Thermal stability of hexameric and tetrameric nucleoside diphosphate kinases. Effect of subunit interaction.


Abstract

The eukaryotic nucleoside diphosphate (NDP) kinases are hexamers, while the bacterial NDP kinases are tetramers made of small, single domain subunits. These enzymes represent an ideal model for studying the effect of subunit interaction on protein stability. The thermostability of NDP kinases of each class was studied by differential scanning calorimetry and biochemical methods. The hexameric NDP kinase from Dictyostelium discoideum displays one single, irreversible differential scanning calorimetry peak (Tm 62 degrees C) over a broad protein concentration, indicating a single step denaturation. The thermal stability of the protein was increased by ADP. The P105G substitution, which affects a loop implicated in subunit contacts, yields a protein that reversibly dissociates to folded monomers at 38 degrees C before the irreversible denaturation occurs (Tm 47 degrees C). ADP delays the dissociation, but does not change the Tm. These data indicate a "coupling" of the quaternary structure with the tertiary structure in the wild-type, but not in the mutated protein. We describe the x-ray structure of the P105G mutant at 2.2-A resolution. It is very similar to that of the wild-type protein. Therefore, a minimal change in the structure leads to a dramatic change of protein thermostability. The NDP kinase from Escherichia coli behaves like the P105G mutant of the Dictyostelium NDP kinase. The detailed study of their thermostability is important, since biological effects of thermolabile NDP kinases have been described in several organisms. Study holds ProTherm entries: 5254, 5255, 5256, 5257, 5258 Extra Details: hexamers; domain subunits; single step denaturation; coupling

Submission Details

ID: eUQoYLEJ4

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:29 p.m.

Version: 1

Publication Details
Giartosio A;Erent M;Cervoni L;Moréra S;Janin J;Konrad M;Lascu I,J. Biol. Chem. (1996) Thermal stability of hexameric and tetrameric nucleoside diphosphate kinases. Effect of subunit interaction. PMID:8663370
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
4C6A 2013-11-20 1.25 High Resolution Structure of the Nucleoside diphosphate kinase
3FKB 2009-09-29 1.65 Structure of NDPK H122G and tenofovir-diphosphate
1NPK 1994-11-01 1.8 REFINED X-RAY STRUCTURE OF DICTYOSTELIUM NUCLEOSIDE DIPHOSPHATE KINASE AT 1,8 ANGSTROMS RESOLUTION
1F3F 2000-09-13 1.85 STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX
1HLW 2001-02-28 1.9 STRUCTURE OF THE H122A MUTANT OF THE NUCLEOSIDE DIPHOSPHATE KINASE
1F6T 2000-09-13 1.92 STRUCTURE OF THE NUCLEOSIDE DIPHOSPHATE KINASE/ALPHA-BORANO(RP)-TDP.MG COMPLEX
1S5Z 2005-02-01 2.0 NDP kinase in complex with adenosine phosphonoacetic acid
1NDC 1994-06-22 2.0 X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP AND MG2+ AT 2 A RESOLUTION
1KDN 1997-04-21 2.0 STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE
1HHQ 2001-05-31 2.1 Role of active site resiude Lys16 in Nucleoside Diphosphate Kinase
1NSP 1995-07-10 2.1 MECHANISM OF PHOSPHATE TRANSFER BY NUCLEOSIDE DIPHOSPHATE KINASE: X-RAY STRUCTURES OF A PHOSPHO-HISTIDINE INTERMEDIATE OF THE ENZYMES FROM DROSOPHILA AND DICTYOSTELIUM
1MN7 2002-10-02 2.15 NDP kinase mutant (H122G;N119S;F64W) in complex with aBAZTTP
1NDK 1993-10-31 2.2 X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE
1NCL 1996-11-08 2.2 THERMAL STABILITY OF HEXAMERIC AND TETRAMERIC NUCLEOSIDE, DIPHOSPHATE KINASES
1NDP 1994-04-30 2.2 ADENOSINE 5'-DIPHOSPHATE BINDING AND THE ACTIVE SITE OF NUCLEOSIDE DIPHOSPHATE KINASE
1LWX 1997-08-20 2.3 AZT DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE
2BEF 1998-08-12 2.3 CRYSTAL STRUCTURE OF NDP KINASE COMPLEXED WITH MG, ADP, AND BEF3
4CP5 2015-02-11 2.32 ndpK in complex with (Rp)-SPMPApp
1B4S 1999-06-15 2.5 STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE H122G MUTANT
1LEO 1996-11-08 2.6 P100S NUCLEOSIDE DIPHOSPHATE KINASE
1HIY 2001-05-31 2.6 Binding of nucleotides to NDP kinase
1B99 1999-06-28 2.7 3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE
1PAE 2003-11-11 2.7 nucleoside diphosphate kinase
1BUX 1999-04-27 2.8 3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE
1MN9 2003-03-18 2.9 NDP kinase mutant (H122G) complex with RTP

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Nucleoside diphosphate kinase, mitochondrial P34093 NDKM_DICDI
100.0 Nucleoside diphosphate kinase, cytosolic P22887 NDKC_DICDI