DB code: S00294

RLCP classification 3.1144.1800.89 : Transfer
CATH domain 3.40.50.170 : Rossmann fold Catalytic domain
E.C. 2.1.2.2
CSA 1grc 1cde 1c2t
M-CSA 1grc 1cde 1c2t
MACiE

CATH domain Related DB codes (homologues)
3.40.50.170 : Rossmann fold D00087

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P08179 Phosphoribosylglycinamide formyltransferase
EC 2.1.2.2
5''-phosphoribosylglycinamide transformylase
GAR transformylase
GART
NP_416995.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490728.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00551 (Formyl_trans_N)
[Graphical View]

KEGG enzyme name
phosphoribosylglycinamide formyltransferase
2-amino-N-ribosylacetamide 5'-phosphate transformylase
GAR formyltransferase
GAR transformylase
glycinamide ribonucleotide transformylase
GAR TFase
5,10-methenyltetrahydrofolate:2-amino-N-ribosylacetamideribonucleotide transformylase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P08179 PUR3_ECOLI 10-formyltetrahydrofolate + N(1)-(5-phospho-D- ribosyl)glycinamide = tetrahydrofolate + N(2)-formyl-N(1)-(5- phospho-D-ribosyl)glycinamide. Monomer. Homodimer below pH 6.8.

KEGG Pathways
Map code Pathways E.C.
MAP00230 Purine metabolism
MAP00670 One carbon pool by folate

Compound table
Substrates Products Intermediates
KEGG-id C00234 C03838 C00101 C04376
E.C.
Compound 10-Formyltetrahydrofolate 5'-Phosphoribosylglycinamide Tetrahydrofolate 5'-Phosphoribosyl-N-formylglycinamide
Type amino acids,amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carboxyl group amide group,amine group,carbohydrate,phosphate group/phosphate ion amino acids,amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carboxyl group amide group,amine group,carbohydrate,phosphate group/phosphate ion
ChEBI 15637
15635
20506
PubChem 122347
6326742
160913
5460413
91443
130805
1c2tA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:NHS Bound:GAR Unbound Unbound Unbound
1c2tB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:NHS Bound:GAR Unbound Unbound Unbound
1c3eA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:NHR Bound:GAR Unbound Unbound Unbound
1c3eB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:NHR Bound:GAR Unbound Unbound Unbound
1cddA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1cddB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1cdeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:GAR Analogue:DZF Unbound Unbound
1cdeB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:GAR Analogue:DZF Unbound Unbound
1cdeC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:GAR Analogue:DZF Unbound Unbound
1cdeD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:GAR Analogue:DZF Unbound Unbound
1garA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:U89 Unbound Unbound Unbound Unbound
1garB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:U89 Unbound Unbound Unbound Unbound
1grcA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1grcB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1jkxA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-analogue:138
1jkxB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-analogue:138
1jkxC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-analogue:138
1jkxD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-analogue:138
2garA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
3garA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [2]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1c2tA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1c2tB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1c3eA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1c3eB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1cddA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1cddB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1cdeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1cdeB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1cdeC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1cdeD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1garA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1garB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1grcA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1grcB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1jkxA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1jkxB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1jkxC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
1jkxD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
2garA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144
3garA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 106;HIS 108;ASP 144

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.9, p.6686
[2]
p.6118
[4]
Fig.8, p.167 3
[5]
Fig.2
[12]
Fig.7, Fig.8 3
[15]
Fig.9, p.10029

References
[1]
Resource
Comments
Medline ID
PubMed ID 2204419
Journal Biochemistry
Year 1990
Volume 29
Pages 6678-87
Authors Inglese J, Smith JM, Benkovic SJ
Title Active-site mapping and site-specific mutagenesis of glycinamide ribonucleotide transformylase from Escherichia coli.
Related PDB
Related UniProtKB P08179
[2]
Resource
Comments
Medline ID
PubMed ID 1631098
Journal Proc Natl Acad Sci U S A
Year 1992
Volume 89
Pages 6114-8
Authors Almassy RJ, Janson CA, Kan CC, Hostomska Z
Title Structures of apo and complexed Escherichia coli glycinamide ribonucleotide transformylase.
Related PDB 1cdd 1cde
Related UniProtKB P08179
[3]
Resource
Comments
Medline ID
PubMed ID 1522592
Journal J Mol Biol
Year 1992
Volume 227
Pages 283-92
Authors 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.
Related PDB 1grc
Related UniProtKB P08179
[4]
Resource
Comments
Medline ID
PubMed ID 7776369
Journal J Mol Biol
Year 1995
Volume 249
Pages 153-75
Authors 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.
Related PDB 1gar
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8688421
Journal Biochemistry
Year 1996
Volume 35
Pages 8855-62
Authors Warren MS, Marolewski AE, Benkovic SJ
Title A rapid screen of active site mutants in glycinamide ribonucleotide transformylase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 8876651
Journal J Mol Biol
Year 1996
Volume 262
Pages 746-55
Authors Mullen CA, Jennings PA
Title Glycinamide ribonucleotide transformylase undergoes pH-dependent dimerization.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9037007
Journal Proc Natl Acad Sci U S A
Year 1997
Volume 94
Pages 1069-73
Authors Nixon AE, Warren MS, Benkovic SJ
Title Assembly of an active enzyme by the linkage of two protein modules.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9354237
Journal Bioorg Med Chem
Year 1997
Volume 5
Pages 1817-30
Authors Boger DL, Haynes NE, Kitos PA, Warren MS, Ramcharan J, Marolewski AE, Benkovic SJ
Title 10-Formyl-5,8,10-trideazafolic acid (10-formyl-TDAF): a potent inhibitor of glycinamide ribonucleotide transformylase.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 9143358
Journal Arch Biochem Biophys
Year 1997
Volume 341
Pages 98-103
Authors Caperelli CA, Giroux EL
Title The human glycinamide ribonucleotide transformylase domain: purification, characterization, and kinetic mechanism.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 9051735
Journal Protein Eng
Year 1997
Volume 10
Pages 63-8
Authors Warren MS, Benkovic SJ
Title Combinatorial manipulation of three key active site residues in glycinamide ribonucleotide transformylase.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 9628739
Journal Biochemistry
Year 1998
Volume 37
Pages 8776-82
Authors Shim JH, Benkovic SJ
Title Evaluation of the kinetic mechanism of Escherichia coli glycinamide ribonucleotide transformylase.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 9698564
Journal J Mol Biol
Year 1998
Volume 281
Pages 485-99
Authors Su Y, Yamashita MM, Greasley SE, Mullen CA, Shim JH, Jennings PA, Benkovic SJ, Wilson IA
Title A pH-dependent stabilization of an active site loop observed from low and high pH crystal structures of mutant monomeric glycinamide ribonucleotide transformylase at 1.8 to 1.9 A.
Related PDB 2gar 3gar
Related UniProtKB P08179
[13]
Resource
Comments
Medline ID
PubMed ID 9500916
Journal J Mol Biol
Year 1998
Volume 276
Pages 819-27
Authors Mullen CA, Jennings PA
Title A single mutation disrupts the pH-dependent dimerization of glycinamide ribonucleotide transformylase.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 10606510
Journal Biochemistry
Year 1999
Volume 38
Pages 16783-93
Authors Greasley SE, Yamashita MM, Cai H, Benkovic SJ, Boger DL, Wilson IA
Title 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.
Related PDB 1c2t 1c3e
Related UniProtKB P08179
[15]
Resource
Comments
Medline ID
PubMed ID 10433709
Journal Biochemistry
Year 1999
Volume 38
Pages 10024-31
Authors Shim JH, Benkovic SJ
Title Catalytic mechanism of Escherichia coli glycinamide ribonucleotide transformylase probed by site-directed mutagenesis and pH-dependent studies.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 10577357
Journal Arch Biochem Biophys
Year 1999
Volume 370
Pages 231-5
Authors Antle VD, Donat N, Hua M, Liao PL, Vince R, Carperelli CA
Title Substrate specificity of human glycinamide ribonucleotide transformylase.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 10835105
Journal Protein Eng
Year 2000
Volume 13
Pages 323-7
Authors Nixon AE, Benkovic SJ
Title Improvement in the efficiency of formyl transfer of a GAR transformylase hybrid enzyme.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11604542
Journal Protein Sci
Year 2001
Volume 10
Pages 2363-78
Authors Morikis D, Elcock AH, Jennings PA, McCammon JA
Title Native-state conformational dynamics of GART: a regulatory pH-dependent coil-helix transition examined by electrostatic calculations.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11604543
Journal Protein Sci
Year 2001
Volume 10
Pages 2379-92
Authors Morikis D, Elcock AH, Jennings PA, McCammon JA
Title Proton transfer dynamics of GART: the pH-dependent catalytic mechanism examined by electrostatic calculations.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 11695901
Journal Biochemistry
Year 2001
Volume 40
Pages 13538-47
Authors Greasley SE, Marsilje TH, Cai H, Baker S, Benkovic SJ, Boger DL, Wilson IA
Title Unexpected formation of an epoxide-derived multisubstrate adduct inhibitor on the active site of GAR transformylase.
Related PDB 1jkx
Related UniProtKB

Comments
According to the literature [15], the catalytic reaction of this enzyme proceeds as follows:
(1) The transferred group, the formyl group of the CHO-THF substrate, is stabilized by the sidechains of His108 and Asn106. The imidazole ring of His108 is protonated by the interaction with Asp144.
(2) The acceptor group, the amine group of the GAR substrate, is in a free base form, and makes a nucleophilic attack on the formyl group, forming a tetrahedral intermediate.
(3) A proton transfer from the amine group of GAR to the leaving amine group is mediated by a catalytic water. This catalytic water may be assisted by Asp144.
(4) A breakdown of the tetrahedral intermediate leads to the release of products.

Created Updated
2002-05-01 2010-12-17