMPS Go to UniProtKB:  P49915

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
XMP	A, B	XANTHOSINE-5'-MONOPHOSPHATE 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE C10 H14 N4 O9 P DCTLYFZHFGENCW-UUOKFMHZSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.256 
• R-Value Work: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 98.520	α = 90.00
b = 123.420	β = 90.00
c = 127.960	γ = 90.00

Software Package:

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

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
  Type: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2013-11-13
  Type: Database references