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PDBsum entry 1a98

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protein Protein-protein interface(s) links
Phosphoribosyltransferase PDB id
1a98
Jmol
Contents
Protein chains
129 a.a. *
Waters ×66
* Residue conservation analysis
PDB id:
1a98
Name: Phosphoribosyltransferase
Title: Xprtase from e. Coli complexed with gmp
Structure: Xanthine-guanine phosphoribosyltransferase. Chain: a, b. Synonym: xprt. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: hb101. Atcc: atcc 37145. Collection: atcc 37145. Cellular_location: cytoplasm. Gene: gpt. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Homo-Tetramer (from PDB file)
Resolution:
2.25Å     R-factor:   0.210     R-free:   0.224
Authors: S.Vos,R.J.Parry,M.R.Burns,J.De Jersey,J.L.Martin
Key ref:
S.Vos et al. (1998). Structures of free and complexed forms of Escherichia coli xanthine-guanine phosphoribosyltransferase. J Mol Biol, 282, 875-889. PubMed id: 9743633 DOI: 10.1006/jmbi.1998.2051
Date:
16-Apr-98     Release date:   17-Jun-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A9M5  (XGPT_ECOLI) -  Xanthine phosphoribosyltransferase
Seq:
Struc:
152 a.a.
129 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.22  - Xanthine phosphoribosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: XMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + xanthine
XMP
+ diphosphate
= 5-phospho-alpha-D-ribose 1-diphosphate
+ xanthine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     nucleoside metabolic process   5 terms 
  Biochemical function     transferase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1998.2051 J Mol Biol 282:875-889 (1998)
PubMed id: 9743633  
 
 
Structures of free and complexed forms of Escherichia coli xanthine-guanine phosphoribosyltransferase.
S.Vos, R.J.Parry, M.R.Burns, J.de Jersey, J.L.Martin.
 
  ABSTRACT  
 
Structures of free, substrate-bound and product-bound forms of Escherichia coli xanthine-guanine phosphoribosyltransferase (XGPRT) have been determined by X-ray crystallography. These are compared with the previously determined structure of magnesium and sulphate-bound XPRT. The structure of free XGPRT at 2.25 A resolution confirms the flexibility of residues in and around a mobile loop identified in other PRTases and shows that the cis-peptide conformation of Arg37 at the active site is maintained in the absence of bound ligands. The structures of XGPRT complexed with the purine base substrates guanine or xanthine in combination with cPRib-PP, an analog of the second substrate PRib-PP, have been solved to 2.0 A resolution. In these two structures the disordered phosphate-binding loop of uncomplexed XGPRT becomes ordered through interactions with the 5'-phosphate group of cPRib-PP. The cyclopentane ring of cPRib-PP has the C3 exo pucker conformation, stabilised by the cPRib-PP-bound Mg2+. The purine base specificity of XGPRT appears to be due to water-mediated interactions between the 2-exocyclic groups of guanine or xanthine and side-chains of Glu136 and Asp140, as well as the main-chain oxygen atom of Ile135. Asp92, together with Lys115, could help stabilise the N7-protonated tautomer of the incoming base and could act as a general base to remove the proton from N7 when the nucleotide product is formed. The 2.6 A resolution structure of XGPRT complexed with product GMP is similar to the substrate-bound complexes. However, the ribose ring of GMP is rotated by approximately 24 degrees compared with the equivalent ring in cPRib-PP. This rotation results in the loss of all interactions between the ribosyl group and the enzyme in the product complex.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Packing of XGPRT molecules in the tetragonal crystal form. The mobile loop of subunit C (green) in tetramer 1 interacts with the active site of subunit A (yellow) in tetramer 2. The mobile loop of subunit A in tetramer 2 is only partially modelled (residues 64 to 66 are not included) but it may prevent the C-terminal tail of subunit B (blue) of tetramer 1 interacting with the active site of subunit C in tetramer 1. The guanine and cPRib-PP molecules bound in the active site of subunit C in tetramer 1 are shown in purple as stick models and the magnesium and two water molecules associated with cPRib-PP are shown as purple spheres. Asp88 and Asp89 in the active site of subunit A in tetramer 2 are shown in pink. This Figure was generated using InsightII.
Figure 3.
Figure 3. Stereo diagram of the active site of XGPRT showing the interactions formed with substrate and product. A, The XGPRT active site in the absence of ligands. B, Binding of Mg:cPRib-PP and guanine to XGPRT. C, Binding of GMP (and borate) to XGPRT. Water molecules are shown as red spheres, magnesium as a pink sphere, and hydrogen bond interactions are indicated by broken lines. For clarity, the interactions of cPRib-PP with water molecules are not shown. The side-chain of Trp134, which is relatively disordered in XGPRT[free] and XGPRT[MgSO4], is stabilised in XGPRT[prpgua], XGPRT[prpxan] and XGPRT[GMP] through interaction with the purine ring. Guanine has an exocyclic amino group in the 2 position of the purine ring that interacts with Glu136 and Asp140 via a water molecule. Binding of cPRib-PP in the active site results in a conformational change in the phosphate-binding loop, thereby bringing Asp92 within hydrogen bonding distance of the N7 atom of guanine. This figure was generated using MOLSCRIPT [Kraulis 1991] and Raster3D [Bacon and Anderson 1988 and Merritt and Murphy 1994].
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 282, 875-889) copyright 1998.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16882332 M.Duckworth, A.Ménard, F.Megraud, and G.L.Mendz (2006).
Bioinformatic analysis of Helicobacter pylori XGPRTase: a potential therapeutic target.
  Helicobacter, 11, 287-295.  
12171924 A.E.Sarver, and C.C.Wang (2002).
The adenine phosphoribosyltransferase from Giardia lamblia has a unique reaction mechanism and unusual substrate binding properties.
  J Biol Chem, 277, 39973-39980.  
12037295 A.Kadziola, J.Neuhard, and S.Larsen (2002).
Structure of product-bound Bacillus caldolyticus uracil phosphoribosyltransferase confirms ordered sequential substrate binding.
  Acta Crystallogr D Biol Crystallogr, 58, 936-945.
PDB code: 1i5e
12180982 G.Stoychev, B.Kierdaszuk, and D.Shugar (2002).
Xanthosine and xanthine. Substrate properties with purine nucleoside phosphorylases, and relevance to other enzyme systems.
  Eur J Biochem, 269, 4048-4057.  
12004061 L.J.Wallace, D.Candlish, and H.P.De Koning (2002).
Different substrate recognition motifs of human and trypanosome nucleobase transporters. Selective uptake of purine antimetabolites.
  J Biol Chem, 277, 26149-26156.  
12070315 L.W.Guddat, S.Vos, J.L.Martin, D.T.Keough, and J.de Jersey (2002).
Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase.
  Protein Sci, 11, 1626-1638.
PDB codes: 1g9s 1g9t 1grv
11502531 A.M.Aronov, N.R.Munagala, I.D.Kuntz, and C.C.Wang (2001).
Virtual screening of combinatorial libraries across a gene family: in search of inhibitors of Giardia lamblia guanine phosphoribosyltransferase.
  Antimicrob Agents Chemother, 45, 2571-2576.  
11258886 B.Canyuk, P.J.Focia, and A.E.Eakin (2001).
The role for an invariant aspartic acid in hypoxanthine phosphoribosyltransferases is examined using saturation mutagenesis, functional analysis, and X-ray crystallography.
  Biochemistry, 40, 2754-2765.
PDB codes: 1i0i 1i0l 1i13 1i14
10841757 W.Shi, N.R.Munagala, C.C.Wang, C.M.Li, P.C.Tyler, R.H.Furneaux, C.Grubmeyer, V.L.Schramm, and S.C.Almo (2000).
Crystal structures of Giardia lamblia guanine phosphoribosyltransferase at 1.75 A(,).
  Biochemistry, 39, 6781-6790.
PDB codes: 1dqn 1dqp
10545170 A.Héroux, E.L.White, L.J.Ross, and D.W.Borhani (1999).
Crystal structures of the Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase-GMP and -IMP complexes: comparison of purine binding interactions with the XMP complex.
  Biochemistry, 38, 14485-14494.
PDB codes: 1qk3 1qk4
10506138 A.T.Deyrup, B.Singh, S.Krishnan, S.Lyle, and N.B.Schwartz (1999).
Chemical modification and site-directed mutagenesis of conserved HXXH and PP-loop motif arginines and histidines in the murine bifunctional ATP sulfurylase/adenosine 5'-phosphosulfate kinase.
  J Biol Chem, 274, 28929-28936.  
  10338013 G.K.Balendiran, J.A.Molina, Y.Xu, J.Torres-Martinez, R.Stevens, P.J.Focia, A.E.Eakin, J.C.Sacchettini, and S.P.Craig (1999).
Ternary complex structure of human HGPRTase, PRPP, Mg2+, and the inhibitor HPP reveals the involvement of the flexible loop in substrate binding.
  Protein Sci, 8, 1023-1031.
PDB code: 1d6n
9860824 P.J.Focia, S.P.Craig, and A.E.Eakin (1998).
Approaching the transition state in the crystal structure of a phosphoribosyltransferase.
  Biochemistry, 37, 17120-17127.
PDB code: 1tc2
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 code is shown on the right.