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PDBsum entry 1c2t

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1c2t
Jmol
Contents
Protein chains
209 a.a. *
Ligands
NHS ×2
GAR ×2
Waters ×197
* Residue conservation analysis
PDB id:
1c2t
Name: Transferase
Title: New insights into inhibitor design from the crystal structur studies of e. Coli gar transformylase in complex with beta- 10-formyl-5,8,10-trideazafolic acid.
Structure: Glycinamide ribonucleotide transformylase. Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.227     R-free:   0.265
Authors: S.E.Greasley,M.M.Yamashita,H.Cai,S.J.Benkovic,D.L.Boger,I.A.
Key ref:
S.E.Greasley et al. (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. Biochemistry, 38, 16783-16793. PubMed id: 10606510 DOI: 10.1021/bi991888a
Date:
26-Jul-99     Release date:   05-Jan-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P08179  (PUR3_ECOLI) -  Phosphoribosylglycinamide formyltransferase
Seq:
Struc:
212 a.a.
209 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.1.2.2  - Phosphoribosylglycinamide formyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Purine Biosynthesis (early stages)
      Reaction: 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide
10-formyltetrahydrofolate
+
N(1)-(5-phospho-D-ribosyl)glycinamide
Bound ligand (Het Group name = GAR)
corresponds exactly
= tetrahydrofolate
+ N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biosynthetic process   5 terms 
  Biochemical function     transferase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi991888a Biochemistry 38:16783-16793 (1999)
PubMed id: 10606510  
 
 
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.
S.E.Greasley, M.M.Yamashita, H.Cai, S.J.Benkovic, D.L.Boger, I.A.Wilson.
 
  ABSTRACT  
 
The crystal structure of Escherichia coli GAR Tfase at 2.1 A resolution in complex with 10-formyl-5,8,10-trideazafolic acid (10-formyl-TDAF, K(i) = 260 nM), an inhibitor designed to form an enzyme-assembled multisubstrate adduct with the substrate, beta-GAR, was studied to determine the exact nature of its inhibitory properties. Rather than forming the expected covalent adduct, the folate inhibitor binds as the hydrated aldehyde (gem-diol) in the enzyme active site, in a manner that mimics the tetrahedral intermediate of the formyl transfer reaction. In this hydrated form, the inhibitor not only provides unexpected insights into the catalytic mechanism but also explains the 10-fold difference in inhibitor potency between 10-formyl-TDAF and the corresponding alcohol, and a further 10-fold difference for inhibitors that lack the alcohol. The presence of the hydrated aldehyde was confirmed in solution by (13)C-(1)H NMR spectroscopy of the ternary GAR Tfase-beta-GAR-10-formyl-TDAF complex using the (13)C-labeled 10-formyl-TDAF. This insight into the behavior of the inhibitor, which is analogous to protease or transaminase inhibitors, provides a novel and previously unrecognized basis for the design of more potent inhibitors of the folate-dependent formyl transfer enzymes of the purine biosynthetic pathway and development of anti-neoplastic agents.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20823548 E.Pozharski (2010).
Percentile-based spread: a more accurate way to compare crystallographic models.
  Acta Crystallogr D Biol Crystallogr, 66, 970-978.  
18686942 J.K.DeMartino, I.Hwang, S.Connelly, I.A.Wilson, and D.L.Boger (2008).
Asymmetric synthesis of inhibitors of glycinamide ribonucleotide transformylase.
  J Med Chem, 51, 5441-5448.  
18712276 Y.Zhang, M.Morar, and S.E.Ealick (2008).
Structural biology of the purine biosynthetic pathway.
  Cell Mol Life Sci, 65, 3699-3724.  
17452785 T.C.Terwilliger, R.W.Grosse-Kunstleve, P.V.Afonine, P.D.Adams, N.W.Moriarty, P.Zwart, R.J.Read, D.Turk, and L.W.Hung (2007).
Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models.
  Acta Crystallogr D Biol Crystallogr, 63, 597-610.  
17198385 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.
  Biochemistry, 46, 156-163.  
17057331 P.Kursula, H.Schüler, S.Flodin, P.Nilsson-Ehle, D.J.Ogg, P.Savitsky, P.Nordlund, and P.Stenmark (2006).
Structures of the hydrolase domain of human 10-formyltetrahydrofolate dehydrogenase and its complex with a substrate analogue.
  Acta Crystallogr D Biol Crystallogr, 62, 1294-1299.
PDB codes: 2bw0 2cfi
16597835 S.N.Reuland, A.P.Vlasov, and S.A.Krupenko (2006).
Modular organization of FDH: Exploring the basis of hydrolase catalysis.
  Protein Sci, 15, 1076-1084.  
15355974 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.
  J Biol Chem, 279, 50555-50565.
PDB code: 1thz
11604542 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.
  Protein Sci, 10, 2363-2378.  
11604543 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.
  Protein Sci, 10, 2379-2392.  
10944351 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.
  Acta Crystallogr D Biol Crystallogr, 56, 1051-1054.  
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.