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* Residue conservation analysis
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Enzyme class:
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Chains A, B:
E.C.2.1.2.2
- Phosphoribosylglycinamide formyltransferase.
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Pathway:
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Purine Biosynthesis (early stages)
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Reaction:
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10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide
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10-formyltetrahydrofolate
Bound ligand (Het Group name = )
matches with 41.00% similarity
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+
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N(1)-(5-phospho-D-ribosyl)glycinamide
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=
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tetrahydrofolate
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+
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N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Biological process
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biosynthetic process
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3 terms
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Biochemical function
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transferase activity
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4 terms
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DOI no:
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J Mol Biol
249:153-175
(1995)
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PubMed id:
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Towards structure-based drug design: crystal structure of a multisubstrate adduct complex of glycinamide ribonucleotide transformylase at 1.96 A resolution.
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C.Klein,
P.Chen,
J.H.Arevalo,
E.A.Stura,
A.Marolewski,
M.S.Warren,
S.J.Benkovic,
I.A.Wilson.
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ABSTRACT
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An inhibitor complex structure of glycinamide ribonucleotide transformylase
(GAR-Tfase; EC 2.1.2.2) from Escherichia coli has been determined with a
multisubstrate adduct BW1476U89 to an R-value of 19.1% at 1.96 A resolution. The
structure was determined by a combination of molecular and single isomorphous
replacement using data from two different monoclinic crystal lattices and
collecting data from crystals soaked in 20% (w/v) methyl-pentanediol as
cryoprotectant for shock-freezing at -150 degrees C. The multisubstrate adduct
is bound in an extended crevice at the interface between the two functional
domains of the enzyme. This inhibitor is positioned in the binding site by three
sets of tight interactions with its phosphate, glutamate and pyrimidone ring
moieties, while its interventing linker atoms are more flexible and adopt two
distinct sets of conformations. The highly conserved Arg103, His108 and Gln170
residues that are key in ligand binding and catalysis (His108), have
compensatory conformational variation that gives some clues as to their role in
substrate specificity and in the formyl transfer. The molecular design of
1476U89 as a multisubstrate adduct inhibitor (Ki approximately 100 pM at pH
8.5), is confirmed as it closely mimics the shape, molecular interaction and
combined binding constants of the natural 10-formyltetrahydrofolate (10-CHO-H4F;
Km approximately 77.4 microM at pH 8.5) and glycinamide-ribonucleotide (GAR; Km
approximately 8.1 microM at pH 8.5) substrates. The stereochemistry of this
ligand complex suggests that His108 may act as an electrophile stabilizing the
oxyanion of the tetrahedral intermediate that is formed as a result of the
direct attack on the 10-CHO-H4F by the amino group of GAR. Structural comparison
of the folate binding modes among GAR-Tfase, dihydrofolate reductase and
thymidylate synthase reveals that folate derivates bound to GAR-Tfase
differentially adopt the trans conformation for the dihedral angle between atoms
C-6 and C-9 providing a handle for targeting specific folate-dependent enzymes.
The structural information derived from two different discrete conformations of
the ligand in the binding site also suggests several leads for the de novo
design of inhibitors of GAR-Tfase that may develop into useful chemotherapeutic
agents.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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H.Li,
W.Fast,
and
S.J.Benkovic
(2009).
Structural and functional modularity of proteins in the de novo purine biosynthetic pathway.
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Protein Sci, 18,
881-892.
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S.A.Krupenko
(2009).
FDH: an aldehyde dehydrogenase fusion enzyme in folate metabolism.
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Chem Biol Interact, 178,
84-93.
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Y.Zhang,
M.Morar,
and
S.E.Ealick
(2008).
Structural biology of the purine biosynthetic pathway.
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Cell Mol Life Sci, 65,
3699-3724.
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W.Manieri,
M.E.Moore,
M.B.Soellner,
P.Tsang,
and
C.A.Caperelli
(2007).
Human glycinamide ribonucleotide transformylase: active site mutants as mechanistic probes.
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Biochemistry, 46,
156-163.
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J.W.Teo,
P.Thayalan,
D.Beer,
A.S.Yap,
M.Nanjundappa,
X.Ngew,
J.Duraiswamy,
S.Liung,
V.Dartois,
M.Schreiber,
S.Hasan,
M.Cynamon,
N.S.Ryder,
X.Yang,
B.Weidmann,
K.Bracken,
T.Dick,
and
K.Mukherjee
(2006).
Peptide deformylase inhibitors as potent antimycobacterial agents.
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Antimicrob Agents Chemother, 50,
3665-3673.
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P.Z.Gatzeva-Topalova,
A.P.May,
and
M.C.Sousa
(2005).
Crystal structure and mechanism of the Escherichia coli ArnA (PmrI) transformylase domain. An enzyme for lipid A modification with 4-amino-4-deoxy-L-arabinose and polymyxin resistance.
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Biochemistry, 44,
5328-5338.
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PDB code:
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A.A.Chumanevich,
S.A.Krupenko,
and
C.Davies
(2004).
The crystal structure of the hydrolase domain of 10-formyltetrahydrofolate dehydrogenase: mechanism of hydrolysis and its interplay with the dehydrogenase domain.
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J Biol Chem, 279,
14355-14364.
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PDB code:
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L.Xu,
C.Li,
A.J.Olson,
and
I.A.Wilson
(2004).
Crystal structure of avian aminoimidazole-4-carboxamide ribonucleotide transformylase in complex with a novel non-folate inhibitor identified by virtual ligand screening.
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J Biol Chem, 279,
50555-50565.
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PDB code:
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G.L.Moore,
and
C.D.Maranas
(2003).
Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach.
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Proc Natl Acad Sci U S A, 100,
5091-5096.
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S.G.Lee,
S.Lutz,
and
S.J.Benkovic
(2003).
On the structural and functional modularity of glycinamide ribonucleotide formyltransferases.
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Protein Sci, 12,
2206-2214.
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T.F.Fu,
J.N.Scarsdale,
G.Kazanina,
V.Schirch,
and
H.T.Wright
(2003).
Location of the pteroylpolyglutamate-binding site on rabbit cytosolic serine hydroxymethyltransferase.
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J Biol Chem, 278,
2645-2653.
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PDB code:
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D.Morikis,
A.H.Elcock,
P.A.Jennings,
and
J.A.McCammon
(2001).
Native-state conformational dynamics of GART: a regulatory pH-dependent coil-helix transition examined by electrostatic calculations.
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Protein Sci, 10,
2363-2378.
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D.Morikis,
A.H.Elcock,
P.A.Jennings,
and
J.A.McCammon
(2001).
Proton transfer dynamics of GART: the pH-dependent catalytic mechanism examined by electrostatic calculations.
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Protein Sci, 10,
2379-2392.
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S.Gite,
Y.Li,
V.Ramesh,
and
U.L.RajBhandary
(2000).
Escherichia coli methionyl-tRNA formyltransferase: role of amino acids conserved in the linker region and in the C-terminal domain on the specific recognition of the initiator tRNA.
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Biochemistry, 39,
2218-2226.
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V.M.Reyes,
S.E.Greasley,
E.A.Stura,
G.P.Beardsley,
and
I.A.Wilson
(2000).
Crystallization and preliminary crystallographic investigations of avian 5-aminoimidazole-4-carboxamide ribonucleotide transformylase-inosine monophosphate cyclohydrolase expressed in Escherichia coli.
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Acta Crystallogr D Biol Crystallogr, 56,
1051-1054.
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M.Ostermeier,
A.E.Nixon,
J.H.Shim,
and
S.J.Benkovic
(1999).
Combinatorial protein engineering by incremental truncation.
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Proc Natl Acad Sci U S A, 96,
3562-3567.
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S.A.Krupenko,
and
C.Wagner
(1999).
Aspartate 142 is involved in both hydrolase and dehydrogenase catalytic centers of 10-formyltetrahydrofolate dehydrogenase.
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J Biol Chem, 274,
35777-35784.
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S.E.Greasley,
M.M.Yamashita,
H.Cai,
S.J.Benkovic,
D.L.Boger,
and
I.A.Wilson
(1999).
New insights into inhibitor design from the crystal structure and NMR studies of Escherichia coli GAR transformylase in complex with beta-GAR and 10-formyl-5,8,10-trideazafolic acid.
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Biochemistry, 38,
16783-16793.
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PDB codes:
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T.J.Stout,
D.Tondi,
M.Rinaldi,
D.Barlocco,
P.Pecorari,
D.V.Santi,
I.D.Kuntz,
R.M.Stroud,
B.K.Shoichet,
and
M.P.Costi
(1999).
Structure-based design of inhibitors specific for bacterial thymidylate synthase.
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Biochemistry, 38,
1607-1617.
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PDB codes:
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V.Ramesh,
C.Mayer,
M.R.Dyson,
S.Gite,
and
U.L.RajBhandary
(1999).
Induced fit of a peptide loop of methionyl-tRNA formyltransferase triggered by the initiator tRNA substrate.
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Proc Natl Acad Sci U S A, 96,
875-880.
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J.H.Shim,
and
S.J.Benkovic
(1998).
Evaluation of the kinetic mechanism of Escherichia coli glycinamide ribonucleotide transformylase.
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Biochemistry, 37,
8776-8782.
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V.Ramesh,
S.Gite,
and
U.L.RajBhandary
(1998).
Functional interaction of an arginine conserved in the sixteen amino acid insertion module of Escherichia coli methionyl-tRNA formyltransferase with determinants for formylation in the initiator tRNA.
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Biochemistry, 37,
15925-15932.
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A.E.Nixon,
M.S.Warren,
and
S.J.Benkovic
(1997).
Assembly of an active enzyme by the linkage of two protein modules.
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Proc Natl Acad Sci U S A, 94,
1069-1073.
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A.V.Efimov
(1997).
Structural trees for protein superfamilies.
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Proteins, 28,
241-260.
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D.L.Boger,
N.E.Haynes,
M.S.Warren,
J.Ramcharan,
A.E.Marolewski,
P.A.Kitos,
and
S.J.Benkovic
(1997).
Abenzyl 10-formyl-trideazafolic acid (abenzyl 10-formyl-TDAF): an effective inhibitor of glycinamide ribonucleotide transformylase.
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Bioorg Med Chem, 5,
1847-1852.
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J.A.Bertrand,
G.Auger,
E.Fanchon,
L.Martin,
D.Blanot,
J.van Heijenoort,
and
O.Dideberg
(1997).
Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli.
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EMBO J, 16,
3416-3425.
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PDB codes:
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S.A.Krupenko,
C.Wagner,
and
R.J.Cook
(1997).
Domain structure of rat 10-formyltetrahydrofolate dehydrogenase. Resolution of the amino-terminal domain as 10-formyltetrahydrofolate hydrolase.
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J Biol Chem, 272,
10273-10278.
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S.P.Sanghani,
and
R.G.Moran
(1997).
Tight binding of folate substrates and inhibitors to recombinant mouse glycinamide ribonucleotide formyltransferase.
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Biochemistry, 36,
10506-10516.
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V.Ramesh,
S.Gite,
Y.Li,
and
U.L.RajBhandary
(1997).
Suppressor mutations in Escherichia coli methionyl-tRNA formyltransferase: role of a 16-amino acid insertion module in initiator tRNA recognition.
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Proc Natl Acad Sci U S A, 94,
13524-13529.
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H.Lee,
V.M.Reyes,
and
J.Kraut
(1996).
Crystal structures of Escherichia coli dihydrofolate reductase complexed with 5-formyltetrahydrofolate (folinic acid) in two space groups: evidence for enolization of pteridine O4.
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Biochemistry, 35,
7012-7020.
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PDB codes:
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L.Rey,
D.Fernández,
B.Brito,
Y.Hernando,
J.M.Palacios,
J.Imperial,
and
T.Ruiz-Argüeso
(1996).
The hydrogenase gene cluster of Rhizobium leguminosarum bv. viciae contains an additional gene (hypX), which encodes a protein with sequence similarity to the N10-formyltetrahydrofolate-dependent enzyme family and is required for nickel-dependent hydrogenase processing and activity.
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Mol Gen Genet, 252,
237-248.
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M.S.Warren,
A.E.Marolewski,
and
S.J.Benkovic
(1996).
A rapid screen of active site mutants in glycinamide ribonucleotide transformylase.
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Biochemistry, 35,
8855-8862.
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J.L.Smith
(1995).
Enzymes of nucleotide synthesis.
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Curr Opin Struct Biol, 5,
752-757.
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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.
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Links
