Equilibrium dissociation and unfolding of nucleoside diphosphate kinase from Dictyostelium discoideum. Role of proline 100 in the stability of the hexameric enzyme.


Abstract

The Killer-of-prune (K-pn) mutation in Drosophila corresponds to a Pro-Ser substitution in nucleoside diphosphate kinase (Lascu, I. Chaffotte, A., Limbourg-Bouchon, B., and Véron, M. (1992) J. Biol. Chem. 267, 12775-12781). We investigated the role of the equivalent proline (Pro100) in the formation and stability of the Dictyostelium nucleoside diphosphate kinase hexamers. Mutations to serine or glycine had only little effect on the properties of the native enzyme. However, the mutant drastically affected the subunit interaction in the hexamer and the ability of the isolated subunits to associate in vitro. While the wild-type hexamer inactivated and unfolded concomitantly at 5-6 M urea, the mutant proteins dissociated to monomers at 0.5-2 M urea and unfolded at 2.5-4 M urea. At intermediate urea concentrations, the unique species present in solution was a folded, partially active monomer as shown by size-exclusion chromatography, UV, fluorescence, and CD spectroscopy. Proline 100 is located in a loop involved in subunits contact. Altered conformation of the loop in P100S and P100S mutants demonstrates its crucial role in subunit assembly. We propose to explain the conditional dominance of the K-pn mutation by the presence of a monomeric form of the enzyme that would have deleterious effects in vivo. Study holds ProTherm entries: 5224 Extra Details: Pro-Ser substitution; subunit interaction;,partially active monomer; loop

Submission Details

ID: saCjZ5ar

Submitter: Connie Wang

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

Version: 1

Publication Details
Lascu I;Deville-Bonne D;Glaser P;Véron M,J. Biol. Chem. (1993) Equilibrium dissociation and unfolding of nucleoside diphosphate kinase from Dictyostelium discoideum. Role of proline 100 in the stability of the hexameric enzyme. PMID:8397202
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
1KDN 1997-04-21 2.0 STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE
1NDC 1994-06-22 2.0 X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP AND MG2+ AT 2 A RESOLUTION
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
1HHQ 2001-05-31 2.1 Role of active site resiude Lys16 in Nucleoside Diphosphate Kinase
1MN7 2002-10-02 2.15 NDP kinase mutant (H122G;N119S;F64W) in complex with aBAZTTP
1NDP 1994-04-30 2.2 ADENOSINE 5'-DIPHOSPHATE BINDING AND THE ACTIVE SITE OF NUCLEOSIDE DIPHOSPHATE KINASE
1NCL 1996-11-08 2.2 THERMAL STABILITY OF HEXAMERIC AND TETRAMERIC NUCLEOSIDE, DIPHOSPHATE KINASES
1NDK 1993-10-31 2.2 X-RAY STRUCTURE 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
1HIY 2001-05-31 2.6 Binding of nucleotides to NDP kinase
1LEO 1996-11-08 2.6 P100S NUCLEOSIDE DIPHOSPHATE KINASE
1PAE 2003-11-11 2.7 nucleoside diphosphate kinase
1B99 1999-06-28 2.7 3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO 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