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Transferase PDB id
1uod
Jmol
Contents
Protein chains
336 a.a. *
Ligands
G3H ×2
SO4 ×2
Waters ×477
* Residue conservation analysis
PDB id:
1uod
Name: Transferase
Title: Crystal structure of the dihydroxyacetone kinase from e. Coli in complex with dihydroxyacetone-phosphate
Structure: Dihydroxyacetone kinase. Chain: a, b. Engineered: yes. Other_details: covalently modified his a230
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
1.90Å     R-factor:   0.168     R-free:   0.206
Authors: C.Siebold,L.F.Garcia-Alles,T.Luthi-Nyffeler,K.Flukiger-Bruhw H.-B.Burgi,U.Baumann,B.Erni
Key ref:
L.F.Garcia-Alles et al. (2004). Phosphoenolpyruvate- and ATP-dependent dihydroxyacetone kinases: covalent substrate-binding and kinetic mechanism. Biochemistry, 43, 13037-13045. PubMed id: 15476397 DOI: 10.1021/bi048575m
Date:
16-Sep-03     Release date:   24-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P76015  (DHAK_ECOLI) -  PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
Seq:
Struc: 		356 a.a.
336 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     glycerol metabolic process   3 terms 
  Biochemical function     protein binding     4 terms  

 

 
DOI no: 10.1021/bi048575m Biochemistry 43:13037-13045 (2004)
PubMed id: 15476397  
 
 
Phosphoenolpyruvate- and ATP-dependent dihydroxyacetone kinases: covalent substrate-binding and kinetic mechanism.
L.F.Garcia-Alles, C.Siebold, T.L.Nyffeler, K.Flükiger-Brühwiler, P.Schneider, H.B.Bürgi, U.Baumann, B.Erni.
 
  ABSTRACT  
 
Dihydroxyacetone (Dha) kinases are a sequence-conserved family of enzymes, which utilize two different phosphoryldonors, ATP in animals, plants, and some bacteria, and a multiphosphoprotein of the phosphoenolpyruvate carbohydrate phosphotransferase system (PTS) in most bacteria. Here, we compare the PTS-dependent kinase of Escherichia coli and the ATP-dependent kinase of Citrobacter freundii. They display 30% sequence identity. The binding constants of the E. coli kinase for eleven short-chain carbonyl compounds were determined by acetone precipitation of the enzyme-substrate complexes. They are 3.4 microM for Dha, 780 microM for Dha-phosphate (DhaP), 50 microM for D,L-glyceraldehyde (GA), and 90 microM for D,L-glyceraldehyde-3-phosphate. The k(cat) for Dha of the PTS-dependent kinase is 290 min(-1), and that of the ATP-dependent kinase is 1050 min(-1). The Km for Dha of both kinases is <6 microM. The X-ray structures of the enzyme-GA and the enzyme-DhaP complex show that substrates as well as products are bound in hemiaminal linkage to an active-site histidine. Quantum-mechanical calculations offer no indication for activation of the reacting hydroxyl group by the formation of the hemiaminal. However, the formation of the hemiaminal bond allows selection for short-chain carbonyl compounds and discrimination against structurally similar polyols. The Dha kinase remains fully active in the presence of 2 M glycerol, and phosphorylates trace impurities of carbonyl compounds present in glycerol.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21404260 J.M.Clomburg, and R.Gonzalez (2011).
Metabolic engineering of Escherichia coli for the production of 1,2-propanediol from glycerol.
  Biotechnol Bioeng, 108, 867-879.  
21209328 R.Shi, L.McDonald, Q.Cui, A.Matte, M.Cygler, and I.Ekiel (2011).
Structural and mechanistic insight into covalent substrate binding by Escherichia coli dihydroxyacetone kinase.
  Proc Natl Acad Sci U S A, 108, 1302-1307.
PDB codes: 3pnk 3pnl 3pnm 3pno 3pnq
19058275 I.Sánchez-Moreno, L.Iturrate, R.Martín-Hoyos, M.L.Jimeno, M.Mena, A.Bastida, and E.García-Junceda (2009).
From kinase to cyclase: an unusual example of catalytic promiscuity modulated by metal switching.
  Chembiochem, 10, 225-229.  
18415986 A.Németh, and B.Sevella (2008).
Development of a new bioprocess for production of 1,3-propanediol I.: Modeling of glycerol bioconversion to 1,3-propanediol with Klebsiella pneumoniae enzymes.
  Appl Biochem Biotechnol, 144, 47-58.  
17158705 J.Deutscher, C.Francke, and P.W.Postma (2006).
How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria.
  Microbiol Mol Biol Rev, 70, 939.  
16760471 S.Christen, A.Srinivas, P.Bähler, A.Zeller, D.Pridmore, C.Bieniossek, U.Baumann, and B.Erni (2006).
Regulation of the Dha operon of Lactococcus lactis: a deviation from the rule followed by the Tetr family of transcription regulators.
  J Biol Chem, 281, 23129-23137.
PDB codes: 2iu4 2iu5 2iu6
15753087 C.Bächler, K.Flükiger-Brühwiler, P.Schneider, P.Bähler, and B.Erni (2005).
From ATP as substrate to ADP as coenzyme: functional evolution of the nucleotide binding subunit of dihydroxyacetone kinases.
  J Biol Chem, 280, 18321-18325.  
15616579 C.Bächler, P.Schneider, P.Bähler, A.Lustig, and B.Erni (2005).
Escherichia coli dihydroxyacetone kinase controls gene expression by binding to transcription factor DhaR.
  EMBO J, 24, 283-293.  
16339738 R.D.Barabote, and M.H.Saier (2005).
Comparative genomic analyses of the bacterial phosphotransferase system.
  Microbiol Mol Biol Rev, 69, 608-634.  
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.