PDBsum entry: 2anb

Transferase

PDB-id: 2anb

Asymmetric unit

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PROCHECK

Protein chain

206 a.a. *

Ligands

SO4

5GP

Waters ×12

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit, hexamer
- as defined in PDB file (see also PQS)

PDB id:

2anb

Name:

Transferase

Title:

Crystal structure of oligomeric e.Coli guanylate kinase in complex with gmp

Structure:

Guanylate kinase. Chain: a. Synonym: gmp kinase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: gmk. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biological unit:

Hexamer (from PDB file)

UniProt:

P60546 (KGUA_ECOLI)

Seq:

207 a.a.

Struc:

206 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

E.C.2.7.4.8   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

ATP + GMP = ADP + GDP (see diagram below)

Resolution:

2.90Å

R-factor:

0.205

R-free:

0.242

Authors:

G.Hible,L.Renault,F.Schaeffer,P.Christova,A.Z.Radulescu, C.Evrin,A.M.Gilles,J.Cherfils

Key ref:

G.Hible et al. (2005). Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase.. J Mol Biol, 352, 1044-1059. [PubMed id: 16140325] [DOI: 10.1016/j.jmb.2005.07.042]

Date:

11-Aug-05

Release date:

30-Aug-05

Related entries:

2an9
crystal structure of oligomeric e.Coli guanylate kinase in
complex with gdp
2anc
crystal structure of unliganded form of oligomeric e.Coli
guanylate kinase

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Key reference

DOI no: 10.1016/j.jmb.2005.07.042

J Mol Biol 352:1044-1059 (2005)

PubMed id: 16140325

Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase.

G.Hible, L.Renault, F.Schaeffer, P.Christova, A.Zoe Radulescu, C.Evrin, A.M.Gilles, J.Cherfils.

ABSTRACT

Guanosine monophosphate kinases (GMPKs), which catalyze the phosphorylation of GMP and dGMP to their diphosphate form, have been characterized as monomeric enzymes in eukaryotes and prokaryotes. Here, we report that GMPK from Escherichia coli (ecGMPK) assembles in solution and in the crystal as several different oligomers. Thermodynamic analysis of ecGMPK using differential scanning calorimetry shows that the enzyme is in equilibrium between a dimer and higher order oligomers, whose relative amounts depend on protein concentration, ionic strength, and the presence of ATP. Crystallographic structures of ecGMPK in the apo, GMP and GDP-bound forms were solved at 3.2A, 2.9A and 2.4A resolution, respectively. ecGMPK forms a hexamer with D3 symmetry in all crystal forms, in which the two nucleotide-binding domains are able to undergo closure comparable to that of monomeric GMPKs. The 2-fold and 3-fold interfaces involve a 20-residue C-terminal extension and a sequence signature, respectively, that are missing from monomeric eukaryotic GMPKs, explaining why ecGMPK forms oligomers. These signatures are found in GMPKs from proteobacteria, some of which are human pathogens. GMPKs from these bacteria are thus likely to form the same quaternary structures. The shift of the thermodynamic equilibrium towards the dimer at low ecGMPK concentration together with the observation that inter-subunit interactions partially occlude the ATP-binding site in the hexameric structure suggest that the dimer may be the active species at physiological enzyme concentration.

Selected figure(s)

Figure 6.
Figure 6. Nucleotide-induced conformational changes in the ecGMPK hexamer. (a) Domain motion within the hexamer. Superimposition of apo (red) and GMP-bound (yellow) NMP-binding and LID domains onto a GDP-bound monomer (blue) within the GDP-bound hexamer (in light blue). (b) NMP-binding and LID domain closure. Superimposition of the apo (red) and GMP-bound (yellow) ecGMPK monomers. GMP and the sulfate ion in ecGMPK·GMP are shown in ball-and-stick and van der Waals surface. Residues involved in subunit interfaces are marked by small spheres.

Figure 7.
Figure 7. The ecGMPK catalytic site. (a) Schematic diagram of the interactions of GDP with ecGMPK. Broken lines in orange, pink and black correspond, respectively, to the interactions found in monomer A, monomer B or both monomers. Labels for the NMP-binding region are in blue, for the CORE region in black. (b) Close-up view of the putative ATP-binding site at the trimeric interface (subunit carrying the ATP-binding site in blue, neighboring subunit in green). The location of ADP in the mGMPK·GMP·ADP structure (ADPm) is overlayed in transparency in grey ball-and-stick. The non-substrate GDP molecule is shown in red. Note that both Tyr31 from the neighboring subunit and the non-substrate GDP molecule would conflict with the binding of the ATP substrate. (c) Schematic diagram of the interactions of the guanosine moiety of the non-substrate GDP. Labels for 3-fold related subunits are in green and blue. (d) A model of catalytic interactions of conserved arginine residues. Overlay of GDP (red) from the ecGMPK·GDP structure onto GMP in the closed conformation of ecGMPK·GMP· Click to view the MathML source- [0?wchp=dGLbVtz-zSkWz] (in yellow), based on the superposition of the NMP-binding domain. Candidate hydrogen bonds of the conserved arginine residues to the phosphate groups are shown in dotted lines. ADP, GMP and the invariant arginine residues from the mGMPK·GMP·ADP structure are superposed to show the equivalence of the sulfate ion with the b-phosphate group of ADP (in blue).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 352, 1044-1059) copyright 2005.

Figures were selected by an automated process.