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PDBsum entry 1je1

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1je1
Jmol
Contents
Protein chains
(+ 0 more) 232 a.a. *
Ligands
SO4 ×6
GMP ×6
Waters ×417
* Residue conservation analysis
PDB id:
1je1
Name: Transferase
Title: 5'-deoxy-5'-methylthioadenosine phosphorylase complex with guanosine and sulfate
Structure: 5'-methylthioadenosine phosphorylase. Chain: a, b, c, d, e, f. Synonym: mta phosphorylase. Mtap. Engineered: yes
Source: Sulfolobus solfataricus. Organism_taxid: 2287. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Hexamer (from PQS)
Resolution:
1.80Å     R-factor:   0.217     R-free:   0.237
Authors: T.C.Appleby,I.I.Mathews,M.Porcelli,G.Cacciapuoti,S.E.Ealick
Key ref:
T.C.Appleby et al. (2001). Three-dimensional structure of a hyperthermophilic 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus. J Biol Chem, 276, 39232-39242. PubMed id: 11489901 DOI: 10.1074/jbc.M105694200
Date:
15-Jun-01     Release date:   26-Oct-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P50389  (PNPH_SULSO) -  Purine nucleoside phosphorylase
Seq:
Struc:
236 a.a.
232 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.1  - Purine-nucleoside phosphorylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate
2. Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Purine nucleoside
Bound ligand (Het Group name = GMP)
matches with 81.00% similarity
+ phosphate
= purine
+ alpha-D-ribose 1-phosphate
Purine deoxynucleoside
+ phosphate
= purine
+ 2'-deoxy-alpha-D-ribose 1-phosphate
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     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M105694200 J Biol Chem 276:39232-39242 (2001)
PubMed id: 11489901  
 
 
Three-dimensional structure of a hyperthermophilic 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus.
T.C.Appleby, I.I.Mathews, M.Porcelli, G.Cacciapuoti, S.E.Ealick.
 
  ABSTRACT  
 
The structure of 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus (SsMTAP) has been determined alone, as ternary complexes with sulfate plus substrates 5'-deoxy-5'-methylthioadenosine, adenosine, or guanosine, or with the noncleavable substrate analog Formycin B and as binary complexes with phosphate or sulfate alone. The structure of unliganded SsMTAP was refined at 2.5-A resolution and the structures of the complexes were refined at resolutions ranging from 1.6 to 2.0 A. SsMTAP is unusual both for its broad substrate specificity and for its extreme thermal stability. The hexameric structure of SsMTAP is similar to that of purine-nucleoside phosphorylase (PNP) from Escherichia coli, however, only SsMTAP accepts 5'-deoxy-5'-methylthioadenosine as a substrate. The active site of SsMTAP is similar to that of E. coli PNP with 13 of 18 nearest residues being identical. The main differences are at Thr(89), which corresponds to serine in E. coli PNP, and Glu(163), which corresponds to proline in E. coli PNP. In addition, a water molecule is found near the purine N-7 position in the guanosine complex of SsMTAP. Thr(89) is near the 5'-position of the nucleoside and may account for the ability of SsMTAP to accept either hydrophobic or hydrophilic substituents in that position. Unlike E. coli PNP, the structures of SsMTAP reveal a substrate-induced conformational change involving Glu(163). This residue is located at the interface between subunits and swings in toward the active site upon nucleoside binding. The high-resolution structures of SsMTAP suggest that the transition state is stabilized in different ways for 6-amino versus 6-oxo substrates. SsMTAP has optimal activity at 120 degrees C and retains full activity after 2 h at 100 degrees C. Examination of the three-dimensional structure of SsMTAP suggests that unlike most thermophilic enzymes, disulfide linkages play a key in role in its thermal stability.
 
  Selected figure(s)  
 
Figure 5.
Fig. 5. Active site drawing of the phosphate-binding site. a, interaction observed when sulfate occupies the site. b, interactions observed when phosphate occupies the binding site. The molecule of Tris is observed only with phosphate. Hydrogen bonds are shown as dashed lines with the corresponding donor-acceptor distance labeled. Residues belongs to the neighboring subunit are designated with an asterisk (*).
Figure 8.
Fig. 8. Active site drawing of the SsMTAP FMB-sulfate complex. a, the binding geometry for FMB. b, the binding geometry for the E. coli PNP-FMB complex for comparison. The coordinates were taken from PDB entry code 1A69 (14). Hydrogen bonds are shown as dashed lines with the corresponding donor-acceptor distance labeled. Residues belongs to the neighboring subunit are designated with an asterisk (*).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 39232-39242) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21166890 N.Parveen, and K.A.Cornell (2011).
Methylthioadenosine/S-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism.
  Mol Microbiol, 79, 7.  
20124695 Y.N.Kang, Y.Zhang, P.W.Allan, W.B.Parker, J.W.Ting, C.Y.Chang, and S.E.Ealick (2010).
Structure of grouper iridovirus purine nucleoside phosphorylase.
  Acta Crystallogr D Biol Crystallogr, 66, 155-162.
PDB code: 3khs
19740110 G.Cacciapuoti, I.Peluso, F.Fuccio, and M.Porcelli (2009).
Purine nucleoside phosphorylases from hyperthermophilic Archaea require a CXC motif for stability and folding.
  FEBS J, 276, 5799-5805.  
18342331 K.K.Siu, J.E.Lee, J.R.Sufrin, B.A.Moffatt, M.McMillan, K.A.Cornell, C.Isom, and P.L.Howell (2008).
Molecular determinants of substrate specificity in plant 5'-methylthioadenosine nucleosidases.
  J Mol Biol, 378, 112-128.
PDB codes: 2qsu 2qtg 2qtt
17334902 M.A.Grillo, and S.Colombatto (2008).
S-adenosylmethionine and its products.
  Amino Acids, 34, 187-193.  
18355316 M.Porcelli, L.Concilio, I.Peluso, A.Marabotti, A.Facchiano, and G.Cacciapuoti (2008).
Pyrimidine-specific ribonucleoside hydrolase from the archaeon Sulfolobus solfataricus--biochemical characterization and homology modeling.
  FEBS J, 275, 1900-1914.  
18299797 X.Li, X.Jiang, H.Li, and D.Ren (2008).
Purine nucleoside phosphorylase from Pseudoalteromonas sp. Bsi590: molecular cloning, gene expression and characterization of the recombinant protein.
  Extremophiles, 12, 325-333.  
17983264 C.H.Yeang, and D.Haussler (2007).
Detecting coevolution in and among protein domains.
  PLoS Comput Biol, 3, e211.  
16131758 C.Schnick, M.A.Robien, A.M.Brzozowski, E.J.Dodson, G.N.Murshudov, L.Anderson, J.R.Luft, C.Mehlin, W.G.Hol, J.A.Brannigan, and A.J.Wilkinson (2005).
Structures of Plasmodium falciparum purine nucleoside phosphorylase complexed with sulfate and its natural substrate inosine.
  Acta Crystallogr D Biol Crystallogr, 61, 1245-1254.
PDB codes: 1sq6 2bsx
15819883 G.Cacciapuoti, S.Forte, M.A.Moretti, A.Brio, V.Zappia, and M.Porcelli (2005).
A novel hyperthermostable 5'-deoxy-5'-methylthioadenosine phosphorylase from the archaeon Sulfolobus solfataricus.
  FEBS J, 272, 1886-1899.  
16148304 J.Eichler, and M.W.Adams (2005).
Posttranslational protein modification in Archaea.
  Microbiol Mol Biol Rev, 69, 393-425.  
16356270 K.Usui, S.Katayama, M.Kanamori-Katayama, C.Ogawa, C.Kai, M.Okada, J.Kawai, T.Arakawa, P.Carninci, M.Itoh, K.Takio, M.Miyano, S.Kidoaki, T.Matsuda, Y.Hayashizaki, and H.Suzuki (2005).
Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
  Genome Biol, 6, R98.  
16111437 M.Beeby, B.D.O'Connor, C.Ryttersgaard, D.R.Boutz, L.J.Perry, and T.O.Yeates (2005).
The genomics of disulfide bonding and protein stabilization in thermophiles.
  PLoS Biol, 3, e309.
PDB code: 1rki
15784569 P.B.Bertin, S.P.Lozzi, J.K.Howell, G.Restrepo-Cadavid, D.Neves, A.R.Teixeira, M.V.de Sousa, S.J.Norris, and J.M.Santana (2005).
The thermophilic, homohexameric aminopeptidase of Borrelia burgdorferi is a member of the M29 family of metallopeptidases.
  Infect Immun, 73, 2253-2261.  
15983408 W.Bu, E.C.Settembre, M.H.el Kouni, and S.E.Ealick (2005).
Structural basis for inhibition of Escherichia coli uridine phosphorylase by 5-substituted acyclouridines.
  Acta Crystallogr D Biol Crystallogr, 61, 863-872.
PDB codes: 1u1c 1u1d 1u1e 1u1f 1u1g
15606771 G.Cacciapuoti, M.A.Moretti, S.Forte, A.Brio, L.Camardella, V.Zappia, and M.Porcelli (2004).
Methylthioadenosine phosphorylase from the archaeon Pyrococcus furiosus. Mechanism of the reaction and assignment of disulfide bonds.
  Eur J Biochem, 271, 4834-4844.  
14739239 M.Roovers, J.Wouters, J.M.Bujnicki, C.Tricot, V.Stalon, H.Grosjean, and L.Droogmans (2004).
A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase.
  Nucleic Acids Res, 32, 465-476.  
15296732 Y.Zhang, S.E.Cottet, and S.E.Ealick (2004).
Structure of Escherichia coli AMP nucleosidase reveals similarity to nucleoside phosphorylases.
  Structure, 12, 1383-1394.
PDB codes: 1t8r 1t8s 1t8w 1t8y
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.