PDBsum entry: 1pae

Transferase

PDB id: 1pae

Contents

Protein chain

148 a.a. *

Metals

_SE ×2

Waters ×15

* Residue conservation analysis

PDB id:

1pae

Name:

Transferase

Title:

Nucleoside diphosphate kinase

Structure:

Nucleoside diphosphate kinase, cytosolic. Chain: x. Synonym: ndk, ndp kinase. Engineered: yes. Mutation: yes

Source:

Dictyostelium discoideum. Organism_taxid: 44689. Gene: ndk. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.70Å R-factor: 0.188 R-free: 0.232

Authors:

M.-P.Strub,F.Hoh,J.-F.Sanchez,J.M.Strub,A.Bock,A.Aumelas,C.D

Key ref:

M.P.Strub et al. (2003). Selenomethionine and selenocysteine double labeling strategy for crystallographic phasing. Structure, 11, 1359-1367. PubMed id: 14604526 DOI: 10.1016/j.str.2003.09.014

Date:

14-May-03 Release date: 11-Nov-03

Protein chain

P22887  (NDKC_DICDI) -  Nucleoside diphosphate kinase, cytosolic

Seq: 155 a.a.

Struc: 148 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.7.4.6 - Nucleoside-diphosphate kinase.
• Reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate

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

 Gene Ontology (GO) functional annotation 

• Cellular component: plasma membrane (6 terms)
• Biological process: cytoskeleton organization (13 terms)
• Biochemical function: nucleotide binding (6 terms)

reference

DOI no: 10.1016/j.str.2003.09.014

Structure 11:1359-1367 (2003)

PubMed id: 14604526

Selenomethionine and selenocysteine double labeling strategy for crystallographic phasing.

M.P.Strub, F.Hoh, J.F.Sanchez, J.M.Strub, A.Böck, A.Aumelas, C.Dumas.

ABSTRACT

A protocol for the quantitative incorporation of both selenomethionine and selenocysteine into recombinant proteins overexpressed in Escherichia coli is described. This methodology is based on the use of a suitable cysteine auxotrophic strain and a minimal medium supplemented with selenium-labeled methionine and cysteine. The proteins chosen for these studies are the cathelin-like motif of protegrin-3 and a nucleoside-diphosphate kinase. Analysis of the purified proteins by electrospray mass spectrometry and X-ray crystallography revealed that both cysteine and methionine residues were isomorphously replaced by selenocysteine and selenomethionine. Moreover, selenocysteines allowed the formation of unstrained and stable diselenide bridges in place of the canonical disulfide bonds. In addition, we showed that NDP kinase contains a selenocysteine adduct on Cys122. This novel selenium double-labeling method is proposed as a general approach to increase the efficiency of the MAD technique used for phase determination in protein crystallography.

Selected figure(s)

Figure 2.
Figure 2. Sulfur-Selenium Isomorphism in ProS and NDP Kinase Structures(A and B) Comparison of 3D structures of native ProS (gray) (PDB entry 1KWI) and [SeMet, SeCys]-ProS derivative in the surroundings of the C107-C124 (A) and C85-C96 (B) disulfide bridges. The diselenide bonds are colored in yellow and N, C, O atoms are colored in blue, green, and red, respectively.(C) Comparison of the X-ray structure of [SetMet, SeCys]-NDP kinase H122C mutant with the unlabeled one (PDB entry 1NDK) in the vicinity of the SeCys122 residue. The unlabeled protein is colored in gray.

The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 1359-1367) copyright 2003.

Figure was selected by the author.