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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1s4e
Jmol
Contents
Protein chains
337 a.a. *
310 a.a. *
337 a.a. *
346 a.a. *
255 a.a. *
Ligands
GLA ×9
ADP ×9
Metals
_MG ×9
* Residue conservation analysis
PDB id:
1s4e
Name: Transferase
Title: Pyrococcus furiosus galactokinase in complex with galactose, adp and magnesium
Structure: Galactokinase. Chain: a, b, c, d, e, f, g, h, i. Synonym: galactose kinase. Engineered: yes
Source: Pyrococcus furiosus. Organism_taxid: 2261. Gene: galk. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.90Å     R-factor:   0.232     R-free:   0.270
Authors: A.Hartley,S.E.Glynn,V.Barynin,P.J.Baker,S.E.Sedelnikova, C.Verhees,D.De Geus,J.Van Der Oost,D.J.Timson,R.J.Reece, D.W.Rice
Key ref:
A.Hartley et al. (2004). Substrate specificity and mechanism from the structure of Pyrococcus furiosus galactokinase. J Mol Biol, 337, 387-398. PubMed id: 15003454 DOI: 10.1016/j.jmb.2004.01.043
Date:
16-Jan-04     Release date:   06-Apr-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9HHB6  (GAL1_PYRFU) -  Galactokinase
Seq:
Struc: 		352 a.a.
337 a.a.*
Protein chain
Pfam   ArchSchema ?
Q9HHB6  (GAL1_PYRFU) -  Galactokinase
Seq:
Struc: 		352 a.a.
310 a.a.
Protein chain
Pfam   ArchSchema ?
Q9HHB6  (GAL1_PYRFU) -  Galactokinase
Seq:
Struc: 		352 a.a.
337 a.a.
Protein chains
Pfam   ArchSchema ?
Q9HHB6  (GAL1_PYRFU) -  Galactokinase
Seq:
Struc: 		352 a.a.
346 a.a.
Protein chain
Pfam   ArchSchema ?
Q9HHB6  (GAL1_PYRFU) -  Galactokinase
Seq:
Struc: 		352 a.a.
255 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H, I: E.C.2.7.1.6  - Galactokinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + D-galactose = ADP + alpha-D-galactose 1-phosphate
ATP
 +
D-galactose
Bound ligand (Het Group name = GLA)
corresponds exactly 		=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly 		+ alpha-D-galactose 1-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   5 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2004.01.043 J Mol Biol 337:387-398 (2004)
PubMed id: 15003454  
 
 
Substrate specificity and mechanism from the structure of Pyrococcus furiosus galactokinase.
A.Hartley, S.E.Glynn, V.Barynin, P.J.Baker, S.E.Sedelnikova, C.Verhees, D.de Geus, J.van der Oost, D.J.Timson, R.J.Reece, D.W.Rice.
 
  ABSTRACT  
 
Galactokinase (GalK) catalyses the first step of the Leloir pathway of galactose metabolism, the ATP-dependent phosphorylation of galactose to galactose-1-phosphate. In man, defects in galactose metabolism can result in disorders with severe clinical consequences, and deficiencies in galactokinase have been linked with the development of cataracts within the first few months of life. The crystal structure of GalK from Pyrococcus furiosus in complex with MgADP and galactose has been determined to 2.9 A resolution to provide insights into the substrate specificity and catalytic mechanism of the enzyme. The structure consists of two domains with the active site in a cleft at the domain interface. Inspection of the substrate binding pocket identifies the amino acid residues involved in galactose and nucleotide binding and points to both structural and mechanistic similarities with other enzymes of the GHMP kinase superfamily to which GalK belongs. Comparison of the sequence of the Gal3p inducer protein, which is related to GalK and which forms part of the transcriptional activation of the GAL gene cluster in the yeast Saccharomyces cerevisiae, has led to an understanding of the molecular basis of galactose and nucleotide recognition. Finally, the structure has enabled us to further our understanding on the functional consequences of mutations in human GalK which cause galactosemia.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. (a) Schematic diagram of the crystal packing arrangement of GalK. The positions of all nine monomers are shown and labelled A to I. (b) Schematic diagram of the GalK monomer. The N-terminal domain is shown in blue and the C-terminal domain in green. The three conserved motifs in the GHMP kinase superfamily are highlighted (1, red; 2, beige; 3, gold). Helices are labelled aA through aJ and b-strands labelled B1 to B13. ADP and galactose are represented with a stick diagram (atom-coloured). Mg2+ is coloured cyan. Both the N and C termini are labelled. Label colours are not significant. 		Figure 3.
Figure 3. (a) Final electron density map (2F[o] -F[c]) in the vicinity of the galactose-binding site contoured at the 1s level. The galactose molecule and surrounding protein residues are labelled and shown in stick format. (b) Final electron density map, as in (a), in the vicinity of the enzyme-bound MgADP. The ADP molecule is shown as sticks and the magnesium ion is shown with an orange ball.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 337, 387-398) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18957435 C.A.Sellick, T.A.Jowitt, and R.J.Reece (2009).
The effect of ligand binding on the galactokinase activity of yeast gal1p and its ability to activate transcription.
  J Biol Chem, 284, 229-236.  
19509296 C.Fan, H.J.Fromm, and T.A.Bobik (2009).
Kinetic and functional analysis of L-threonine kinase, the PduX enzyme of Salmonella enterica.
  J Biol Chem, 284, 20240-20248.  
19509290 T.Yang, L.Bar-Peled, L.Gebhart, S.G.Lee, and M.Bar-Peled (2009).
Identification of galacturonic acid-1-phosphate kinase, a new member of the GHMP kinase superfamily in plants, and comparison with galactose-1-phosphate kinase.
  J Biol Chem, 284, 21526-21535.  
19666462 Y.Yokooji, H.Tomita, H.Atomi, and T.Imanaka (2009).
Pantoate kinase and phosphopantothenate synthetase, two novel enzymes necessary for CoA biosynthesis in the Archaea.
  J Biol Chem, 284, 28137-28145.  
18199744 T.Kotake, S.Hojo, N.Tajima, K.Matsuoka, T.Koyama, and Y.Tsumuraya (2008).
A bifunctional enzyme with L-fucokinase and GDP-L-fucose pyrophosphorylase activities salvages free L-fucose in Arabidopsis.
  J Biol Chem, 283, 8125-8135.  
16603548 C.A.Sellick, and R.J.Reece (2006).
Contribution of amino acid side chains to sugar binding specificity in a galactokinase, Gal1p, and a transcriptional inducer, Gal3p.
  J Biol Chem, 281, 17150-17155.  
16219783 C.Q.Diep, G.Peng, M.Bewley, V.Pilauri, I.Ropson, and J.E.Hopper (2006).
Intragenic suppression of Gal3C interaction with Gal80 in the Saccharomyces cerevisiae GAL gene switch.
  Genetics, 172, 77-87.  
  16511293 E.Inagaki, K.Sakamoto, N.Obayashi, T.Terada, M.Shirouzu, Y.Bessho, C.Kuroishi, S.Kuramitsu, A.Shinkai, and S.Yokoyama (2006).
Expression, purification, crystallization and preliminary X-ray diffraction analysis of galactokinase from Pyrococcus horikoshii.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 169-171.  
16160853 A.Lakshminarasimhan, and P.J.Bhat (2005).
Replacement of a conserved tyrosine by tryptophan in Gal3p of Saccharomyces cerevisiae reduces constitutive activity: implications for signal transduction in the GAL regulon.
  Mol Genet Genomics, 274, 384-393.  
15950477 C.A.Sellick, and R.J.Reece (2005).
Eukaryotic transcription factors as direct nutrient sensors.
  Trends Biochem Sci, 30, 405-412.  
  16511101 E.Byres, D.M.Martin, and W.N.Hunter (2005).
A preliminary crystallographic analysis of the putative mevalonate diphosphate decarboxylase from Trypanosoma brucei.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 581-584.  
16115868 J.B.Thoden, C.A.Sellick, D.J.Timson, R.J.Reece, and H.M.Holden (2005).
Molecular structure of Saccharomyces cerevisiae Gal1p, a bifunctional galactokinase and transcriptional inducer.
  J Biol Chem, 280, 36905-36911.
PDB code: 2aj4
15590630 J.B.Thoden, D.J.Timson, R.J.Reece, and H.M.Holden (2005).
Molecular structure of human galactokinase: implications for type II galactosemia.
  J Biol Chem, 280, 9662-9670.
PDB code: 1wuu
15795221 J.B.Thoden, and H.M.Holden (2005).
The molecular architecture of galactose mutarotase/UDP-galactose 4-epimerase from Saccharomyces cerevisiae.
  J Biol Chem, 280, 21900-21907.
PDB code: 1z45
16006554 J.B.Thoden, and H.M.Holden (2005).
The molecular architecture of human N-acetylgalactosamine kinase.
  J Biol Chem, 280, 32784-32791.
PDB codes: 2a2c 2a2d
15239057 D.Hoffmeister, and J.S.Thorson (2004).
Mechanistic implications of Escherichia coli galactokinase structure-based engineering.
  Chembiochem, 5, 989-992.  
15239058 J.Yang, L.Liu, and J.S.Thorson (2004).
Structure-based enhancement of the first anomeric glucokinase.
  Chembiochem, 5, 992-996.  
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.