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PDBsum entry 1b66

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protein ligands metals links
Tetrahydrobiopterin biosynthesis PDB id
1b66
Jmol
Contents
Protein chains
138 a.a. *
Ligands
BIO ×2
Metals
_ZN ×2
Waters ×259
* Residue conservation analysis
PDB id:
1b66
Name: Tetrahydrobiopterin biosynthesis
Title: 6-pyruvoyl tetrahydropterin synthase
Structure: 6-pyruvoyl tetrahydropterin synthase. Chain: a, b. Engineered: yes
Source: Rattus rattus. Black rat. Organism_taxid: 10117. Organ: liver. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Hexamer (from PQS)
Resolution:
1.90Å     R-factor:   0.227     R-free:   0.258
Authors: T.Ploom,B.Thoeny,J.Yim,S.Lee,H.Nar,W.Leimbacher,R.Huber,J.Ri G.Auerbach
Key ref:
T.Ploom et al. (1999). Crystallographic and kinetic investigations on the mechanism of 6-pyruvoyl tetrahydropterin synthase. J Mol Biol, 286, 851-860. PubMed id: 10024455 DOI: 10.1006/jmbi.1998.2511
Date:
20-Jan-99     Release date:   27-Apr-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P27213  (PTPS_RAT) -  6-pyruvoyl tetrahydrobiopterin synthase
Seq:
Struc:
144 a.a.
138 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.3.12  - 6-pyruvoyltetrahydropterin synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Biopterin Biosynthesis
      Reaction: 7,8-dihydroneopterin 3'-triphosphate = 6-pyruvoyl-5,6,7,8- tetrahydropterin + triphosphate
7,8-dihydroneopterin 3'-triphosphate
=
6-pyruvoyl-5,6,7,8- tetrahydropterin
Bound ligand (Het Group name = BIO)
corresponds exactly
+ triphosphate
      Cofactor: Magnesium
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cellular_component   3 terms 
  Biological process     tetrahydrobiopterin biosynthetic process   1 term 
  Biochemical function     lyase activity     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.1998.2511 J Mol Biol 286:851-860 (1999)
PubMed id: 10024455  
 
 
Crystallographic and kinetic investigations on the mechanism of 6-pyruvoyl tetrahydropterin synthase.
T.Ploom, B.Thöny, J.Yim, S.Lee, H.Nar, W.Leimbacher, J.Richardson, R.Huber, G.Auerbach.
 
  ABSTRACT  
 
The enzyme 6-pyruvoyl tetrahydropterin synthase (PTPS) catalyses the second step in the de novo biosynthesis of tetrahydrobiopterin, the conversion of dihydroneopterin triphosphate to 6-pyruvoyl tetrahydropterin. The Zn and Mg-dependent reaction includes a triphosphate elimination, a stereospecific reduction of the N5-C6 double bond and the oxidation of both side-chain hydroxyl groups. The crystal structure of the inactive mutant Cys42Ala of PTPS in complex with its natural substrate dihydroneopterinetriphosphate was determined at 1.9 A resolution. Additionally, the uncomplexed enzyme was refined to 2.0 A resolution. The active site of PTPS consists of the pterin-anchoring Glu A107 neighboured by two catalytic motifs: a Zn(II) binding site and an intersubunit catalytic triad formed by Cys A42, Asp B88 and His B89. In the free enzyme the Zn(II) is in tetravalent co-ordination with three histidine ligands and a water molecule. In the complex the water is replaced by the two substrate side-chain hydroxyl groups yielding a penta-co-ordinated Zn(II) ion. The Zn(II) ion plays a crucial role in catalysis. It activates the protons of the substrate, stabilizes the intermediates and disfavours the breaking of the C1'C2' bond in the pyruvoyl side-chain. Cys A42 is activated by His B89 and Asp B88 for proton abstraction from the two different substrate side-chain atoms C1', and C2'. Replacing Ala A42 in the mutant structure by the wild-type Cys by modelling shows that the C1' and C2' substrate side-chain protons are at equal distances to Cys A42 Sgamma. The basicity of Cys A42 may be increased by a catalytic triad His B89 and Asp B88. The active site of PTPS seems to be optimised to carry out proton abstractions from two different side-chain C1' and C2' atoms, with no obvious preference for one of them. Kinetic studies with dihydroneopterin monophosphate reveal that the triphosphate moiety of the substrate is necessary for enzyme specifity.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Complex of the inactive mutant Cys42Ala with the substrate. The 2F[o] − F[c] electron density of the pterin is contoured at lσ.
Figure 7.
Figure 7. Hypothetical reaction mechanism for PTPS catalysis. We suggest that the reaction starts with a substrate (S) protonated at N5, which increases the acidicity of C1′---H. The intermediate I1 is stereospecifically protonated yielding the 6-R pterin. In the intermediate 12 the C2′---H is significantly more acidic than in the substrate S. It will be abstracted by the Cys A42 S^γ leading to triphosphate elimination and keto-enol tautomerization yielding the product 6-R-pyruvoyl-5,6,7,8-tetrahydropterin.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 286, 851-860) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
18805734 J.E.Hyde, S.Dittrich, P.Wang, P.F.Sims, V.de Crécy-Lagard, and A.D.Hanson (2008).
Plasmodium falciparum: a paradigm for alternative folate biosynthesis in diverse microorganisms?
  Trends Parasitol, 24, 502-508.  
  18931427 J.E.Spoonamore, S.A.Roberts, A.Heroux, and V.Bandarian (2008).
Structure of a 6-pyruvoyltetrahydropterin synthase homolog from Streptomyces coelicolor.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 875-879.
PDB code: 3d7j
18093090 S.Dittrich, S.L.Mitchell, A.M.Blagborough, Q.Wang, P.Wang, P.F.Sims, and J.E.Hyde (2008).
An atypical orthologue of 6-pyruvoyltetrahydropterin synthase can provide the missing link in the folate biosynthesis pathway of malaria parasites.
  Mol Microbiol, 67, 609-618.  
  17183164 B.Bagautdinov, M.Sugahara, and N.Kunishima (2007).
Purification, crystallization and preliminary crystallographic analysis of archaeal 6-pyruvoyl tetrahydrobiopterin synthase homologue PH0634 from Pyrococcus horikoshii OT3.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 15-17.  
11087827 G.Auerbach, A.Herrmann, A.Bracher, G.Bader, M.Gutlich, M.Fischer, M.Neukamm, M.Garrido-Franco, J.Richardson, H.Nar, R.Huber, and A.Bacher (2000).
Zinc plays a key role in human and bacterial GTP cyclohydrolase I.
  Proc Natl Acad Sci U S A, 97, 13567-13572.
PDB codes: 1fb1 1fbx
10874306 N.Blau, T.Scherer-Oppliger, A.Baumer, M.Riegel, A.Matasovic, A.Schinzel, J.Jaeken, and B.Thöny (2000).
Isolated central form of tetrahydrobiopterin deficiency associated with hemizygosity on chromosome 11q and a mutant allele of PTPS.
  Hum Mutat, 16, 54-60.  
10765502 S.Laufs, S.H.Kim, S.Kim, N.Blau, and B.Thöny (2000).
Reconstitution of a metabolic pathway with triple-cistronic IRES-containing retroviral vectors for correction of tetrahydrobiopterin deficiency.
  J Gene Med, 2, 22-31.  
10531334 T.Scherer-Oppliger, W.Leimbacher, N.Blau, and B.Thöny (1999).
Serine 19 of human 6-pyruvoyltetrahydropterin synthase is phosphorylated by cGMP protein kinase II.
  J Biol Chem, 274, 31341-31348.  
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.