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Escherichia coli K-12 substr. MG1655 Enzyme: pyridoxamine kinase / hydroxymethylpyrimidine kinase / pyridoxal kinase



Gene: pdxK Accession Numbers: G7259 (EcoCyc), b2418, ECK2413

Synonyms: yfeI, thiJ, pdxL

Regulation Summary Diagram: ?

Subunit composition of pyridoxamine kinase / hydroxymethylpyrimidine kinase / pyridoxal kinase = [PdxK]4

Summary:
PdxK is a bifunctional enzyme which can function as a hydroxymethylpyrimidine (HMP) kinase in the thiamine phosphate biosynthesis pathway and also as a pyridoxal (PL) kinase in the scavenger/salvage pathway of pyridoxal 5'-phosphate.

The HMP kinase catalyzes the conversion of hydroxymethylpyrimidine to its monophosphate (HMP-P) in the presence of ATP. [Mizote89, Mizote99] There are two HMP kinases in E. coli. PdxK, is encoded by the pdxK gene product and the other HMP kinase is encoded by the thiD gene product. Mutations in both genes in the same cell resulted in the complete loss of HMP kinase activity [Mizote96, Reddick98].

The PL kinase is an ATP dependent kinase that phosphorylates pyridoxal, pyridoxine and pyridoxamine forming their respective 5'-phosphorylated esters. There are two PL kinases in E. coli, one is the pdxK gene product and the other is the pdxY gene product. The major activity for PL kinase is expressed by the pdxK gene, while PdxY has very low activity and binds PL covalently at the active site. Both enzymes function in the scavenger/salvage pathway of pyridoxal 5'-phosphate. [diSalvo04, Yang98b, Zhao96a]

The crystal structure of PdxK has been determined at 2.1 Å resolution. PdxK complexed with MgATP and also with pyridoxal has been determined with both the ATP and metal binding sites described. Kinetic studies showed that potassium as a monovalent cation was required for kinase activity. Magnesium is needed by the kinase for catalysis and has been shown to be the favored substrate under physiological conditions. [Safo06, diSalvo04]

Locations: cytosol

Map Position: [2,534,408 <- 2,535,259] (54.62 centisomes)
Length: 852 bp / 283 aa

Molecular Weight of Polypeptide: 30.847 kD (from nucleotide sequence), 28.8 kD (experimental) [diSalvo04 ]

Unification Links: ASAP:ABE-0007973 , EchoBASE:EB2519 , EcoGene:EG12642 , EcoliWiki:b2418 , ModBase:P40191 , OU-Microarray:b2418 , PortEco:pdxK , PR:PRO_000023506 , Pride:P40191 , Protein Model Portal:P40191 , RefSeq:NP_416913 , RegulonDB:G7259 , SMR:P40191 , String:511145.b2418 , UniProt:P40191

Relationship Links: InterPro:IN-FAMILY:IPR004625 , InterPro:IN-FAMILY:IPR013749 , InterPro:IN-FAMILY:IPR023479 , Panther:IN-FAMILY:PTHR10534 , PDB:Structure:2DDM , PDB:Structure:2DDO , PDB:Structure:2DDW , Pfam:IN-FAMILY:PF08543

In Paralogous Gene Group: 416 (2 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0008615 - pyridoxine biosynthetic process Inferred from experiment [Yang96e, Gamerman92]
GO:0009443 - pyridoxal 5'-phosphate salvage Inferred from experiment Inferred by computational analysis [GOA01a, Safo06]
GO:0016310 - phosphorylation Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Safo06]
GO:0006096 - glycolytic process Inferred by computational analysis [GOA06]
GO:0051156 - glucose 6-phosphate metabolic process Inferred by computational analysis [GOA06]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment Inferred by computational analysis [GOA06, Safo06, Gamerman92]
GO:0005524 - ATP binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, Safo06, Gamerman92]
GO:0008478 - pyridoxal kinase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, diSalvo04, White70, Yang96e, Gamerman92]
GO:0008902 - hydroxymethylpyrimidine kinase activity Inferred from experiment [Mizote96]
GO:0016301 - kinase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Gamerman92]
GO:0046872 - metal ion binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Safo06]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0004340 - glucokinase activity Inferred by computational analysis [GOA06]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA06]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: metabolism central intermediary metabolism pyridoxal 5'-phosphate salvage

Essentiality data for pdxK knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 02-Aug-2013 by Kubo A , SRI International


Enzymatic reaction of: pyridoxamine kinase

EC Number: 2.7.1.35

ATP + pyridoxamine <=> ADP + pyridoxamine 5'-phosphate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

In Pathways: superpathway of pyridoxal 5'-phosphate biosynthesis and salvage , pyridoxal 5'-phosphate salvage I


Enzymatic reaction of: hydroxymethylpyrimidine kinase

Synonyms: HMP kinase, ATP:4-amino-5-hydroxymethyl-2-methylpyrimidine 5-phosphotransferase

EC Number: 2.7.1.49

ATP + hydroxymethylpyrimidine <=> ADP + 4-amino-2-methyl-5-phosphomethylpyrimidine + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Alternative Substrates for hydroxymethylpyrimidine: pyridoxamine [Mizote89 ] , pyridoxal [Mizote89 ] , pyridoxine [Mizote89 ]

Alternative Substrates for ATP: GTP , UTP , CTP

In Pathways: thiamin salvage II , hydroxymethylpyrimidine salvage

Inhibitors (Competitive): hydroxymethylpyrimidine [Mizote89, Comment 5] , pyridoxine [Mizote89, Comment 6]


Enzymatic reaction of: pyridoxal kinase

Synonyms: pyridoxine kinase, ATP:pyridoxal 5'-phosphotransferase

EC Number: 2.7.1.35

ATP + pyridoxine <=> ADP + pyridoxine 5'-phosphate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

EC Number: 2.7.1.35

ATP + pyridoxal <=> ADP + pyridoxal 5'-phosphate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for pyridoxine: pyridoxal [White70 , Mizote89 , Webb92 ] , hydroxymethylpyrimidine [Webb92 , Mizote89 , White70 ] , pyridoxamine [Webb92 , Mizote89 , White70 ]

In Pathways: superpathway of pyridoxal 5'-phosphate biosynthesis and salvage , pyridoxal 5'-phosphate salvage I

Cofactors or Prosthetic Groups [White70]: Mg2+ [Safo06], K+ [Safo06]

Alternative Cofactors for Zn2+: Mg2+

Inhibitors (Competitive): 5-deoxypyridoxal [White70] , pyridoxamine [White70] , pyridoxal [White70, Furukawa81]

Inhibitors (Unknown Mechanism): pyridoxine 5'-phosphate [White70] , pyridoxal 5'-phosphate [White70, Comment 7] , pyridoxamine 5'-phosphate [White70, Comment 7]

Kinetic Parameters:

Substrate
Km (μM)
Citations
pyridoxamine
30.0
[diSalvo04]
pyridoxine
25.0
[diSalvo04]
pyridoxal
100.0
[diSalvo04]


Sequence Features

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 23
[UniProt10b]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 136
[UniProt10b]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 195 -> 196
[UniProt10b]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 220 -> 232
[UniProt10b]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 233
[UniProt10b]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

diSalvo04: di Salvo ML, Hunt S, Schirch V (2004). "Expression, purification, and kinetic constants for human and Escherichia coli pyridoxal kinases." Protein Expr Purif 36(2);300-6. PMID: 15249053

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Furukawa81: Furukawa Y, Yamada R, Iwashima A (1981). "Inactivation of microbial pyridoxal kinase by pyridoxal." Acta Vitaminol Enzymol 3(3);145-56. PMID: 6289642

Gamerman92: Gamerman GE (1992). "FDA regulation of biomedical software." Proc Annu Symp Comput Appl Med Care ;745-9. PMID: 1482971

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Mizote89: Mizote T, Nakayama H (1989). "Purification and properties of hydroxymethylpyrimidine kinase from Escherichia coli." Biochim Biophys Acta 1989;991(1);109-13. PMID: 2540841

Mizote96: Mizote T, Tsuda M, Nakazawa T, Nakayama H (1996). "The thiJ locus and its relation to phosphorylation of hydroxymethylpyrimidine in Escherichia coli." Microbiology 1996;142 ( Pt 10);2969-74. PMID: 8885414

Mizote99: Mizote T, Tsuda M, Smith DD, Nakayama H, Nakazawa T (1999). "Cloning and characterization of the thiD/J gene of Escherichia coli encoding a thiamin-synthesizing bifunctional enzyme, hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase." Microbiology 1999;145 ( Pt 2);495-501. PMID: 10075431

Reddick98: Reddick JJ, Kinsland C, Nicewonger R, Christian T, Downs DM, Winkler ME, Begley TP "Overexpression, purification and characterization of two pyrimidine kinases involved in the biosynthesis of thiamin: 4-amino-5-hydroxymethyl-2-methylpyrimidine kinase and 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase." Tetrahedron 54:15983-15991 (1998).

Safo06: Safo MK, Musayev FN, di Salvo ML, Hunt S, Claude JB, Schirch V (2006). "Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases." J Bacteriol 188(12);4542-52. PMID: 16740960

UniProt10b: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Webb92: Webb EC "Enzyme Nomenclature 1992." Academic Press, Inc., San Diego, 1992.

White70: White RS, Dempsey WB (1970). "Purification and properties of vitamin B6 kinase from Escherichia coli B." Biochemistry 1970;9(21);4057-64. PMID: 4917899

Yang96e: Yang Y, Zhao G, Winkler ME (1996). "Identification of the pdxK gene that encodes pyridoxine (vitamin B6) kinase in Escherichia coli K-12." FEMS Microbiol Lett 141(1);89-95. PMID: 8764513

Yang98b: Yang Y, Tsui HC, Man TK, Winkler ME (1998). "Identification and function of the pdxY gene, which encodes a novel pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate biosynthesis in Escherichia coli K-12." J Bacteriol 1998;180(7);1814-21. PMID: 9537380

Zhao96a: Zhao G, Winkler ME (1996). "4-Phospho-hydroxy-L-threonine is an obligatory intermediate in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12." FEMS Microbiol Lett 1996;135(2-3);275-80. PMID: 8595869

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Mon Dec 22, 2014, BIOCYC13A.