PDBsum entry: 2j41

Transferase

PDB id: 2j41

Contents

Protein chains

167 a.a. *

174 a.a. *

Ligands

SO4 ×5

5GP ×3

Metals

__K ×3

Waters ×471

* Residue conservation analysis

PDB id:

2j41

Name:

Transferase

Title:

Crystal structure of staphylococcus aureus guanylate monophosphate kinase

Structure:

Guanylate kinase. Chain: a, b, c, d. Synonym: gmp kinase, staphylococcus aureus guanylate monophosphate kinase. Engineered: yes

Source:

Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.9Å R-factor: 0.209 R-free: 0.239

Authors:

K.El Omari,B.Dhaliwal,M.Lockyer,I.Charles,A.R.Hawkins, D.K.Stammers

Key ref:

K.El Omari et al. (2006). Structure of Staphylococcus aureus guanylate monophosphate kinase. Acta Crystallograph Sect F Struct Biol Cryst Commun, 62, 949-953. PubMed id: 17012781 Ref: Full text

Date:

24-Aug-06 Release date: 11-Oct-06

Protein chains

Q5HGM3  (KGUA_STAAC) -  Guanylate kinase

Seq: 207 a.a.

Struc: 167 a.a.

Protein chains

Q5HGM3  (KGUA_STAAC) -  Guanylate kinase

Seq: 207 a.a.

Struc: 174 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.2.7.4.8 - Guanylate kinase.
• Reaction: ATP + GMP = ADP + GDP

ATP + GMP (Bound ligand (Het Group name = 5GP) corresponds exactly) = ADP + GDP

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: purine nucleotide metabolic process (1 term)
• Biochemical function: nucleotide binding (5 terms)

reference

Full text	Acta Crystallograph Sect F Struct Biol Cryst Commun 62:949-953 (2006)
PubMed id: 17012781

Structure of Staphylococcus aureus guanylate monophosphate kinase.

K.El Omari, B.Dhaliwal, M.Lockyer, I.Charles, A.R.Hawkins, D.K.Stammers.

ABSTRACT

Nucleotide monophosphate kinases (NMPKs) are potential antimicrobial drug targets owing to their role in supplying DNA and RNA precursors. The present work reports the crystal structure of Staphylococcus aureus guanylate monophosphate kinase (SaGMK) at 1.9 A resolution. The structure shows that unlike most GMKs SaGMK is dimeric, confirming the role of the extended C-terminus in dimer formation as first observed for Escherichia coli GMK (EcGMK). One of the two SaGMK dimers within the crystal asymmetric unit has two monomers in different conformations: an open form with a bound sulfate ion (mimicking the beta-phosphate of ATP) and a closed form with bound GMP and sulfate ion. GMP-induced domain movements in SaGMK can thus be defined by comparison of these conformational states. Like other GMKs, the binding of GMP firstly triggers a partial closure of the enzyme, diminishing the distance between the GMP-binding and ATP-binding sites. In addition, the closed structure shows the presence of a potassium ion in contact with the guanine ring of GMP. The potassium ion appears to form an integral part of the GMP-binding site, as the Tyr36 side chain has significantly moved to form a metal ion-ligand coordination involving the lone pair of the side-chain O atom. The potassium-binding site might also be exploited in the design of novel inhibitors.

Selected figure(s)

Figure 2.
Representative DLS mass particle size distribution of SaGMK (1 mg ml^[minus sign]1) in 20 mM Tris pH 7, 150 mM NaCl, 1 mM DTT. The protein displays a hydrodynamic radius of 3.1 nm, which gives an extrapolated molecular weight of 47.5 kDa corresponding to a dimer of SaGMK. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 October 1; 62(Pt 10): 949–953. Published online 2006 September 19. doi: 10.1107/S174430910603613X. Copyright [copyright] International Union of Crystallography 2006

Figure 4.
(a) Ribbon diagram showing the superimposition of the SaGMK open state (coloured yellow), closed state (coloured raspberry) and the mouse GMK closed state (coloured blue). The SaGMK ligands, sulfate and GMP, are in grey. (b) Stereo diagram showing the superimposition of the open conformation of the SaGMK active site (transparent representation) onto the closed conformation. The GMP and sulfate are in standard atom colours; the potassium ion is coloured cyan. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 October 1; 62(Pt 10): 949–953. Published online 2006 September 19. doi: 10.1107/S174430910603613X. Copyright [copyright] International Union of Crystallography 2006

The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallograph Sect F Struct Biol Cryst Commun (2006, 62, 949-953) copyright 2006.

Figures were selected by an automated process.