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PDBsum entry 1kj9

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1kj9
Jmol
Contents
Protein chains
386 a.a. *
Ligands
ATP ×2
MPO
EDO ×6
Metals
_MG ×5
_NA ×2
_CL ×2
Waters ×993
* Residue conservation analysis
PDB id:
1kj9
Name: Transferase
Title: Crystal structure of purt-encoded glycinamide ribonucleotide transformylase complexed with mg-atp
Structure: Phosphoribosylglycinamide formyltransferase 2. Chain: a, b. Synonym: gart 2. Gar transformylase 2. 5'- phosphoribosylglycinamide. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: purt. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.60Å     R-factor:   0.180     R-free:   0.230
Authors: J.B.Thoden,S.M.Firestine,S.J.Benkovic,H.M.Holden
Key ref:
J.B.Thoden et al. (2002). PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site. J Biol Chem, 277, 23898-23908. PubMed id: 11953435 DOI: 10.1074/jbc.M202251200
Date:
04-Dec-01     Release date:   28-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P33221  (PURT_ECOLI) -  Phosphoribosylglycinamide formyltransferase 2
Seq:
Struc:
392 a.a.
386 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: 10.1074/jbc.M202251200 J Biol Chem 277:23898-23908 (2002)
PubMed id: 11953435  
 
 
PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site.
J.B.Thoden, S.M.Firestine, S.J.Benkovic, H.M.Holden.
 
  ABSTRACT  
 
PurT-encoded glycinamide ribonucleotide transformylase, or PurT transformylase, functions in purine biosynthesis by catalyzing the formylation of glycinamide ribonucleotide through a catalytic mechanism requiring Mg(2+)ATP and formate. From previous x-ray diffraction analyses, it has been demonstrated that PurT transformylase from Escherichia coli belongs to the ATP-grasp superfamily of enzymes, which are characterized by three structural motifs referred to as the A-, B-, and C-domains. In all of the ATP-grasp enzymes studied to date, the adenosine nucleotide ligands are invariably wedged between the B- and C-domains, and in some cases, such as biotin carboxylase and carbamoyl phosphate synthetase, the B-domains move significantly upon nucleotide binding. Here we present a systematic and high-resolution structural investigation of PurT transformylase complexed with various adenosine nucleotides or nucleotide analogs including Mg(2+)ATP, Mg(2+)-5'-adenylylimidodiphosphate, Mg(2+)-beta,gamma-methyleneadenosine 5'-triphosphate, Mg(2+)ATPgammaS, or Mg(2+)ADP. Taken together, these studies indicate that the conformation of the so-called "T-loop," delineated by Lys-155 to Gln-165, is highly sensitive to the chemical identity of the nucleotide situated in the binding pocket. This sensitivity to nucleotide identity is in sharp contrast to that observed for the "P-loop"-containing enzymes, in which the conformation of the binding motif is virtually unchanged in the presence or absence of nucleotides.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Close-up view of the active site of PurT transformylase. The AMPPNP and GAR moieties are highlighted in yellow and pink bonds, respectively. Those amino acids located within ~3.2 Å of the AMPPNP and GAR moieties are shown in stereo. The amino group of GAR that is formylated during the reaction mechanism is indicated by the asterisk.
Figure 6.
Fig. 6. Structure of PurT transformylase complexed with Mg2+ATP and GAR. Electron densities for the Mg 2+ATP and the T-loop are shown in a, whereas the hydrogen bonding interactions between the nucleotide and the protein are indicated by the dashed lines in b.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 23898-23908) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19182782 S.Schmelz, N.Kadi, S.A.McMahon, L.Song, D.Oves-Costales, M.Oke, H.Liu, K.A.Johnson, L.G.Carter, C.H.Botting, M.F.White, G.L.Challis, and J.H.Naismith (2009).
AcsD catalyzes enantioselective citrate desymmetrization in siderophore biosynthesis.
  Nat Chem Biol, 5, 174-182.
PDB codes: 2w02 2w03 2w04
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
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.  
18954462 T.A.Binkowski, and A.Joachimiak (2008).
Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites.
  BMC Struct Biol, 8, 45.  
18712276 Y.Zhang, M.Morar, and S.E.Ealick (2008).
Structural biology of the purine biosynthetic pathway.
  Cell Mol Life Sci, 65, 3699-3724.  
17154526 M.Morar, R.Anand, A.A.Hoskins, J.Stubbe, and S.E.Ealick (2006).
Complexed structures of formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima describe a novel ATP binding protein superfamily.
  Biochemistry, 45, 14880-14895.
PDB codes: 2hru 2hry 2hs0 2hs3 2hs4
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.