PDBsum entry 1pae

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protein metals links
Transferase PDB id
Protein chain
148 a.a. *
_SE ×2
Waters ×15
* Residue conservation analysis
PDB id:
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)
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
14-May-03     Release date:   11-Nov-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P22887  (NDKC_DICDI) -  Nucleoside diphosphate kinase, cytosolic
155 a.a.
148 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Nucleoside-diphosphate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
+ nucleoside diphosphate
+ nucleoside triphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     plasma membrane   7 terms 
  Biological process     macropinocytosis   18 terms 
  Biochemical function     nucleotide binding     6 terms  


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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20382987 H.Walden (2010).
Selenium incorporation using recombinant techniques.
  Acta Crystallogr D Biol Crystallogr, 66, 352-357.  
19135260 Y.Jiang, M.J.Trnka, K.F.Medzihradszky, H.Ouellet, Y.Wang, and P.R.Ortiz de Montellano (2009).
Covalent heme attachment to the protein in human heme oxygenase-1 with selenocysteine replacing the His25 proximal iron ligand.
  J Inorg Biochem, 103, 316-325.  
18458339 L.Banci, I.Bertini, S.Ciofi-Baffoni, T.Hadjiloi, M.Martinelli, and P.Palumaa (2008).
Mitochondrial copper(I) transfer from Cox17 to Sco1 is coupled to electron transfer.
  Proc Natl Acad Sci U S A, 105, 6803-6808.  
18357559 M.Iwaoka, R.Ooka, T.Nakazato, S.Yoshida, and S.Oishi (2008).
Synthesis of selenocysteine and selenomethionine derivatives from sulfur-containing amino acids.
  Chem Biodivers, 5, 359-374.  
18951416 M.Muttenthaler, and P.F.Alewood (2008).
Selenopeptide chemistry.
  J Pept Sci, 14, 1223-1239.  
18953414 P.F.Egea, J.Napetschnig, P.Walter, and R.M.Stroud (2008).
Structures of SRP54 and SRP19, the two proteins that organize the ribonucleic core of the signal recognition particle from Pyrococcus furiosus.
  PLoS ONE, 3, e3528.
PDB codes: 3dlu 3dlv 3dm5
16887798 M.Korbas, S.Vogt, W.Meyer-Klaucke, E.Bill, E.J.Lyon, R.K.Thauer, and S.Shima (2006).
The iron-sulfur cluster-free hydrogenase (Hmd) is a metalloenzyme with a novel iron binding motif.
  J Biol Chem, 281, 30804-30813.  
16823037 W.A.Barton, D.Tzvetkova-Robev, H.Erdjument-Bromage, P.Tempst, and D.B.Nikolov (2006).
Highly efficient selenomethionine labeling of recombinant proteins produced in mammalian cells.
  Protein Sci, 15, 2008-2013.  
15612050 L.Moroder, H.J.Musiol, M.Götz, and C.Renner (2005).
Synthesis of single- and multiple-stranded cystine-rich peptides.
  Biopolymers, 80, 85-97.  
15782428 L.Moroder (2005).
Isosteric replacement of sulfur with other chalcogens in peptides and proteins.
  J Pept Sci, 11, 187-214.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.