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PDBsum entry 1thz

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protein ligands metals Protein-protein interface(s) links
Transferase, hydrolase PDB id
1thz
Jmol
Contents
Protein chains
590 a.a. *
Ligands
326 ×2
Metals
__K ×2
Waters ×748
* Residue conservation analysis
PDB id:
1thz
Name: Transferase, hydrolase
Title: Crystal structure of avian aicar transformylase in complex with a novel inhibitor identified by virtual ligand screening
Structure: Bifunctional purine biosynthesis protein purh. Chain: a, b. Engineered: yes. Other_details: purh contains phosphoribosylaminoimidazolecarboxamide formyltransferase and imp cyclohydrolase
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Gene: atic, purh. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.214     R-free:   0.240
Authors: L.Xu,C.Li,A.J.Olson,I.A.Wilson
Key ref:
L.Xu et al. (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. PubMed id: 15355974 DOI: 10.1074/jbc.M406801200
Date:
01-Jun-04     Release date:   07-Sep-04    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P31335  (PUR9_CHICK) -  Bifunctional purine biosynthesis protein PURH
Seq:
Struc:
 
Seq:
Struc:
593 a.a.
590 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.2.1.2.3  - Phosphoribosylaminoimidazolecarboxamide formyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Purine Biosynthesis (late stages)
      Reaction: 10-formyltetrahydrofolate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamide = tetrahydrofolate + 5-formamido-1-(5-phospho-D- ribosyl)imidazole-4-carboxamide
10-formyltetrahydrofolate
+ 5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamide
= tetrahydrofolate
+ 5-formamido-1-(5-phospho-D- ribosyl)imidazole-4-carboxamide
   Enzyme class 3: E.C.3.5.4.10  - Imp cyclohydrolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: IMP + H2O = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
IMP
+ H(2)O
= 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M406801200 J Biol Chem 279:50555-50565 (2004)
PubMed id: 15355974  
 
 
Crystal structure of avian aminoimidazole-4-carboxamide ribonucleotide transformylase in complex with a novel non-folate inhibitor identified by virtual ligand screening.
L.Xu, C.Li, A.J.Olson, I.A.Wilson.
 
  ABSTRACT  
 
Aminoimidazole-4-carboxamide ribonucleotide transformylase (AICAR Tfase), one of the two folate-dependent enzymes in the de novo purine biosynthesis pathway, is a promising target for anti-neoplastic chemotherapy. Although classic antifolates, such as methotrexate, have been developed as anticancer agents, their general toxicity and drug resistance are major issues associated with their clinical use and future development. Identification of inhibitors with novel scaffolds could be an attractive alternative. We present here the crystal structure of avian AICAR Tfase complexed with the first non-folate based inhibitor identified through virtual ligand screening of the National Cancer Institute Diversity Set. The inhibitor 326203-A (2-[5-hydroxy-3-methyl-1-(2-methyl-4-sulfophenyl)-1H-pyrazol-4-ylazo]-4-sulfo-benzoic acid) displayed competitive inhibition against the natural cofactor, 10-formyl-tetrahydrofolate, with a K(i) of 7.1 mum. The crystal structure of AICAR Tfase with 326203-A at 1.8 A resolution revealed a unique binding mode compared with antifolate inhibitors. The inhibitor also accessed an additional binding pocket that is not occupied by antifolates. The sulfonate group of 326203-A appears to form the dominant interaction of the inhibitor with the proposed oxyanion hole through interaction with a helix dipole and Lys(267). An aromatic interaction with Phe(316) also likely contributes to favorable binding. Based on these structural insights, several inhibitors with improved potency were subsequently identified in the National Cancer Institute Compound Library and the Available Chemical Directory by similarity search and molecular modeling methods. These results provide further support for our combined virtual ligand screening rational design approach for the discovery of novel, non-folate-based inhibitors of AICAR Tfase.
 
  Selected figure(s)  
 
Figure 2.
FIG. 2. Chemical structures of inhibitor 326203-A and the active site of AICAR Tfase. A, the structure of 326203-A is shown as depicted in National Cancer Institute Compound library; the Cr^3+ chelation site is highlighted in red. B, the crystal structure of the inhibitor did not show any bound Cr^3+ but instead an intramolecular hydrogen bond array, which is colored in red. C, stereo view of the AICAR Tfase active site with bound 326203-A. The two different subunits of the dimer that compose the active site are colored in sky blue and pink, respectively. The bound inhibitor is depicted in ball-and-stick representation, with the oxygen atoms in red, carbons in yellow, sulfurs in green, and nitrogens in blue. The 2F[o] - F[c] electron density map (blue) for the inhibitor is contoured at 1.0 . The key interactions of the inhibitor with AICAR Tfase involve three moieties of the inhibitor: benzene ring A, pyrazole ring, and benzene ring B.
Figure 4.
FIG. 4. AICAR Tfase-326203-A interactions. A, residues in the AICAR Tfase active site interact with the inhibitor. The side chains of the protein and the inhibitor are depicted in ball-and-stick representations. The protein and inhibitor are colored as in Fig. 2C. The side chains of the protein are colored in gray. Asn^490 has a different conformation in the apo human enzyme and is colored in green. B, schematic drawing of AICAR Tfase interactions with 326203-A, generated by LIGPLOT (31). Residues forming van der Waals' interactions are indicated by an arc with radiating spokes toward the ligand atom they contact; those participating in the hydrogen bonding are shown in ball-and-stick representations. Hydrogen bonds are illustrated as dotted lines with the donor-acceptor distance given in Å. Water molecules are colored in cyan, and carbon atoms are in black; other atom types are colored according to Fig. 2C.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 50555-50565) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18712276 Y.Zhang, M.Morar, and S.E.Ealick (2008).
Structural biology of the purine biosynthetic pathway.
  Cell Mol Life Sci, 65, 3699-3724.  
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