PDBsum entry 1eyz

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
Protein chains
389 a.a. *
ANP ×2
_MG ×5
_NA ×2
Waters ×846
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Structure of escherichia coli purt-encoded glycinamide ribonucleotide transformylase complexed with mg and amppnp
Structure: Phosphoribosylglycinamide formyltransferase 2. Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
1.75Å     R-factor:   0.187     R-free:   0.228
Authors: J.B.Thoden,S.Firestine,A.Nixon,S.J.Benkovic,H.M.Holden
Key ref:
J.B.Thoden et al. (2000). Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase. Biochemistry, 39, 8791-8802. PubMed id: 10913290 DOI: 10.1021/bi000926j
09-May-00     Release date:   02-Aug-00    
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Protein chains
Pfam   ArchSchema ?
P33221  (PURT_ECOLI) -  Phosphoribosylglycinamide formyltransferase 2
392 a.a.
389 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     phosphorylation   4 terms 
  Biochemical function     catalytic activity     11 terms  


DOI no: 10.1021/bi000926j Biochemistry 39:8791-8802 (2000)
PubMed id: 10913290  
Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase.
J.B.Thoden, S.Firestine, A.Nixon, S.J.Benkovic, H.M.Holden.
In Escherichia coli, the PurT-encoded glycinamide ribonucleotide transformylase, or PurT transformylase, catalyzes an alternative formylation of glycinamide ribonucleotide (GAR) in the de novo pathway for purine biosynthesis. On the basis of amino acid sequence analyses, it is known that the PurT transformylase belongs to the ATP-grasp superfamily of proteins. The common theme among members of this superfamily is a catalytic reaction mechanism that requires ATP and proceeds through an acyl phosphate intermediate. All of the enzymes belonging to the ATP-grasp superfamily are composed of three structural motifs, termed the A-, B-, and C-domains, and in each case, the ATP is wedged between the B- and C-domains. Here we describe two high-resolution X-ray crystallographic structures of PurT transformylase from E. coli: one form complexed with the nonhydrolyzable ATP analogue AMPPNP and the second with bound AMPPNP and GAR. The latter structure is of special significance because it represents the first ternary complex to be determined for a member of the ATP-grasp superfamily involved in purine biosynthesis and as such provides new information about the active site region involved in ribonucleotide binding. Specifically in PurT transformylase, the GAR substrate is anchored to the protein via Glu 82, Asp 286, Lys 355, Arg 362, and Arg 363. Key amino acid side chains involved in binding the AMPPNP to the enzyme include Arg 114, Lys 155, Glu 195, Glu 203, and Glu 267. Strikingly, the amino group of GAR that is formylated during the reaction lies at 2.8 A from one of the gamma-phosphoryl oxygens of the AMPPNP.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20631005 M.Welin, J.G.Grossmann, S.Flodin, T.Nyman, P.Stenmark, L.Trésaugues, T.Kotenyova, I.Johansson, P.Nordlund, and L.Lehtiö (2010).
Structural studies of tri-functional human GART.
  Nucleic Acids Res, 38, 7308-7319.
PDB codes: 2qk4 2v9y
19384989 H.Li, W.Fast, and S.J.Benkovic (2009).
Structural and functional modularity of proteins in the de novo purine biosynthetic pathway.
  Protein Sci, 18, 881-892.  
19362848 S.M.Firestine, H.Paritala, J.E.McDonnell, J.B.Thoden, and H.M.Holden (2009).
Identification of inhibitors of N5-carboxyaminoimidazole ribonucleotide synthetase by high-throughput screening.
  Bioorg Med Chem, 17, 3317-3323.  
18725455 I.Mochalkin, J.R.Miller, A.Evdokimov, S.Lightle, C.Yan, C.K.Stover, and G.L.Waldrop (2008).
Structural evidence for substrate-induced synergism and half-sites reactivity in biotin carboxylase.
  Protein Sci, 17, 1706-1718.
PDB codes: 2c00 2j9g 2vpq 2vqd 2vr1
19053251 J.B.Thoden, H.M.Holden, and S.M.Firestine (2008).
Structural analysis of the active site geometry of N5-carboxyaminoimidazole ribonucleotide synthetase from Escherichia coli.
  Biochemistry, 47, 13346-13353.
PDB codes: 3eth 3etj
18271571 S.O.Nilsson Lill, J.Gao, and G.L.Waldrop (2008).
Molecular dynamics simulations of biotin carboxylase.
  J Phys Chem B, 112, 3149-3156.  
18712276 Y.Zhang, M.Morar, and S.E.Ealick (2008).
Structural biology of the purine biosynthetic pathway.
  Cell Mol Life Sci, 65, 3699-3724.  
18069798 Y.Zhang, R.H.White, and S.E.Ealick (2008).
Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii.
  Biochemistry, 47, 205-217.
PDB codes: 2r7k 2r7l 2r7m 2r7n 2r84 2r85 2r86 2r87
17717183 M.St Maurice, L.Reinhardt, K.H.Surinya, P.V.Attwood, J.C.Wallace, W.W.Cleland, and I.Rayment (2007).
Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme.
  Science, 317, 1076-1079.
PDB code: 2qf7
16481318 M.E.Fraser, K.Hayakawa, M.S.Hume, D.G.Ryan, and E.R.Brownie (2006).
Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase.
  J Biol Chem, 281, 11058-11065.
PDB codes: 2fp4 2fpg 2fpi 2fpp
15975512 Y.Li, N.M.Llewellyn, R.Giri, F.Huang, and J.B.Spencer (2005).
Biosynthesis of the unique amino acid side chain of butirosin: possible protective-group chemistry in an acyl carrier protein-mediated pathway.
  Chem Biol, 12, 665-675.  
14990577 A.Dinescu, T.R.Cundari, V.S.Bhansali, J.L.Luo, and M.E.Anderson (2004).
Function of conserved residues of human glutathione synthetase: implications for the ATP-grasp enzymes.
  J Biol Chem, 279, 22412-22421.  
14500881 K.Matsuda, T.Nishioka, K.Kinoshita, T.Kawabata, and N.Go (2003).
Finding evolutionary relations beyond superfamilies: fold-based superfamilies.
  Protein Sci, 12, 2239-2251.  
11953435 J.B.Thoden, S.M.Firestine, S.J.Benkovic, and H.M.Holden (2002).
PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site.
  J Biol Chem, 277, 23898-23908.
PDB codes: 1kj8 1kj9 1kji 1kjj 1kjq
11006546 T.J.Kappock, S.E.Ealick, and J.Stubbe (2000).
Modular evolution of the purine biosynthetic pathway.
  Curr Opin Chem Biol, 4, 567-572.  
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 codes are shown on the right.