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


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. Study holds ProTherm entries: 19539, 19540, 19541, 19542, 19543, 19544, 19545 Extra Details: Transition 1 nucleoside monophosphate kinase; differential scanning calorimetry; X-ray crystallography; guanosine monophosphate kinase; oligomerization

Submission Details

ID: sigtNpML4

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:51 p.m.

Version: 1

Publication Details
Hible G;Renault L;Schaeffer F;Christova P;Zoe Radulescu A;Evrin C;Gilles AM;Cherfils J,J. Mol. Biol. (2005) Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase. PMID:16140325
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1S96 2004-02-10 2.0 The 2.0 A X-ray structure of Guanylate Kinase from E.coli
2AN9 2005-08-30 2.35 Crystal Structure Of Oligomeric E.coli Guanylate Kinase In Complex With GDP
2F3R 2006-05-30 2.5 Crystal Structure Of E.coli Guanylate Kinase In Complex With Ap5G
2ANB 2005-08-30 2.9 Crystal Structure Of Oligomeric E.coli Guanylate Kinase In Complex With GMP
2F3T 2006-05-30 3.16 Crystal Structure Of E.coli Guanylate Kinase In Complex With Ganciclovir monophosphate
2ANC 2005-08-30 3.2 Crystal Structure Of Unliganded Form Of Oligomeric E.coli Guanylate Kinase

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
95.7 Guanylate kinase Q9X6M5 KGUA_SALTY
95.7 Guanylate kinase Q57I92 KGUA_SALCH
96.1 Guanylate kinase Q8Z2H9 KGUA_SALTI
96.1 Guanylate kinase Q5PC40 KGUA_SALPA
99.5 Guanylate kinase Q329K8 KGUA_SHIDS
99.5 Guanylate kinase Q8XD88 KGUA_ECO57
99.5 Guanylate kinase Q31UQ6 KGUA_SHIBS
100.0 Guanylate kinase Q3YW11 KGUA_SHISS
100.0 Guanylate kinase P60548 KGUA_SHIFL
100.0 Guanylate kinase Q1R4U3 KGUA_ECOUT
100.0 Guanylate kinase P60546 KGUA_ECOLI
100.0 Guanylate kinase P60547 KGUA_ECOL6
100.0 Guanylate kinase Q0TBG1 KGUA_ECOL5