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MetaCyc Enzyme: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase

Gene: folK Accession Numbers: EG11374 (MetaCyc), b0142, ECK0141

Synonyms: HPPK

Species: Escherichia coli K-12 substr. MG1655

Summary:
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes a reaction in the folate biosynthesis pathway, the transfer of pyrophosphate from ATP to 6-hydroxymethyl-7,8-dihydropterin [Talarico92]. HPPK is essential in microorganisms, and the enzyme is not present in mammals; it is therefore a target for the development of antimicrobial drugs.

Various crystal and solution structures of HPPK have been solved and have elucidated the reaction mechanism and kinetics. The protein undergoes conformational changes during the catalytic cycle. [Xiao99, Shi99, Stammers99, Blaszczyk00, Shi01, Yan01, Xiao01, Blaszczyk03, Blaszczyk04, Blaszczyk04a, Garcon04, Yang05a, Li05b, Li06f, Lescop09, Su09]

The enzyme binds ATP first, which then enables faster binding of 6-hydroxymethyl-7,8-dihydropterin (HMDP) [Bermingham00]. Mg2+ is important for binding of both ATP and HMDP [Li02a]. The roles in substrate binding and catalysis of several amino acid residues in the flexible loop 3 have been investigated by site-directed mutagenesis [Li03a, Blaszczyk04, Li05b].

Reviews: [Derrick08, Yan11]

Locations: cytosol

Map Position: [157,253 <- 157,732]

Molecular Weight of Polypeptide: 18.079 kD (from nucleotide sequence), 23.0 kD (experimental) [Talarico92 ]

pI: 5.58

Unification Links: ASAP:ABE-0000491 , CGSC:29572 , EchoBASE:EB1348 , EcoGene:EG11374 , EcoliWiki:b0142 , EcoO157Cyc:FOLK-MONOMER , ModBase:P26281 , OU-Microarray:b0142 , PortEco:folK , PR:PRO_000022680 , Protein Model Portal:P26281 , RefSeq:NP_414684 , RegulonDB:EG11374 , SMR:P26281 , String:511145.b0142 , UniProt:P26281

Relationship Links: InterPro:IN-FAMILY:IPR000550 , PDB:Structure:1DY3 , PDB:Structure:1EQ0 , PDB:Structure:1EQM , PDB:Structure:1EX8 , PDB:Structure:1F9H , PDB:Structure:1G4C , PDB:Structure:1HKA , PDB:Structure:1HQ2 , PDB:Structure:1IM6 , PDB:Structure:1KBR , PDB:Structure:1Q0N , PDB:Structure:1RAO , PDB:Structure:1RB0 , PDB:Structure:1RTZ , PDB:Structure:1RU1 , PDB:Structure:1RU2 , PDB:Structure:1TMJ , PDB:Structure:1TMM , PDB:Structure:2F63 , PDB:Structure:2F65 , PDB:Structure:3HCX , PDB:Structure:3HD1 , PDB:Structure:3HD2 , PDB:Structure:3HSD , PDB:Structure:3HSG , PDB:Structure:3HSJ , PDB:Structure:3HSZ , PDB:Structure:3HT0 , PDB:Structure:3ILI , PDB:Structure:3ILJ , PDB:Structure:3ILL , PDB:Structure:3ILO , PDB:Structure:3IP0 , PDB:Structure:3KUE , PDB:Structure:3KUG , PDB:Structure:3KUH , PDB:Structure:3UD5 , PDB:Structure:3UDE , PDB:Structure:3UDV , PDB:Structure:4F7V , Pfam:IN-FAMILY:PF01288 , Prosite:IN-FAMILY:PS00794

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0009396 - folic acid-containing compound biosynthetic process Inferred by computational analysis [GOA01]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11a]
GO:0046654 - tetrahydrofolate biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0046656 - folic acid biosynthetic process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [Shi00]
GO:0003848 - 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Talarico91, Talarico92]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers folic acid

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase

Synonyms: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase, PPPK, 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase, HPPK, hydroxymethyldihydropterin pyrophosphokinase, ATP:2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine 6'-pyrophosphotransferase

EC Number: 2.7.6.3

6-hydroxymethyl-7,8-dihydropterin + ATP <=> (2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl diphosphate + AMP + 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.

In Pathways: superpathway of tetrahydrofolate biosynthesis and salvage , superpathway of chorismate metabolism , superpathway of tetrahydrofolate biosynthesis , 6-hydroxymethyl-dihydropterin diphosphate biosynthesis I

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Summary:
The enzyme was first purified from E. coli B [Richey69].

The enzyme is highly specific for ATP [Bermingham00].

Cofactors or Prosthetic Groups: Mg2+ [Shi00, Richey69]

Kinetic Parameters:

Substrate
Km (μM)
Citations
ATP
15.0
[Ballantine94, BRENDA14]
ATP
17.0
[Talarico91, BRENDA14]
6-hydroxymethyl-7,8-dihydropterin
1.6
[Talarico91]

pH(opt): 8.5 [BRENDA14, Ballantine94]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Talarico91, Talarico92, UniProt11]
UniProt: Removed.
Chain 2 -> 159
[UniProt09]
UniProt: 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase;

History:
10/20/97 Gene b0142 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11374; confirmed by SwissProt match.


References

Ballantine94: Ballantine SP, Volpe F, Delves CJ (1994). "The hydroxymethyldihydropterin pyrophosphokinase domain of the multifunctional folic acid synthesis Fas protein of Pneumocystis carinii expressed as an independent enzyme in Escherichia coli: refolding and characterization of the recombinant enzyme." Protein Expr Purif 5(4);371-8. PMID: 7950384

Bermingham00: Bermingham A, Bottomley JR, Primrose WU, Derrick JP (2000). "Equilibrium and kinetic studies of substrate binding to 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase from Escherichia coli." J Biol Chem 275(24);17962-7. PMID: 10751386

Blaszczyk00: Blaszczyk J, Shi G, Yan H, Ji X (2000). "Catalytic center assembly of HPPK as revealed by the crystal structure of a ternary complex at 1.25 A resolution." Structure 8(10);1049-58. PMID: 11080626

Blaszczyk03: Blaszczyk J, Li Y, Shi G, Yan H, Ji X (2003). "Dynamic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: crystallographic studies." Biochemistry 42(6);1573-80. PMID: 12578370

Blaszczyk04: Blaszczyk J, Li Y, Wu Y, Shi G, Ji X, Yan H (2004). "Essential roles of a dynamic loop in the catalysis of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase." Biochemistry 43(6);1469-77. PMID: 14769023

Blaszczyk04a: Blaszczyk J, Shi G, Li Y, Yan H, Ji X (2004). "Reaction trajectory of pyrophosphoryl transfer catalyzed by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase." Structure (Camb) 12(3);467-75. PMID: 15016362

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Derrick08: Derrick JP (2008). "The structure and mechanism of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase." Vitam Horm 79;411-33. PMID: 18804704

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

Garcon04: Garcon A, Bermingham A, Lian LY, Derrick JP (2004). "Kinetic and structural characterization of a product complex of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase from Escherichia coli." Biochem J 380(Pt 3);867-73. PMID: 15018613

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Lescop09: Lescop E, Lu Z, Liu Q, Xu H, Li G, Xia B, Yan H, Jin C (2009). "Dynamics of the conformational transitions in the assembling of the Michaelis complex of a bisubstrate enzyme: a (15)N relaxation study of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase." Biochemistry 48(2);302-12. PMID: 19108643

Li02a: Li Y, Gong Y, Shi G, Blaszczyk J, Ji X, Yan H (2002). "Chemical transformation is not rate-limiting in the reaction catalyzed by Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase." Biochemistry 41(27);8777-83. PMID: 12093297

Li03a: Li Y, Wu Y, Blaszczyk J, Ji X, Yan H (2003). "Catalytic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: site-directed mutagenesis and biochemical studies." Biochemistry 42(6);1581-8. PMID: 12578371

Li05b: Li Y, Blaszczyk J, Wu Y, Shi G, Ji X, Yan H (2005). "Is the critical role of loop 3 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase in catalysis due to loop-3 residues arginine-84 and tryptophan-89? Site-directed mutagenesis, biochemical, and crystallographic studies." Biochemistry 44(24);8590-9. PMID: 15952765

Li06f: Li G, Felczak K, Shi G, Yan H (2006). "Mechanism of the conformational transitions in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by NMR spectroscopy." Biochemistry 45(41);12573-81. PMID: 17029412

Richey69: Richey DP, Brown GM (1969). "The biosynthesis of folic acid. IX. Purification and properties of the enzymes required for the formation of dihydropteroic acid." J Biol Chem 1969;244(6);1582-92. PMID: 4304228

Shi00: Shi G, Gong Y, Savchenko A, Zeikus JG, Xiao B, Ji X, Yan H (2000). "Dissecting the nucleotide binding properties of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase with fluorescent 3'(2)'-o-anthraniloyladenosine 5'-triphosphate." Biochim Biophys Acta 1478(2);289-99. PMID: 10825540

Shi01: Shi G, Blaszczyk J, Ji X, Yan H (2001). "Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: synthesis and biochemical and crystallographic studies." J Med Chem 44(9);1364-71. PMID: 11311059

Shi99: Shi G, Gao J, Yan H (1999). "1H, 13C and 15N resonance assignments of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase and its complex with MgAMPPCP." J Biomol NMR 14(2);189-90. PMID: 10427747

Stammers99: Stammers DK, Achari A, Somers DO, Bryant PK, Rosemond J, Scott DL, Champness JN (1999). "2.0 A X-ray structure of the ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue." FEBS Lett 456(1);49-53. PMID: 10452528

Su09: Su L, Cukier RI (2009). "Hamiltonian replica exchange method study of Escherichia coli and Yersinia pestis HPPK." J Phys Chem B 113(50);16197-208. PMID: 19924845

Talarico91: Talarico TL, Dev IK, Dallas WS, Ferone R, Ray PH (1991). "Purification and partial characterization of 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase and 7,8-dihydropteroate synthase from Escherichia coli MC4100." J Bacteriol 173(21);7029-32. PMID: 1657875

Talarico92: Talarico TL, Ray PH, Dev IK, Merrill BM, Dallas WS (1992). "Cloning, sequence analysis, and overexpression of Escherichia coli folK, the gene coding for 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase." J Bacteriol 1992;174(18);5971-7. PMID: 1325970

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Xiao01: Xiao B, Shi G, Gao J, Blaszczyk J, Liu Q, Ji X, Yan H (2001). "Unusual conformational changes in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by X-ray crystallography and NMR." J Biol Chem 276(43);40274-81. PMID: 11546767

Xiao99: Xiao B, Shi G, Chen X, Yan H, Ji X (1999). "Crystal structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, a potential target for the development of novel antimicrobial agents." Structure 7(5);489-96. PMID: 10378268

Yan01: Yan H, Blaszczyk J, Xiao B, Shi G, Ji X (2001). "Structure and dynamics of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase." J Mol Graph Model 19(1);70-7. PMID: 11381532

Yan11: Yan H, Ji X (2011). "Role of protein conformational dynamics in the catalysis by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase." Protein Pept Lett 18(4);328-35. PMID: 21222642

Yang05a: Yang R, Lee MC, Yan H, Duan Y (2005). "Loop conformation and dynamics of the Escherichia coli HPPK apo-enzyme and its binary complex with MgATP." Biophys J 89(1);95-106. PMID: 15821168


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Thu Dec 18, 2014, biocyc13.