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PDBsum entry 1l1r

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protein ligands metals links
Transferase PDB id
1l1r
Jmol PyMol
Contents
Protein chain
179 a.a. *
Ligands
9DA
PRP
Metals
_MG
Waters ×79
* Residue conservation analysis
PDB id:
1l1r
Name: Transferase
Title: Crystal structure of aprtase from giardia lamblia complexed deazaadenine, mg2+ and prpp
Structure: Adenine phosphoribosyltransferase. Chain: a. Engineered: yes
Source: Giardia intestinalis. Organism_taxid: 5741. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
1.95Å     R-factor:   0.218     R-free:   0.262
Authors: W.Shi,A.E.Sarver,C.C.Wang,K.S.Tanaka,S.C.Almo,V.L.Schramm
Key ref:
W.Shi et al. (2002). Closed site complexes of adenine phosphoribosyltransferase from Giardia lamblia reveal a mechanism of ribosyl migration. J Biol Chem, 277, 39981-39988. PubMed id: 12171925 DOI: 10.1074/jbc.M205596200
Date:
19-Feb-02     Release date:   27-Nov-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q967M2  (Q967M2_GIAIN) -  Adenine phosphoribosyltransferase
Seq:
Struc:
180 a.a.
179 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.7  - Adenine phosphoribosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Ribose activation
      Reaction: AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate
AMP
+ diphosphate
=
adenine
Bound ligand (Het Group name = 9DA)
matches with 81.82% similarity
+
5-phospho-alpha-D-ribose 1-diphosphate
Bound ligand (Het Group name = PRP)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleoside metabolic process   1 term 
  Biochemical function     transferase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M205596200 J Biol Chem 277:39981-39988 (2002)
PubMed id: 12171925  
 
 
Closed site complexes of adenine phosphoribosyltransferase from Giardia lamblia reveal a mechanism of ribosyl migration.
W.Shi, A.E.Sarver, C.C.Wang, K.S.Tanaka, S.C.Almo, V.L.Schramm.
 
  ABSTRACT  
 
The adenine phosphoribosyltransferase (APRTase) from Giardia lamblia was co-crystallized with 9-deazaadenine and sulfate or with 9-deazaadenine and Mg-phosphoribosylpyrophosphate. The complexes were solved and refined to 1.85 and 1.95 A resolution. Giardia APRTase is a symmetric homodimer with the monomers built around Rossman fold cores, an element common to all known purine phosphoribosyltransferases. The catalytic sites are capped with a small hood domain that is unique to the APRTases. These structures reveal several features relevant to the catalytic function of APRTase: 1) a non-proline cis peptide bond (Glu(61)-Ser(62)) is required to form the pyrophosphate binding site in the APRTase.9dA.MgPRPP complex but is a trans peptide bond in the absence of pyrophosphate group, as observed in the APRTase.9dA.SO4 complex; 2) a catalytic site loop is closed and fully ordered in both complexes, with Glu(100) from the catalytic loop acting as the acid/base for protonation/deprotonation of N-7 of the adenine ring; 3) the pyrophosphoryl charge is neutralized by a single Mg2+ ion and Arg(63), in contrast to the hypoxanthine-guanine phosphoribosyltransferases, which use two Mg2+ ions; and 4) the nearest structural neighbors to APRTases are the orotate phosphoribosyltransferases, suggesting different paths of evolution for adenine relative to other purine PRTases. An overlap comparison of AMP and 9-deazaadenine plus Mg-PRPP at the catalytic sites of APRTases indicated that reaction coordinate motion involves a 2.1-A excursion of the ribosyl anomeric carbon, whereas the adenine ring and the 5-phosphoryl group remained fixed. G. lamblia APRTase therefore provides another example of nucleophilic displacement by electrophile migration.
 
  Selected figure(s)  
 
Figure 5.
Fig. 5. Peptide conformation of Glu61-Ser62. a, stereoview of trans conformation of Glu61-Ser62 in the Giardia APRTase·9dA·SO[4] complex. The peptide segment connecting Glu61 and Ser62 is stabilized in the trans conformation by a sulfate ion. b, stereoview of the cis conformation of the same peptide in APRTase·9dA·MgPRPP complex. The unusual cis conformation in the peptide link between Glu61 and Ser62 orients the amide nitrogen atoms of Ser62 and Arg63 to bind PRPP.
Figure 7.
Fig. 7. Hydrogen bond network in Giardia APRTase·9dA·MgPRPP complex. Distances (<3.2 Å) are in angstroms.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 39981-39988) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21190580 A.R.Zomorrodi, and C.D.Maranas (2010).
Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data.
  BMC Syst Biol, 4, 178.  
19819904 R.Takahashi, S.Nakamura, T.Nakazawa, K.Minoura, T.Yoshida, Y.Nishi, Y.Kobayashi, and T.Ohkubo (2010).
Structure and reaction mechanism of human nicotinamide phosphoribosyltransferase.
  J Biochem, 147, 95.
PDB codes: 2e5b 2e5c 2e5d
19666527 E.S.Burgos, M.C.Ho, S.C.Almo, and V.L.Schramm (2009).
A phosphoenzyme mimic, overlapping catalytic sites and reaction coordinate motion for human NAMPT.
  Proc Natl Acad Sci U S A, 106, 13748-13753.
PDB codes: 3dgr 3dhd 3dhf 3dkj 3dkl
16152602 P.H.Rehse, and T.H.Tahirov (2005).
Crystal structure of a purine/pyrimidine phosphoribosyltransferase-related protein from Thermus thermophilus HB8.
  Proteins, 61, 658-665.
PDB codes: 1vch 2cvb
12951162 M.H.el Kouni (2003).
Potential chemotherapeutic targets in the purine metabolism of parasites.
  Pharmacol Ther, 99, 283-309.  
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.

 

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