PDBsum entry 1jxh

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Transferase PDB id
Protein chains
248 a.a. *
SO4 ×4
Waters ×139
* Residue conservation analysis
PDB id:
Name: Transferase
Title: 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from salmonella typhimurium
Structure: Phosphomethylpyrimidine kinase. Chain: a, b. Synonym: hmp-phosphate kinase. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602. Gene: thid. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
2.30Å     R-factor:   0.235     R-free:   0.272
Authors: G.Cheng,E.M.Bennett,T.P.Begley,S.E.Ealick
Key ref:
G.Cheng et al. (2002). Crystal structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from Salmonella typhimurium at 2.3 A resolution. Structure, 10, 225-235. PubMed id: 11839308 DOI: 10.1016/S0969-2126(02)00708-6
07-Sep-01     Release date:   27-Feb-02    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P55882  (THID_SALTY) -  Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase
266 a.a.
248 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 2: E.C.  - Hydroxymethylpyrimidine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine = ADP + 4-amino-5- phosphonooxymethyl-2-methylpyrimidine
+ 4-amino-5-hydroxymethyl-2-methylpyrimidine
+ 4-amino-5- phosphonooxymethyl-2-methylpyrimidine
   Enzyme class 3: E.C.  - Phosphomethylpyrimidine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine = ADP + 4-amino-2- methyl-5-diphosphomethylpyrimidine
+ 4-amino-2-methyl-5-phosphomethylpyrimidine
+ 4-amino-2- methyl-5-diphosphomethylpyrimidine
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
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     6 terms  


DOI no: 10.1016/S0969-2126(02)00708-6 Structure 10:225-235 (2002)
PubMed id: 11839308  
Crystal structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from Salmonella typhimurium at 2.3 A resolution.
G.Cheng, E.M.Bennett, T.P.Begley, S.E.Ealick.
The crystal structures of Salmonella typhimurium 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMPP kinase) and its complex with substrate HMP have been determined. HMPP kinase catalyzes two separate ATP-dependent phosphorylation reactions and is an essential enzyme in the thiamin biosynthetic pathway. HMPP kinase is a homodimer with one active site per monomer and is structurally homologous to members of the ribokinase family. A comparison of the structure of HMPP kinase with other members of the ribokinase family suggests an evolutionary progression. Modeling studies suggest that HMPP kinase catalyzes both of its phosphorylation reactions using in-line displacement mechanisms. We propose that the active site accommodates the two separate reactions by providing two different binding modes for the phosphate group of HMP phosphate.
  Selected figure(s)  
Figure 3.
Figure 3. Ribbon Diagram of HMPP Kinase Dimer Viewed along the 2-Fold AxisThe a helices are blue, and the b strands are green. The HMP molecules and sulfate ions are shown as ball and stick models. The HMP and sulfate binding sites and the binding site flap are labeled for each monomer. The closest contact between the two HMP molecules is about 20 .
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 225-235) copyright 2002.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20693694 H.Xu (2010).
Enhancing MAD F(A) data for substructure determination.
  Acta Crystallogr D Biol Crystallogr, 66, 945-949.  
19237742 C.H.Trinh, A.Asipu, D.T.Bonthron, and S.E.Phillips (2009).
Structures of alternatively spliced isoforms of human ketohexokinase.
  Acta Crystallogr D Biol Crystallogr, 65, 201-211.
PDB codes: 2hqq 2hw1
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.  
18219117 H.Xu, and C.M.Weeks (2008).
Rapid and automated substructure solution by Shake-and-Bake.
  Acta Crystallogr D Biol Crystallogr, 64, 172-177.  
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.  
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
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.  
  17012797 J.A.Newman, S.K.Das, S.E.Sedelnikova, and D.W.Rice (2006).
Cloning, purification and preliminary crystallographic analysis of a putative pyridoxal kinase from Bacillus subtilis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1006-1009.  
16826377 K.Nosaka (2006).
Recent progress in understanding thiamin biosynthesis and its genetic regulation in Saccharomyces cerevisiae.
  Appl Microbiol Biotechnol, 72, 30-40.  
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
15906321 A.J.Bordner, and R.Abagyan (2005).
Statistical analysis and prediction of protein-protein interfaces.
  Proteins, 60, 353-366.  
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.  
15983421 H.Xu, C.M.Weeks, and H.A.Hauptman (2005).
Optimizing statistical Shake-and-Bake for Se-atom substructure determination.
  Acta Crystallogr D Biol Crystallogr, 61, 976-981.  
15858269 J.Benach, W.C.Edstrom, I.Lee, K.Das, B.Cooper, R.Xiao, J.Liu, B.Rost, T.B.Acton, G.T.Montelione, and J.F.Hunt (2005).
The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism.
  Acta Crystallogr D Biol Crystallogr, 61, 589-598.
PDB code: 1rtw
15614489 Y.Kawasaki, M.Onozuka, T.Mizote, and K.Nosaka (2005).
Biosynthesis of hydroxymethylpyrimidine pyrophosphate in Saccharomyces cerevisiae.
  Curr Genet, 47, 156-162.  
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
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.