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PDBsum entry 1d8h
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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1d8h

 

 

 

 

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Contents
Protein chains
288 a.a. *
Ligands
SO4 ×3
Metals
_MN ×3
Waters ×669
* Residue conservation analysis
PDB id:
1d8h
Name: Hydrolase
Title: X-ray crystal structure of yeast RNA triphosphatase in complex with sulfate and manganese ions.
Structure: mRNA triphosphatase cet1. Chain: a, b, c. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Hexamer (from PDB file)
Resolution:
2.00Å     R-factor:   0.229     R-free:   0.310
Authors: C.D.Lima,L.K.Wang,S.Shuman
Key ref:
C.D.Lima et al. (1999). Structure and mechanism of yeast RNA triphosphatase: an essential component of the mRNA capping apparatus. Cell, 99, 533-543. PubMed id: 10589681 DOI: 10.1016/S0092-8674(00)81541-X
Date:
24-Oct-99     Release date:   29-Nov-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O13297  (CET1_YEAST) -  mRNA-capping enzyme subunit beta from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		549 a.a.
288 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.6.1.74  - mRNA 5'-phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: a 5'-end triphospho-ribonucleoside in mRNA + H2O = a 5'-end diphospho- ribonucleoside in mRNA + phosphate + H+
5'-end triphospho-ribonucleoside in mRNA
 + H2O
 = 5'-end diphospho- ribonucleoside in mRNA
 + phosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Key reference    
 
 
DOI no: 10.1016/S0092-8674(00)81541-X Cell 99:533-543 (1999)
PubMed id: 10589681  
 
 
Structure and mechanism of yeast RNA triphosphatase: an essential component of the mRNA capping apparatus.
C.D.Lima, L.K.Wang, S.Shuman.
 
  ABSTRACT  
 
RNA triphosphatase is an essential mRNA processing enzyme that catalyzes the first step in cap formation. The 2.05 A crystal structure of yeast RNA triphosphatase Cet1p reveals a novel active site fold whereby an eight-stranded beta barrel forms a topologically closed triphosphate tunnel. Interactions of a sulfate in the center of the tunnel with a divalent cation and basic amino acids projecting into the tunnel suggest a catalytic mechanism that is supported by mutational data. Discrete surface domains mediate Cet1p homodimerization and Cet1p binding to the guanylyltransferase component of the capping apparatus. The structure and mechanism of fungal RNA triphosphatases are completely different from those of mammalian mRNA capping enzymes. Hence, RNA triphosphatase presents an ideal target for structure-based antifungal drug discovery.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereo View of the RNA Triphosphatase MonomerA stereo image of the Cα trace of the Cet1(241–539)p monomer was prepared with the program SETOR ([7]). The view is looking into the tunnel entrance (as in Figure 4A). An enzyme-bound sulfate coordinated within the tunnel is shown as a stick model. Basic amino acid side chains that point into the tunnel are shown in blue. Acidic side chains that point into the tunnel are shown in red. 		Figure 6.
Figure 6. The Triphosphate Tunnel and the Metal-Binding Site(A) Stereo image of the refined 2Fo-Fc density of a cross section of the tunnel in the manganese-soaked crystal. Blue density is contoured at 1.25 σ. Red density contoured at 4 σ highlights the sulfate ion (located in the center of the tunnel) and the manganese ion, which is coordinated by acidic side chains projecting from the tunnel floor.(B) Stereo view of a cross section of the tunnel highlighting the network of side chain interactions that coordinate the sulfate and manganese ions. The manganese (blue sphere) interacts with octahedral geometry with the sulfate, Glu-305, Glu-307, Glu-496, and two waters (red spheres).The images were prepared using SETOR ([7]).
 
  The above figures are reprinted by permission from Cell Press: Cell (1999, 99, 533-543) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22138959 E.Decroly, F.Ferron, J.Lescar, and B.Canard (2012).
Conventional and unconventional mechanisms for capping viral mRNA.
  Nat Rev Microbiol, 10, 51-65.  
20664792 A.Simoes-Barbosa, R.P.Hirt, and P.J.Johnson (2010).
A metazoan/plant-like capping enzyme and cap modified nucleotides in the unicellular eukaryote Trichomonas vaginalis.
  PLoS Pathog, 6, e1000999.  
20159466 M.Gu, K.R.Rajashankar, and C.D.Lima (2010).
Structure of the Saccharomyces cerevisiae Cet1-Ceg1 mRNA capping apparatus.
  Structure, 18, 216-227.
PDB code: 3kyh
20007273 M.Lelke, L.Brunotte, C.Busch, and S.Günther (2010).
An N-terminal region of Lassa virus L protein plays a critical role in transcription but not replication of the virus genome.
  J Virol, 84, 1934-1944.  
20616014 P.A.Nair, P.Smith, and S.Shuman (2010).
Structure of bacterial LigD 3'-phosphoesterase unveils a DNA repair superfamily.
  Proc Natl Acad Sci U S A, 107, 12822-12827.
PDB codes: 3n9b 3n9d
19490098 L.Bettendorff, and P.Wins (2009).
Thiamin diphosphate in biological chemistry: new aspects of thiamin metabolism, especially triphosphate derivatives acting other than as cofactors.
  FEBS J, 276, 2917-2925.  
19390046 M.Hothorn, H.Neumann, E.D.Lenherr, M.Wehner, V.Rybin, P.O.Hassa, A.Uttenweiler, M.Reinhardt, A.Schmidt, J.Seiler, A.G.Ladurner, C.Herrmann, K.Scheffzek, and A.Mayer (2009).
Catalytic core of a membrane-associated eukaryotic polyphosphate polymerase.
  Science, 324, 513-516.
PDB codes: 3g3o 3g3q 3g3r 3g3t 3g3u
19372271 M.Issur, S.Despins, I.Bougie, and M.Bisaillon (2009).
Nucleotide analogs and molecular modeling studies reveal key interactions involved in substrate recognition by the yeast RNA triphosphatase.
  Nucleic Acids Res, 37, 3714-3722.  
18400173 D.Benarroch, P.Smith, and S.Shuman (2008).
Characterization of a trifunctional mimivirus mRNA capping enzyme and crystal structure of the RNA triphosphatase domain.
  Structure, 16, 501-512.
PDB codes: 2qy2 2qze
19047636 D.G.Conrady, C.C.Brescia, K.Horii, A.A.Weiss, D.J.Hassett, and A.B.Herr (2008).
A zinc-dependent adhesion module is responsible for intercellular adhesion in staphylococcal biofilms.
  Proc Natl Acad Sci U S A, 105, 19456-19461.  
18276586 J.Song, L.Bettendorff, M.Tonelli, and J.L.Markley (2008).
Structural basis for the catalytic mechanism of mammalian 25-kDa thiamine triphosphatase.
  J Biol Chem, 283, 10939-10948.
PDB code: 2jmu
18039706 M.F.Soulière, J.P.Perreault, and M.Bisaillon (2008).
Magnesium-binding studies reveal fundamental differences between closely related RNA triphosphatases.
  Nucleic Acids Res, 36, 451-461.  
18782773 R.Jain, and S.Shuman (2008).
Polyphosphatase Activity of CthTTM, a Bacterial Triphosphate Tunnel Metalloenzyme.
  J Biol Chem, 283, 31047-31057.  
18385232 Y.Li, and L.A.Guarino (2008).
Roles of LEF-4 and PTP/BVP RNA triphosphatases in processing of baculovirus late mRNAs.
  J Virol, 82, 5573-5583.  
17949828 J.P.Ruan, S.Shen, E.Ullu, and C.Tschudi (2007).
Evidence for a capping enzyme with specificity for the trypanosome spliced leader RNA.
  Mol Biochem Parasitol, 156, 246-254.  
17534848 M.K.Sung, and W.K.Huh (2007).
Bimolecular fluorescence complementation analysis system for in vivo detection of protein-protein interaction in Saccharomyces cerevisiae.
  Yeast, 24, 767-775.  
17303560 N.Keppetipola, R.Jain, and S.Shuman (2007).
Novel triphosphate phosphohydrolase activity of Clostridium thermocellum TTM, a member of the triphosphate tunnel metalloenzyme superfamily.
  J Biol Chem, 282, 11941-11949.  
16809816 C.Gong, P.Smith, and S.Shuman (2006).
Structure-function analysis of Plasmodium RNA triphosphatase and description of a triphosphate tunnel metalloenzyme superfamily that includes Cet1-like RNA triphosphatases and CYTH proteins.
  RNA, 12, 1468-1474.  
16352561 D.L.Sawicki, S.Perri, J.M.Polo, and S.G.Sawicki (2006).
Role for nsP2 proteins in the cessation of alphavirus minus-strand synthesis by host cells.
  J Virol, 80, 360-371.  
16709677 J.Li, J.T.Wang, and S.P.Whelan (2006).
A unique strategy for mRNA cap methylation used by vesicular stomatitis virus.
  Proc Natl Acad Sci U S A, 103, 8493-8498.  
16964259 L.Larivière, S.Geiger, S.Hoeppner, S.Röther, K.Strässer, and P.Cramer (2006).
Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20.
  Nat Struct Mol Biol, 13, 895-901.
PDB codes: 2hzm 2hzs
16934294 R.Vasquez-Del Carpio, F.D.Gonzalez-Nilo, G.Riadi, Z.F.Taraporewala, and J.T.Patton (2006).
Histidine triad-like motif of the rotavirus NSP2 octamer mediates both RTPase and NTPase activities.
  J Mol Biol, 362, 539-554.  
15556935 S.Hausmann, M.A.Altura, M.Witmer, S.M.Singer, H.G.Elmendorf, and S.Shuman (2005).
Yeast-like mRNA capping apparatus in Giardia lamblia.
  J Biol Chem, 280, 12077-12086.  
12595553 A.Martins, and S.Shuman (2003).
Mapping the triphosphatase active site of baculovirus mRNA capping enzyme LEF4 and evidence for a two-metal mechanism.
  Nucleic Acids Res, 31, 1455-1463.  
12820968 C.Fabrega, V.Shen, S.Shuman, and C.D.Lima (2003).
Structure of an mRNA capping enzyme bound to the phosphorylated carboxy-terminal domain of RNA polymerase II.
  Mol Cell, 11, 1549-1561.
PDB code: 1p16
14525979 C.Gong, A.Martins, and S.Shuman (2003).
Structure-function analysis of Trypanosoma brucei RNA triphosphatase and evidence for a two-metal mechanism.
  J Biol Chem, 278, 50843-50852.  
12819229 M.Bisaillon, and I.Bougie (2003).
Investigating the role of metal ions in the catalytic mechanism of the yeast RNA triphosphatase.
  J Biol Chem, 278, 33963-33971.  
12788946 S.Hausmann, Y.Pei, and S.Shuman (2003).
Homodimeric quaternary structure is required for the in vivo function and thermal stability of Saccharomyces cerevisiae and Schizosaccharomyces pombe RNA triphosphatases.
  J Biol Chem, 278, 30487-30496.  
12576476 T.Takagi, A.K.Walker, C.Sawa, F.Diehn, Y.Takase, T.K.Blackwell, and S.Buratowski (2003).
The Caenorhabditis elegans mRNA 5'-capping enzyme. In vitro and in vivo characterization.
  J Biol Chem, 278, 14174-14184.  
12637515 Y.Mukai, J.K.Davie, and S.Y.Dent (2003).
Physical and functional interaction of the yeast corepressor Tup1 with mRNA 5'-triphosphatase.
  J Biol Chem, 278, 18895-18901.  
12475973 Y.Pei, B.Schwer, and S.Shuman (2003).
Interactions between fission yeast Cdk9, its cyclin partner Pch1, and mRNA capping enzyme Pct1 suggest an elongation checkpoint for mRNA quality control.
  J Biol Chem, 278, 7180-7188.  
11844801 C.Gong, and S.Shuman (2002).
Chlorella virus RNA triphosphatase. Mutational analysis and mechanism of inhibition by tripolyphosphate.
  J Biol Chem, 277, 15317-15324.  
12032088 M.P.Egloff, D.Benarroch, B.Selisko, J.L.Romette, and B.Canard (2002).
An RNA cap (nucleoside-2'-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization.
  EMBO J, 21, 2757-2768.
PDB codes: 1l9k 2p1d
12154373 S.Shuman (2002).
What messenger RNA capping tells us about eukaryotic evolution.
  Nat Rev Mol Cell Biol, 3, 619-625.  
11917006 V.Anantharaman, E.V.Koonin, and L.Aravind (2002).
Comparative genomics and evolution of proteins involved in RNA metabolism.
  Nucleic Acids Res, 30, 1427-1464.  
11893740 Y.Pei, and S.Shuman (2002).
Interactions between fission yeast mRNA capping enzymes and elongation factor Spt5.
  J Biol Chem, 277, 19639-19648.  
11350947 A.Changela, C.K.Ho, A.Martins, S.Shuman, and A.Mondragón (2001).
Structure and mechanism of the RNA triphosphatase component of mammalian mRNA capping enzyme.
  EMBO J, 20, 2575-2586.
PDB codes: 1i9s 1i9t
11553638 A.Martins, and S.Shuman (2001).
Mutational analysis of baculovirus capping enzyme Lef4 delineates an autonomous triphosphatase domain and structural determinants of divalent cation specificity.
  J Biol Chem, 276, 45522-45529.  
11160672 C.K.Ho, C.Gong, and S.Shuman (2001).
RNA triphosphatase component of the mRNA capping apparatus of Paramecium bursaria Chlorella virus 1.
  J Virol, 75, 1744-1750.  
11553645 C.K.Ho, and S.Shuman (2001).
Trypanosoma brucei RNA triphosphatase. Antiprotozoal drug target and guide to eukaryotic phylogeny.
  J Biol Chem, 276, 46182-46186.  
11248030 C.K.Ho, and S.Shuman (2001).
A yeast-like mRNA capping apparatus in Plasmodium falciparum.
  Proc Natl Acad Sci U S A, 98, 3050-3055.  
11472630 J.M.Bujnicki, M.Feder, M.Radlinska, and L.Rychlewski (2001).
mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships.
  BMC Bioinformatics, 2, 2.
PDB code: 1ic3
12762032 S.Shuman (2001).
The mRNA capping apparatus as drug target and guide to eukaryotic phylogeny.
  Cold Spring Harb Symp Quant Biol, 66, 301-312.  
11737862 Y.Pei, B.Schwer, J.Saiz, R.P.Fisher, and S.Shuman (2001).
RNA triphosphatase is essential in Schizosaccharomyces pombe and Candida albicans.
  BMC Microbiol, 1, 29.  
11139608 Y.Pei, B.Schwer, S.Hausmann, and S.Shuman (2001).
Characterization of Schizosaccharomyces pombe RNA triphosphatase.
  Nucleic Acids Res, 29, 387-396.  
10823853 C.K.Ho, A.Martins, and S.Shuman (2000).
A yeast-based genetic system for functional analysis of viral mRNA capping enzymes.
  J Virol, 74, 5486-5494.  
  10756187 Y.Pei, K.Lehman, L.Tian, and S.Shuman (2000).
Characterization of Candida albicans RNA triphosphatase and mutational analysis of its active site.
  Nucleic Acids Res, 28, 1885-1892.  
11094081 Y.Takase, T.Takagi, P.B.Komarnitsky, and S.Buratowski (2000).
The essential interaction between yeast mRNA capping enzyme subunits is not required for triphosphatase function in vivo.
  Mol Cell Biol, 20, 9307-9316.  
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.

 

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