View source for Biology:Phosphoribosylglycinamide formyltransferase

{{Infobox enzyme
| Name       = Phosphoribosylglycinamide formyltransferase
| EC_number  = 2.1.2.2
| CAS_number = 2604945
| GO_code    =
| image      = 1rby.jpg
| width      = 270
| caption    = GAR formyltransferase monomer, Human 
}}
'''Phosphoribosylglycinamide formyltransferase''' ({{EC number|2.1.2.2}}, ''2-amino-N-ribosylacetamide 5'-phosphate transformylase'', ''GAR formyltransferase'', ''GAR transformylase'', ''glycinamide ribonucleotide transformylase'', ''GAR TFase'', ''5,10-methenyltetrahydrofolate:2-amino-N-ribosylacetamide ribonucleotide transformylase'') is an [[Biology:Enzyme|enzyme]] with [[Biology:List of enzymes|systematic name]] ''10-formyltetrahydrofolate:5'-phosphoribosylglycinamide N-formyltransferase''.<ref name = "pmid|13672969">{{cite journal | vauthors = Hartman SC, Buchanan JM | title = Biosynthesis of the purines. XXVI. The identification of the formyl donors of the transformylation reactions | journal = The Journal of Biological Chemistry | volume = 234 | issue = 7 | pages = 1812–6 | date = July 1959 | pmid = 13672969 }}</ref><ref name = "pmid|7284307">{{cite journal | vauthors = Smith GK, Benkovic PA, Benkovic SJ | title = L(-)-10-Formyltetrahydrofolate is the cofactor for glycinamide ribonucleotide transformylase from chicken liver | journal = Biochemistry | volume = 20 | issue = 14 | pages = 4034–6 | date = July 1981 | pmid = 7284307 | doi = 10.1021/bi00517a013 }}</ref><ref name = "pmid|13502326">{{cite journal | vauthors = Warren L, Buchanan JM | title = Biosynthesis of the purines. XIX. 2-Amino-N-ribosylacetamide 5'-phosphate (glycinamide ribotide) transformylase | journal = The Journal of Biological Chemistry | volume = 229 | issue = 2 | pages = 613–26 | date = December 1957 | pmid = 13502326 }}</ref> This enzyme [[Chemistry:Catalysis|catalyses]] the following [[Chemistry:Chemical reaction|chemical reaction]]

:[[Chemistry:10-Formyltetrahydrofolate|10-formyltetrahydrofolate]] + [[Chemistry:Glycineamide ribonucleotide|N<sup>1</sup>-(5-phospho-D-ribosyl)glycinamide]] <math>\rightleftharpoons</math> tetrahydrofolate  + [[Chemistry:Phosphoribosyl-N-formylglycineamide|N<sup>2</sup>-formyl-N<sup>1</sup>-(5-phospho-D-ribosyl)glycinamide]]

[[File:Overall Reaction of GAR transformylase.jpg|thumb|center|upright=1.2|Overall reaction of GAR transformylase]]
This THF dependent enzyme catalyzes a nucleophilic acyl substitution of the formyl group from 10-formyltetrahydrofolate (fTHF) to N<sup>1</sup>-(5-phospho-D-ribosyl)glycinamide (GAR) to form N<sup>2</sup>-formyl-N<sup>1</sup>-(5-phospho-D-ribosyl)glycinamide (fGAR) as shown above.<ref>McMurry, J. and Tadhg, B. The Organic Chemistry of Biological Pathways</ref> This reaction plays an important role in the formation of purine through the ''de novo'' [[Biology:Purine metabolism|purine biosynthesis]] pathway. This pathway creates [[Chemistry:Inosinic acid|inosine monophosphate]] (IMP), a precursor to [[Chemistry:Adenosine monophosphate|adenosine monophosphate]] (AMP) and [[Chemistry:Guanosine monophosphate|guanosine monophosphate]] (GMP). AMP is a building block for important energy carriers such as ATP, [[Chemistry:Nicotinamide adenine dinucleotide|NAD<sup>+</sup>]] and [[Chemistry:Flavin adenine dinucleotide|FAD]], and signaling molecules such as [[Chemistry:Cyclic adenosine monophosphate|cAMP]].   GARTfase's role in ''de novo'' purine biosynthesis makes it a target for anti-cancer drugs<ref name="pmid23869564">{{cite journal | vauthors = Connelly S, DeMartino JK, Boger DL, Wilson IA | title = Biological and structural evaluation of 10R- and 10S-methylthio-DDACTHF reveals a new role for sulfur in inhibition of glycinamide ribonucleotide transformylase | journal = Biochemistry | volume = 52 | issue = 30 | pages = 5133–44 | date = July 2013 | pmid = 23869564 | pmc = 3823235 | doi = 10.1021/bi4005182 }}</ref> and its overexpression during postnatal development has been connected to [[Medicine:Down syndrome|Down syndrome]].<ref name ="pmid17902044">{{cite journal | vauthors = Banerjee D, Nandagopal K | title = Potential interaction between the GARS-AIRS-GART Gene and CP2/LBP-1c/LSF transcription factor in Down syndrome-related Alzheimer disease | journal = Cellular and Molecular Neurobiology | volume = 27 | issue = 8 | pages = 1117–26 | date = December 2007 | pmid = 17902044 | doi = 10.1007/s10571-007-9217-2 }}</ref> There are two known types of genes encoding GAR transformylase in E.coli: purN and purT, while only purN is found in humans.<ref name ="pmid8501063">{{cite journal | vauthors = Nygaard P, Smith JM | title = Evidence for a novel glycinamide ribonucleotide transformylase in Escherichia coli | journal = Journal of Bacteriology | volume = 175 | issue = 11 | pages = 3591–7 | date = June 1993 | pmid = 8501063 | pmc = 204760 | doi = 10.1128/jb.175.11.3591-3597.1993 }}</ref> Many residues in the active site are conserved across bacterial, yeast, avian and human enzymes.<ref name = "pmid|1522592"/>

== Enzyme Structure ==
[[File:GAR transformylase.png|thumb|left|Structure of GAR transformylase in rainbow from N(blue)->C(red). Folate binding loop is highlighted in black. GAR substrate (red) and THF analogue (blue) are shown in binding pockets.<ref>Zhang, Y., Desharnais, J., Boger, D.L., Wilson, I.A. (2005) "Human GAR Tfase complex structure with 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid and substrate beta-GAR." Unplubished. PDB: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1RBY 1RBY].</ref>]]

In humans, GARTfase is part of trifunctional enzyme which also includes glycinamide ribonucleotide synthase ([[Biology:Phosphoribosylamine—glycine ligase|GARS]])  and aminoimidazole ribonucleotide synthetase ([[Biology:AIR synthetase (FGAM cyclase)|AIRS]]). This protein (110kDa) catalyzes steps 2, 3 and 5 of de novo purine biosynthesis. The proximity of these enzyme units and flexibility of the protein serves to increase pathway throughput. GARTfase is located on the C-terminal end of the protein.<ref name="pmid|20631005">{{cite journal | vauthors = Welin M, Grossmann JG, Flodin S, Nyman T, Stenmark P, Trésaugues L, Kotenyova T, Johansson I, Nordlund P, Lehtiö L | title = Structural studies of tri-functional human GART | journal = Nucleic Acids Research | volume = 38 | issue = 20 | pages = 7308–19 | date = November 2010 | pmid = 20631005 | pmc = 2978367 | doi = 10.1093/nar/gkq595 }}</ref>

Human GARTfase has been crystallized by vapor-diffusion sitting drop method and imaged at the Stanford Synchrotron Radiation Laboratory (SSRL) by at least two groups.<ref name="pmid23869564" /><ref name="pmid12450384">{{cite journal | vauthors = Zhang Y, Desharnais J, Greasley SE, Beardsley GP, Boger DL, Wilson IA | title = Crystal structures of human GAR Tfase at low and high pH and with substrate beta-GAR | journal = Biochemistry | volume = 41 | issue = 48 | pages = 14206–15 | date = December 2002 | pmid = 12450384 | doi = 10.1021/bi020522m }}</ref>

The structure can be described by two subdomains which are connected by a seven-stranded beta sheet. The N- terminal domain consists of a Rossman type mononucleotide fold, with a four strand part of the beta sheet surrounded on each side by two alpha helices. The beta sheet continues into the C terminal domain, where on one side it is covered by a long alpha helix and on the other it is partially exposed to solvent. It is the cleft between the two subdomains where the active site lies.<ref name = "pmid|1522592">{{cite journal | vauthors = Chen P, Schulze-Gahmen U, Stura EA, Inglese J, Johnson DL, Marolewski A, Benkovic SJ, Wilson IA | title = Crystal structure of glycinamide ribonucleotide transformylase from Escherichia coli at 3.0 A resolution. A target enzyme for chemotherapy | journal = Journal of Molecular Biology | volume = 227 | issue = 1 | pages = 283–92 | date = September 1992 | pmid = 1522592 | doi = 10.1016/0022-2836(92)90698-j }}</ref>

The cleft consists of the GAR binding site and the folate binding pocket. The folate binding pocket is delineated by pteridine-binding cleft, the formyl transfer region and the benzoylglutamate region which  bind thepteridine head and a benzoylglutamate tail connected by a formyl bound nitrogen of  fTHF. This folate binding region has been the subject of much research because its inhibition by small molecules has led to the discovery of antineoplastic drugs. The folate binding loop has been shown to change conformation depending on the pH of solution and as such Human GAR transformylase shows highest activity around pH 7.5-8. Lower pH (~4.2) conditions change the conformation of the substrate (GAR) binding loops as well.<ref name="pmid12450384" />

== Mechanism ==

=== Mechanism of purN GARTfase ===
[[File:GAR transformylase mechanism suggested by Qiao et al.jpg|thumb|right|GAR transformylase water assisted mechanism suggested by Qiao et al]]

Klein et al first suggested a water molecule assisted mechanism. A single water molecule possibly held in place by hydrogen bonding with the carboxylate group of the persistent Asp144 residue transfers protons from the GAR-N to the THF-N. The nucleophilic nitrogen on the terminal amino group of GAR attacks the carbonyl carbon of the formyl group on THF pushing negative charge onto the oxygen. Klein suggests that His108 stabilizes the transition state by hydrogen bonding with the negatively charged oxygen and that the reformation of the carbonyl double bond results in breaking the THF-N - formyl bond. Calculations by Qiao et al suggest that the water assisted stepwise proton transfer from Gar-N to THF-N is 80-100 kj/mol more favorable than the concerted transfer suggested by Klein. The mechanism shown is suggested by Qiao et al, whom admittedly did not consider surrounding residues in their calculations.<ref name="pmid7776369">{{cite journal | vauthors = Klein C, Chen P, Arevalo JH, Stura EA, Marolewski A, Warren MS, Benkovic SJ, Wilson IA | title = Towards structure-based drug design: crystal structure of a multisubstrate adduct complex of glycinamide ribonucleotide transformylase at 1.96 A resolution | journal = Journal of Molecular Biology | volume = 249 | issue = 1 | pages = 153–75 | date = May 1995 | pmid = 7776369 | doi = 10.1006/jmbi.1995.0286 }}</ref><ref name="pmid16198047">{{cite journal | vauthors = Qiao QA, Jin Y, Yang C, Zhang Z, Wang M | title = A quantum chemical study on the mechanism of glycinamide ribonucleotide transformylase inhibitor: 10-Formyl-5,8,10-trideazafolic acid | journal = Biophysical Chemistry | volume = 118 | issue = 2–3 | pages = 78–83 | date = December 2005 | pmid = 16198047 | doi = 10.1016/j.bpc.2005.07.001 }}</ref> Much of the early active site mapping on GAR TFase was determined with the bacterial enzyme owing to the quantity available from its overexpression in E. coli.<ref>{{cite journal | vauthors = Inglese J, Johnson DL, Shiau A, Smith JM, Benkovic SJ | title = Subcloning, characterization, and affinity labeling of Escherichia coli glycinamide ribonucleotide transformylase | journal = Biochemistry | volume = 29 | issue = 6 | pages = 1436–43 | date = February 1990 | pmid = 2185839 | doi = 10.1021/bi00458a014 }}</ref>  Using a bromoacetyl dideazafolate affinity analog [[Biography:James Inglese|James Inglese]] and colleagues first identified Asp144 as an active site residue likely involved in the formyl transfer mechanism.<ref>{{cite journal | vauthors = Inglese J, Smith JM, Benkovic SJ | title = Active-site mapping and site-specific mutagenesis of glycinamide ribonucleotide transformylase from Escherichia coli | journal = Biochemistry | volume = 29 | issue = 28 | pages = 6678–87 | date = July 1990 | pmid = 2204419 | doi = 10.1021/bi00480a018 }}</ref>

=== Mechanism of purT GARTfase ===
Studies of the purT variant of GAR transformylase in E.coli found that the reaction proceeds through a formyl phosphate intermediate.  While the in vitro reaction can proceed without THF, overall the in vivo reaction is the same.<ref name="pmid9184151">{{cite journal | vauthors = Marolewski AE, Mattia KM, Warren MS, Benkovic SJ | title = Formyl phosphate: a proposed intermediate in the reaction catalyzed by Escherichia coli PurT GAR transformylase | journal = Biochemistry | volume = 36 | issue = 22 | pages = 6709–16 | date = June 1997 | pmid = 9184151 | doi = 10.1021/bi962961p }}</ref>

== Involvement in ''de novo'' Purine Biosynthesis ==
GART catalyzes the third step in ''de novo'' purine biosynthesis, the formation of [[Chemistry:Phosphoribosyl-N-formylglycineamide|N<sup>2</sup>-formyl-N<sup>1</sup>-(5-phospho-D-ribosyl)glycinamide]] (fGAR) by formyl addition to N<sup>1</sup>-(5-phospho-D-ribosyl)glycinamide (GAR).<ref name = "pmid|13502326"/> In E. coli, the purN enzyme is a 23 kDa protein<ref name = "pmid|10835105">{{cite journal | vauthors = Nixon AE, Benkovic SJ | title = Improvement in the efficiency of formyl transfer of a GAR transformylase hybrid enzyme | journal = Protein Engineering | volume = 13 | issue = 5 | pages = 323–7 | date = May 2000 | pmid = 10835105 | doi = 10.1093/protein/13.5.323 | doi-access = free }}</ref> but in humans it is part of a trifunctional protein of 110 kDa which includes AIRS and GARS functionalities.<ref name = "pmid|20631005"/> This protein catalyzes three different steps of the ''de novo'' purine pathway.

== Disease Relevance ==

=== Cancer Target ===
Due to their increased growth rate and metabolic requirements, cancer cells rely on ''de novo'' nucleotide biosynthesis to achieve levels of AMP and GMP necessary.<ref name = "pmid19201187">{{cite journal | vauthors = Tong X, Zhao F, Thompson CB | title = The molecular determinants of de novo nucleotide biosynthesis in cancer cells | journal = Current Opinion in Genetics & Development | volume = 19 | issue = 1 | pages = 32–7 | date = February 2009 | pmid = 19201187 | pmc = 2707261 | doi = 10.1016/j.gde.2009.01.002 }}</ref> Being able to block any of the steps of the ''de novo'' purine pathway would present significant reduction in tumor growth. Studies have been done both on the substrate binding<ref name = "pmid10577357">{{cite journal | vauthors = Antle VD, Donat N, Hua M, Liao PL, Vince R, Carperelli CA | title = Substrate specificity of human glycinamide ribonucleotide transformylase | journal = Archives of Biochemistry and Biophysics | volume = 370 | issue = 2 | pages = 231–5 | date = October 1999 | pmid = 10577357 | doi = 10.1006/abbi.1999.1428 }}</ref> and folate binding site<ref name = "pmid11469716">{{cite journal | vauthors = Costi MP, Ferrari S | title = Update on antifolate drugs targets | journal = Current Drug Targets | volume = 2 | issue = 2 | pages = 135–66 | date = June 2001 | pmid = 11469716 | doi = 10.2174/1389450013348669 }}</ref> to find inhibitors.

=== Down Syndrome ===
GARTfase is suspected to be connected with Down syndrome. The gene encoding the trifunctional protein human GARS-AIRS-GART is located on chromosome 21q22.1, in the Down syndrome critical region. The protein is overexpressed in the cerebellum during the postnatal development of individuals with Down syndrome. Typically, this protein is undetectable in cerebellum shortly after birth, but found in high levels in prenatal development.<ref name ="pmid17902044" /><ref name ="PMID 9328467">{{cite journal | vauthors = Brodsky G, Barnes T, Bleskan J, Becker L, Cox M, Patterson D | title = The human GARS-AIRS-GART gene encodes two proteins which are differentially expressed during human brain development and temporally overexpressed in cerebellum of individuals with Down syndrome | journal = Human Molecular Genetics | volume = 6 | issue = 12 | pages = 2043–50 | date = November 1997 | pmid = 9328467 | doi = 10.1093/hmg/6.12.2043 | doi-access = free }}</ref>

== See also ==
* Trifunctional purine biosynthetic protein adenosine-3

== References ==
{{reflist}}

== External links ==
* {{MeshName|Phosphoribosylglycinamide+formyltransferase}}

{{One carbon transferases}}
{{Enzymes}}

[[Category:EC 2.1.2]]

{{Sourceattribution|Phosphoribosylglycinamide formyltransferase}}