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PDBsum entry 1q1k

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Transferase PDB id
1q1k
Jmol
Contents
Protein chain
288 a.a. *
Ligands
PRT
TLA ×2
* Residue conservation analysis
PDB id:
1q1k
Name: Transferase
Title: Structure of atp-phosphoribosyltransferase from e. Coli comp pr-atp
Structure: Atp phosphoribosyltransferase. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: hisg. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PDB file)
Resolution:
2.90Å     R-factor:   0.215     R-free:   0.272
Authors: B.Lohkamp,G.Mcdermott,J.R.Coggins,A.J.Lapthorn
Key ref:
B.Lohkamp et al. (2004). The structure of Escherichia coli ATP-phosphoribosyltransferase: identification of substrate binding sites and mode of AMP inhibition. J Mol Biol, 336, 131-144. PubMed id: 14741209 DOI: 10.1016/j.jmb.2003.12.020
Date:
21-Jul-03     Release date:   02-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P60757  (HIS1_ECOLI) -  ATP phosphoribosyltransferase
Seq:
Struc:
299 a.a.
288 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.17  - Atp phosphoribosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Histidine Biosynthesis (early stages)
      Reaction: 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D- ribose 1-diphosphate
1-(5-phospho-beta-D-ribosyl)-ATP
Bound ligand (Het Group name = PRT)
corresponds exactly
+ diphosphate
= ATP
+ 5-phospho-alpha-D- ribose 1-diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     cellular amino acid biosynthetic process   2 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2003.12.020 J Mol Biol 336:131-144 (2004)
PubMed id: 14741209  
 
 
The structure of Escherichia coli ATP-phosphoribosyltransferase: identification of substrate binding sites and mode of AMP inhibition.
B.Lohkamp, G.McDermott, S.A.Campbell, J.R.Coggins, A.J.Lapthorn.
 
  ABSTRACT  
 
ATP-phosphoribosyltransferase (ATP-PRT), the first enzyme of the histidine pathway, is a complex allosterically regulated enzyme, which controls the flow of intermediates through this biosynthetic pathway. The crystal structures of Escherichia coli ATP-PRT have been solved in complex with the inhibitor AMP at 2.7A and with product PR-ATP at 2.9A (the ribosyl-triphosphate could not be resolved). On the basis of binding of AMP and PR-ATP and comparison with type I PRTs, the PRPP and parts of the ATP-binding site are identified. These structures clearly identify the AMP as binding in the 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP)-binding site, with the adenosine ring occupying the ATP-binding site. Comparison with the recently solved Mycobacterium tuberculosis ATP-PRT structures indicates that histidine is solely responsible for the large conformational changes observed between the hexameric forms of the enzyme. The role of oligomerisation in inhibition and the structural basis for the synergistic inhibition by histidine and AMP are discussed.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Reaction mechanism of ATP-PRT. (a) Condensation of PRPP and ATP to form PR-ATP as catalysed by ATP-PRT in the presence of Mg2+. (b) Proposed reaction sequence of ATP-PRT adapted from Morton & Parsons.[23.] First, the free enzyme binds ATP to form the complex E·ATP. This form can be trapped by addition of PPi (E·ATP·PPi). The E·ATP complex binds PRPP and the condensation to PR-ATP occurs. PPi is released first before the product PR-ATP leaves and the free enzyme is regenerated.
Figure 6.
Figure 6. A ribbon representation of the ATP-PRT hexamer viewed down a crystallographic 2-fold axis. Individual chains are coloured uniquely and molecules of the inhibitor AMP are shown in ball-and-stick representation. The molecular surface is calculated using GRASP,[21.] and highlights the fact that the AMPs and therefore the active site is located on the inside of the hexamer, with only one significant opening to the exterior per monomer formed at the interface of domain 1 and the C-terminal domain. The Figure was composed using DINO (http://www.dino3d.org).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 336, 131-144) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19486323 J.D.Rees, R.A.Ingle, and J.A.Smith (2009).
Relative contributions of nine genes in the pathway of histidine biosynthesis to the control of free histidine concentrations in Arabidopsis thaliana.
  Plant Biotechnol J, 7, 499-511.  
18778048 Y.Cho, T.R.Ioerger, and J.C.Sacchettini (2008).
Discovery of novel nitrobenzothiazole inhibitors for Mycobacterium tuberculosis ATP phosphoribosyl transferase (HisG) through virtual screening.
  J Med Chem, 51, 5984-5992.  
17660285 R.Leipuviene, and G.R.Björk (2007).
Alterations in the two globular domains or in the connecting alpha-helix of bacterial ribosomal protein L9 induces +1 frameshifts.
  J Bacteriol, 189, 7024-7031.  
16987805 G.A.Grant (2006).
The ACT domain: a small molecule binding domain and its role as a common regulatory element.
  J Biol Chem, 281, 33825-33829.  
17154531 K.S.Champagne, E.Piscitelli, and C.S.Francklyn (2006).
Substrate recognition by the hetero-octameric ATP phosphoribosyltransferase from Lactococcus lactis.
  Biochemistry, 45, 14933-14943.  
16955235 R.Fani, M.Brilli, and P.Liò (2006).
Inference from proteobacterial operons shows piecewise organization: a reply to Price et al.
  J Mol Evol, 63, 577-580.  
16051603 K.S.Champagne, M.Sissler, Y.Larrabee, S.Doublié, and C.S.Francklyn (2005).
Activation of the hetero-octameric ATP phosphoribosyl transferase through subunit interface rearrangement by a tRNA synthetase paralog.
  J Biol Chem, 280, 34096-34104.
PDB codes: 1z7m 1z7n
15660995 M.C.Vega, P.Zou, F.J.Fernandez, G.E.Murphy, R.Sterner, A.Popov, and M.Wilmanns (2005).
Regulation of the hetero-octameric ATP phosphoribosyl transferase complex from Thermotoga maritima by a tRNA synthetase-like subunit.
  Mol Microbiol, 55, 675-686.
PDB code: 1usy
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.