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PDBsum entry 1esj

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1esj
Jmol
Contents
Protein chains
284 a.a. *
Ligands
SO4 ×2
Waters ×342
* Residue conservation analysis
PDB id:
1esj
Name: Transferase
Title: Crystal structure of thiazole kinase mutant (c198s)
Structure: Hydroxyethylthiazole kinase. Chain: a, b, c. Synonym: thz kinase. Engineered: yes. Mutation: yes. Other_details: n-terminal his tag
Source: Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
1.80Å     R-factor:   0.229     R-free:   0.253
Authors: N.Campobasso,I.I.Mathews,T.P.Begley,S.E.Ealick
Key ref:
N.Campobasso et al. (2000). Crystal structure of 4-methyl-5-beta-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 A resolution. Biochemistry, 39, 7868-7877. PubMed id: 10891066 DOI: 10.1021/bi0000061
Date:
10-Apr-00     Release date:   09-Aug-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P39593  (THIM_BACSU) -  Hydroxyethylthiazole kinase
Seq:
Struc:
272 a.a.
284 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.2.7.1.50  - Hydroxyethylthiazole kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + 4-methyl-5-(2-hydroxyethyl)thiazole = ADP + 4-methyl-5- (2-phosphonooxyethyl)thiazole
ATP
+ 4-methyl-5-(2-hydroxyethyl)thiazole
= ADP
+ 4-methyl-5- (2-phosphonooxyethyl)thiazole
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     phosphorylation   3 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi0000061 Biochemistry 39:7868-7877 (2000)
PubMed id: 10891066  
 
 
Crystal structure of 4-methyl-5-beta-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 A resolution.
N.Campobasso, I.I.Mathews, T.P.Begley, S.E.Ealick.
 
  ABSTRACT  
 
4-Methyl-5-beta-hydroxyethylthiazole kinase (ThiK) catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (Thz). This enzyme is a salvage enzyme in the thiamin biosynthetic pathway and enables the cell to use recycled Thz as an alternative to its synthesis from 1-deoxy-D-xylulose-5-phosphate, cysteine, and tyrosine. The structure of ThiK in the rhombohedral crystal form has been determined to 1.5 A resolution and refined to a final R-factor of 21. 6% (R-free 25.1%). The structures of the enzyme/Thz complex and the enzyme/Thz-phosphate/ATP complex have also been determined. ThiK is a trimer of identical subunits. Each subunit contains a large nine-stranded central beta-sheet flanked by helices. The overall fold is similar to that of ribokinase and adenosine kinase, although sequence similarity is not immediately apparent. The area of greatest similarity occurs in the ATP-binding site where several key residues are highly conserved. Unlike adenosine kinase and ribokinase, in which the active site is located between two domains within a single subunit, the ThiK active site it formed at the interface between two subunits within the trimer. The structure of the enzyme/ATP/Thz-phosphate complex suggests that phosphate transfer occurs by an inline mechanism. Although this mechanism is similar to that proposed for both ribokinase and adenosine kinase, ThiK lacks an absolutely conserved Asp thought to be important for catalysis in the other two enzymes. Instead, ThiK has a conserved cysteine (Cys198) in this position. When this Cys is mutated to Asp, the enzymatic activity increases 10-fold. Further sequence analysis suggests that another thiamin biosynthetic enzyme (ThiD), which catalyzes the formation of 2-methyl-4-amino-5-hydroxymethylpyrimidine pyrophosphate by two sequential phosphorylation reactions, belongs to the same family of small molecule kinases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19348578 C.T.Jurgenson, T.P.Begley, and S.E.Ealick (2009).
The structural and biochemical foundations of thiamin biosynthesis.
  Annu Rev Biochem, 78, 569-603.  
19888457 I.B.Müller, B.Bergmann, M.R.Groves, I.Couto, L.Amaral, T.P.Begley, R.D.Walter, and C.Wrenger (2009).
The vitamin B1 metabolism of Staphylococcus aureus is controlled at enzymatic and transcriptional levels.
  PLoS One, 4, e7656.  
19548321 V.Guixé, and F.Merino (2009).
The ADP-dependent sugar kinase family: kinetic and evolutionary aspects.
  IUBMB Life, 61, 753-761.  
18054064 A.L.Jenkins, Y.Zhang, S.E.Ealick, and T.P.Begley (2008).
Mutagenesis studies on TenA: a thiamin salvage enzyme from Bacillus subtilis.
  Bioorg Chem, 36, 29-32.
PDB code: 2qcx
18625008 F.Merino, and V.Guixé (2008).
Specificity evolution of the ADP-dependent sugar kinase family: in silico studies of the glucokinase/phosphofructokinase bifunctional enzyme from Methanocaldococcus jannaschii.
  FEBS J, 275, 4033-4044.  
19021762 H.Ota, S.Sakasegawa, Y.Yasuda, S.Imamura, and T.Tamura (2008).
A novel nucleoside kinase from Burkholderia thailandensis.
  FEBS J, 275, 5865-5872.  
18004772 I.I.Mathews, D.McMullan, M.D.Miller, J.M.Canaves, M.A.Elsliger, R.Floyd, S.K.Grzechnik, L.Jaroszewski, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, T.M.McPhillips, A.T.Morse, K.Quijano, C.L.Rife, R.Schwarzenbacher, G.Spraggon, R.C.Stevens, H.van den Bedem, D.Weekes, G.Wolf, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2008).
Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution.
  Proteins, 70, 603-608.
PDB code: 2afb
  18097102 Y.F.Zhou, L.F.Li, C.Yang, Y.H.Liang, and X.D.Su (2008).
Preliminary X-ray crystallographic analysis of SMU.573, a putative sugar kinase from Streptococcus mutans.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 47-49.  
17384969 E.Dyguda-Kazimierowicz, W.A.Sokalski, and J.LeszczyƄski (2007).
Non-empirical study of the phosphorylation reaction catalyzed by 4-methyl-5-beta-hydroxyethylthiazole kinase: relevance of the theory of intermolecular interactions.
  J Mol Model, 13, 839-849.  
17766369 F.N.Musayev, M.L.di Salvo, T.P.Ko, A.K.Gandhi, A.Goswami, V.Schirch, and M.K.Safo (2007).
Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation.
  Protein Sci, 16, 2184-2194.
PDB codes: 2yxt 2yxu
17459874 L.Miallau, W.N.Hunter, S.M.McSweeney, and G.A.Leonard (2007).
Structures of Staphylococcus aureus D-tagatose-6-phosphate kinase implicate domain motions in specificity and mechanism.
  J Biol Chem, 282, 19948-19957.
PDB codes: 2jg1 2jgv
17242506 Y.Zhang, M.H.El Kouni, and S.E.Ealick (2007).
Substrate analogs induce an intermediate conformational change in Toxoplasma gondii adenosine kinase.
  Acta Crystallogr D Biol Crystallogr, 63, 126-134.
PDB codes: 2a9y 2a9z 2aa0 2ab8
16388576 C.Lehmann, T.P.Begley, and S.E.Ealick (2006).
Structure of the Escherichia coli ThiS-ThiF complex, a key component of the sulfur transfer system in thiamin biosynthesis.
  Biochemistry, 45, 11-19.
PDB code: 1zud
16497163 C.Wrenger, M.L.Eschbach, I.B.Müller, N.P.Laun, T.P.Begley, and R.D.Walter (2006).
Vitamin B1 de novo synthesis in the human malaria parasite Plasmodium falciparum depends on external provision of 4-amino-5-hydroxymethyl-2-methylpyrimidine.
  Biol Chem, 387, 41-51.  
16929110 L.Arnfors, T.Hansen, P.Schönheit, R.Ladenstein, and W.Meining (2006).
Structure of Methanocaldococcus jannaschii nucleoside kinase: an archaeal member of the ribokinase family.
  Acta Crystallogr D Biol Crystallogr, 62, 1085-1097.
PDB codes: 2c49 2c4e
16740960 M.K.Safo, F.N.Musayev, M.L.di Salvo, S.Hunt, J.B.Claude, and V.Schirch (2006).
Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases.
  J Bacteriol, 188, 4542-4552.
PDB codes: 2ddm 2ddo 2ddw
16421444 Y.Zhang, M.H.El Kouni, and S.E.Ealick (2006).
Structure of Toxoplasma gondii adenosine kinase in complex with an ATP analog at 1.1 angstroms resolution.
  Acta Crystallogr D Biol Crystallogr, 62, 140-145.
PDB code: 2abs
15590634 C.Wrenger, M.L.Eschbach, I.B.Müller, D.Warnecke, and R.D.Walter (2005).
Analysis of the vitamin B6 biosynthesis pathway in the human malaria parasite Plasmodium falciparum.
  J Biol Chem, 280, 5242-5248.  
15593246 F.J.Stevens, C.Kuemmel, G.Babnigg, and F.R.Collart (2005).
Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: application.
  J Mol Recognit, 18, 150-157.  
16030223 F.McArthur, C.E.Andersson, S.Loutet, S.L.Mowbray, and M.A.Valvano (2005).
Functional analysis of the glycero-manno-heptose 7-phosphate kinase domain from the bifunctional HldE protein, which is involved in ADP-L-glycero-D-manno-heptose biosynthesis.
  J Bacteriol, 187, 5292-5300.  
14973012 J.H.Park, K.Burns, C.Kinsland, and T.P.Begley (2004).
Characterization of two kinases involved in thiamine pyrophosphate and pyridoxal phosphate biosynthesis in Bacillus subtilis: 4-amino-5-hydroxymethyl-2methylpyrimidine kinase and pyridoxal kinase.
  J Bacteriol, 186, 1571-1573.  
15150256 J.Melnick, E.Lis, J.H.Park, C.Kinsland, H.Mori, T.Baba, J.Perkins, G.Schyns, O.Vassieva, A.Osterman, and T.P.Begley (2004).
Identification of the two missing bacterial genes involved in thiamine salvage: thiamine pyrophosphokinase and thiamine kinase.
  J Bacteriol, 186, 3660-3662.  
14722069 M.H.Li, F.Kwok, W.R.Chang, S.Q.Liu, S.C.Lo, J.P.Zhang, T.Jiang, and D.C.Liang (2004).
Conformational changes in the reaction of pyridoxal kinase.
  J Biol Chem, 279, 17459-17465.
PDB codes: 1rft 1rfu 1rfv
15547280 M.K.Safo, F.N.Musayev, S.Hunt, M.L.di Salvo, N.Scarsdale, and V.Schirch (2004).
Crystal structure of the PdxY Protein from Escherichia coli.
  J Bacteriol, 186, 8074-8082.
PDB code: 1td2
15229886 N.Fernandez-Fuentes, A.Hermoso, J.Espadaler, E.Querol, F.X.Aviles, and B.Oliva (2004).
Classification of common functional loops of kinase super-families.
  Proteins, 56, 539-555.  
14675553 E.Settembre, T.P.Begley, and S.E.Ealick (2003).
Structural biology of enzymes of the thiamin biosynthesis pathway.
  Curr Opin Struct Biol, 13, 739-747.  
12906824 N.Manoj, E.Strauss, T.P.Begley, and S.E.Ealick (2003).
Structure of human phosphopantothenoylcysteine synthetase at 2.3 A resolution.
  Structure, 11, 927-936.
PDB code: 1p9o
12235162 M.H.Li, F.Kwok, W.R.Chang, C.K.Lau, J.P.Zhang, S.C.Lo, T.Jiang, and D.C.Liang (2002).
Crystal structure of brain pyridoxal kinase, a novel member of the ribokinase superfamily.
  J Biol Chem, 277, 46385-46390.
PDB codes: 1lhp 1lhr
12457846 R.G.Zhang, J.Grembecka, E.Vinokour, F.Collart, I.Dementieva, W.Minor, and A.Joachimiak (2002).
Structure of Bacillus subtilis YXKO--a member of the UPF0031 family and a putative kinase.
  J Struct Biol, 139, 161-170.
PDB code: 1kyh
11435118 L.J.Baker, J.A.Dorocke, R.A.Harris, and D.E.Timm (2001).
The crystal structure of yeast thiamin pyrophosphokinase.
  Structure, 9, 539-546.
PDB code: 1ig0
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 code is shown on the right.