spacer
spacer

PDBsum entry 1p16

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Transferase PDB id
1p16
Jmol
Contents
Protein chains
390 a.a. *
17 a.a. *
Ligands
THR-SEP-PRO-SER-
TYR-SER-PRO-THR-
SEP
PO4 ×3
__G
GTP
Waters ×433
* Residue conservation analysis
PDB id:
1p16
Name: Transferase
Title: Structure of an mRNA capping enzyme bound to the phosphorylated carboxyl-terminal domain of RNA polymerase ii
Structure: mRNA capping enzyme alpha subunit. Chain: a, b. Fragment: residues 1-395 od sws p78587. Synonym: mRNA guanylyltransferase. Gtp--RNA guanylyltransferase. Gtase. Engineered: yes. Mutation: yes. Phosphorylated peptide from c-terminal of RNA polymerase ii.
Source: Candida albicans. Organism_taxid: 5476. Gene: cgt1. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: b834 (de3). Other_details: modified pet15b (n-terminal sumo fusion). Synthetic: yes. Other_details: naturally occuring repetitive ysptsps
Biol. unit: Dimer (from PQS)
Resolution:
2.70Å     R-factor:   0.200     R-free:   0.266
Authors: C.Fabrega,V.Shen,S.Shuman,C.D.Lima
Key ref:
C.Fabrega et al. (2003). Structure of an mRNA capping enzyme bound to the phosphorylated carboxy-terminal domain of RNA polymerase II. Mol Cell, 11, 1549-1561. PubMed id: 12820968 DOI: 10.1016/S1097-2765(03)00187-4
Date:
11-Apr-03     Release date:   15-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P78587  (MCE1_CANAX) -  mRNA-capping enzyme subunit alpha
Seq:
Struc:
449 a.a.
390 a.a.*
Protein chain
No UniProt id for this chain
Struc: 17 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.2.7.7.50  - mRNA guanylyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: GTP + (5')pp-Pur-mRNA = diphosphate + G(5')ppp-Pur-mRNA
GTP
Bound ligand (Het Group name = GTP)
corresponds exactly
+ (5')pp-Pur-mRNA
=
diphosphate
Bound ligand (Het Group name = PO4)
matches with 55.00% similarity
+ G(5')ppp-Pur-mRNA
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mRNA cap methyltransferase complex   1 term 
  Biological process     mRNA processing   2 terms 
  Biochemical function     mRNA guanylyltransferase activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1016/S1097-2765(03)00187-4 Mol Cell 11:1549-1561 (2003)
PubMed id: 12820968  
 
 
Structure of an mRNA capping enzyme bound to the phosphorylated carboxy-terminal domain of RNA polymerase II.
C.Fabrega, V.Shen, S.Shuman, C.D.Lima.
 
  ABSTRACT  
 
The 2.7 A structure of Candida albicans RNA guanylyltransferase Cgt1 cocrystallized with a carboxy-terminal domain (CTD) peptide composed of four Ser5-PO4 YSPTSPS heptad repeats illuminates distinct CTD-docking sites localized to the Cgt1 N-terminal nucleotidyl transferase domain. Tyr1, Pro3, Pro6, and Ser5-PO4 side chains from each of two YSPTSPS repeats contribute to the interface. Comparison to the Pin1-CTD structure shows that the CTD can assume markedly different conformations that are templated by particular binding partners. Structural plasticity combined with remodeling of CTD primary structure by kinases and phosphatases provides a versatile mechanism by which the CTD can recruit structurally dissimilar proteins during transcription. A binding site for the RNA triphosphatase component of the capping apparatus was also uncovered within the Cgt1 OB domain.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structures of the Guanylyltransferase/CTD-PO[4] Complexes(A) Ribbon diagram of Cgt1 monomer A as an enzyme-guanylate (K67-GMP) in complex with phosphate (P) and 9 residues of phosphorylated CTD.(B) Monomer B shown in complex with GTP and 17 residues of phosphorylated CTD. Cgt1 monomers A and B are colored blue to red from N- to C termini. The CTD is shown by solid bond representation and carbons colored yellow. The N- and C termini of Cgt1 and CTD peptides are indicated. Images generated with SETOR unless noted otherwise (Evans, 1993).
Figure 3.
Figure 3. CTD Docking Sites(A) CDS1 is shown on the left, CDS2 on the right, and CDS3 in the middle. “N” and “C” denote CTD N- and C termini. CTD carbons colored yellow with the Cgt1 backbone colored blue below the CTD residues (from monomer B), and gray above the CTD residues (from monomer A). Hydrogen bonding interactions are depicted by dashed lines and waters shown as red spheres.(B) Serial dilutions of S. cerevisiae ceg1Δ cultures bearing indicated CGT1 alleles containing single point mutations were spotted on YPD agar and tested for growth at 23°C (top panel), 30°C (middle panel), and 37°C (bottom panel).(C) Serial dilutions of S. cerevisiae ceg1Δ cultures bearing indicated CGT1 alleles containing single, double, and triple point mutations were spotted on YPD agar and tested for growth at 23°C (top panel), 30°C (middle panel), and 37°C (bottom panel).
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2003, 11, 1549-1561) copyright 2003.  
  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.  
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
20558594 P.Liu, J.M.Kenney, J.W.Stiller, and A.L.Greenleaf (2010).
Genetic organization, length conservation, and evolution of RNA polymerase II carboxyl-terminal domain.
  Mol Biol Evol, 27, 2628-2641.  
20231361 S.Schneider, Y.Pei, S.Shuman, and B.Schwer (2010).
Separable functions of the fission yeast Spt5 carboxyl-terminal domain (CTD) in capping enzyme binding and transcription elongation overlap with those of the RNA polymerase II CTD.
  Mol Cell Biol, 30, 2353-2364.  
19394294 A.L.Mosley, S.G.Pattenden, M.Carey, S.Venkatesh, J.M.Gilmore, L.Florens, J.L.Workman, and M.P.Washburn (2009).
Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylation.
  Mol Cell, 34, 168-178.  
19176527 B.J.Natalizio, N.D.Robson-Dixon, and M.A.Garcia-Blanco (2009).
The Carboxyl-terminal Domain of RNA Polymerase II Is Not Sufficient to Enhance the Efficiency of Pre-mRNA Capping or Splicing in the Context of a Different Polymerase.
  J Biol Chem, 284, 8692-8702.  
19460865 B.Schwer, S.Schneider, Y.Pei, A.Aronova, and S.Shuman (2009).
Characterization of the Schizosaccharomyces pombe Spt5-Spt4 complex.
  RNA, 15, 1241-1250.  
19723344 J.Kohoutek (2009).
P-TEFb- the final frontier.
  Cell Div, 4, 19.  
19850911 M.Issur, B.J.Geiss, I.Bougie, F.Picard-Jean, S.Despins, J.Mayette, S.E.Hobdey, and M.Bisaillon (2009).
The flavivirus NS5 protein is a true RNA guanylyltransferase that catalyzes a two-step reaction to form the RNA cap structure.
  RNA, 15, 2340-2350.  
19679665 M.Kim, H.Suh, E.J.Cho, and S.Buratowski (2009).
Phosphorylation of the yeast Rpb1 C-terminal domain at serines 2, 5, and 7.
  J Biol Chem, 284, 26421-26426.  
19879837 Y.Shi (2009).
Serine/threonine phosphatases: mechanism through structure.
  Cell, 139, 468-484.  
19026779 A.Ghosh, S.Shuman, and C.D.Lima (2008).
The structure of Fcp1, an essential RNA polymerase II CTD phosphatase.
  Mol Cell, 32, 478-490.
PDB codes: 3ef0 3ef1
18158581 C.R.Mandel, Y.Bai, and L.Tong (2008).
Protein factors in pre-mRNA 3'-end processing.
  Cell Mol Life Sci, 65, 1099-1122.  
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
18660819 L.Vasiljeva, M.Kim, H.Mutschler, S.Buratowski, and A.Meinhart (2008).
The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain.
  Nat Struct Mol Biol, 15, 795-804.
PDB code: 3clj
19008886 M.Fuxreiter, P.Tompa, I.Simon, V.N.Uversky, J.C.Hansen, and F.J.Asturias (2008).
Malleable machines take shape in eukaryotic transcriptional regulation.
  Nat Chem Biol, 4, 728-737.  
18573085 P.Cramer, K.J.Armache, S.Baumli, S.Benkert, F.Brueckner, C.Buchen, G.E.Damsma, S.Dengl, S.R.Geiger, A.J.Jasiak, A.Jawhari, S.Jennebach, T.Kamenski, H.Kettenberger, C.D.Kuhn, E.Lehmann, K.Leike, J.F.Sydow, and A.Vannini (2008).
Structure of eukaryotic RNA polymerases.
  Annu Rev Biophys, 37, 337-352.  
17989694 M.De la Peña, O.J.Kyrieleis, and S.Cusack (2007).
Structural insights into the mechanism and evolution of the vaccinia virus mRNA cap N7 methyl-transferase.
  EMBO J, 26, 4913-4925.
PDB code: 2vdw
17339332 M.Gullerova, A.Barta, and Z.J.Lorkovic (2007).
Rct1, a nuclear RNA recognition motif-containing cyclophilin, regulates phosphorylation of the RNA polymerase II C-terminal domain.
  Mol Cell Biol, 27, 3601-3611.  
17164243 S.Ryser, T.Fujita, S.Tortola, I.Piuz, and W.Schlegel (2007).
The rate of c-fos transcription in vivo is continuously regulated at the level of elongation by dynamic stimulus-coupled recruitment of positive transcription elongation factor b.
  J Biol Chem, 282, 5075-5084.  
18006688 Y.X.Xu, and J.L.Manley (2007).
Pin1 modulates RNA polymerase II activity during the transcription cycle.
  Genes Dev, 21, 2950-2962.  
16732283 A.A.Yunus, and C.D.Lima (2006).
Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway.
  Nat Struct Mol Biol, 13, 491-499.
PDB codes: 2grn 2gro 2grp 2grq 2grr
16253993 A.Gasch, S.Wiesner, P.Martin-Malpartida, X.Ramirez-Espain, L.Ruiz, and M.J.Macias (2006).
The structure of Prp40 FF1 domain and its interaction with the crn-TPR1 motif of Clf1 gives a new insight into the binding mode of FF domains.
  J Biol Chem, 281, 356-364.
PDB code: 2b7e
16829979 B.T.Seet, I.Dikic, M.M.Zhou, and T.Pawson (2006).
Reading protein modifications with interaction domains.
  Nat Rev Mol Cell Biol, 7, 473-483.  
16476729 D.Akey, A.Martins, J.Aniukwu, M.S.Glickman, S.Shuman, and J.M.Berger (2006).
Crystal structure and nonhomologous end-joining function of the ligase component of Mycobacterium DNA ligase D.
  J Biol Chem, 281, 13412-13423.
PDB code: 1vs0
16497660 D.Hollingworth, C.G.Noble, I.A.Taylor, and A.Ramos (2006).
RNA polymerase II CTD phosphopeptides compete with RNA for the interaction with Pcf11.
  RNA, 12, 555-560.  
16286474 E.Vojnic, B.Simon, B.D.Strahl, M.Sattler, and P.Cramer (2006).
Structure and carboxyl-terminal domain (CTD) binding of the Set2 SRI domain that couples histone H3 Lys36 methylation to transcription.
  J Biol Chem, 281, 13-15.
PDB code: 2c5z
16431985 M.P.Hall, and C.K.Ho (2006).
Characterization of a Trypanosoma brucei RNA cap (guanine N-7) methyltransferase.
  RNA, 12, 488-497.  
15702066 C.D.Lima (2005).
Inducing interactions with the CTD.
  Nat Struct Mol Biol, 12, 102-103.  
15665873 C.G.Noble, D.Hollingworth, S.R.Martin, V.Ennis-Adeniran, S.J.Smerdon, G.Kelly, I.A.Taylor, and A.Ramos (2005).
Key features of the interaction between Pcf11 CID and RNA polymerase II CTD.
  Nat Struct Mol Biol, 12, 144-151.
PDB code: 2bf0
15901493 D.L.Bentley (2005).
Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors.
  Curr Opin Cell Biol, 17, 251-256.  
15671015 H.Zhu, and S.Shuman (2005).
Structure-guided mutational analysis of the nucleotidyltransferase domain of Escherichia coli NAD+-dependent DNA ligase (LigA).
  J Biol Chem, 280, 12137-12144.  
15923379 L.K.Wang, and S.Shuman (2005).
Structure-function analysis of yeast tRNA ligase.
  RNA, 11, 966-975.  
16314571 M.Li, H.P.Phatnani, Z.Guan, H.Sage, A.L.Greenleaf, and P.Zhou (2005).
Solution structure of the Set2-Rpb1 interacting domain of human Set2 and its interaction with the hyperphosphorylated C-terminal domain of Rpb1.
  Proc Natl Acad Sci U S A, 102, 17636-17641.
PDB code: 2a7o
16054818 P.Tompa, C.Szász, and L.Buday (2005).
Structural disorder throws new light on moonlighting.
  Trends Biochem Sci, 30, 484-489.  
16148005 S.Hausmann, H.Koiwa, S.Krishnamurthy, M.Hampsey, and S.Shuman (2005).
Different strategies for carboxyl-terminal domain (CTD) recognition by serine 5-specific CTD phosphatases.
  J Biol Chem, 280, 37681-37688.  
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.  
15590684 S.Hausmann, and S.Shuman (2005).
Specificity and mechanism of RNA cap guanine-N2 methyltransferase (Tgs1).
  J Biol Chem, 280, 4021-4024.  
16209948 S.Kaneko, and J.L.Manley (2005).
The mammalian RNA polymerase II C-terminal domain interacts with RNA to suppress transcription-coupled 3' end formation.
  Mol Cell, 20, 91.  
14747466 A.Martins, and S.Shuman (2004).
Characterization of a baculovirus enzyme with RNA ligase, polynucleotide 5'-kinase, and polynucleotide 3'-phosphatase activities.
  J Biol Chem, 279, 18220-18231.  
15333634 A.Martins, and S.Shuman (2004).
An RNA ligase from Deinococcus radiodurans.
  J Biol Chem, 279, 50654-50661.  
15241417 A.Meinhart, and P.Cramer (2004).
Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors.
  Nature, 430, 223-226.
PDB codes: 1sz9 1sza
14962393 C.K.Ho, L.K.Wang, C.D.Lima, and S.Shuman (2004).
Structure and mechanism of RNA ligase.
  Structure, 12, 327-339.
PDB code: 1s68
15037606 I.Bougie, and M.Bisaillon (2004).
The broad spectrum antiviral nucleoside ribavirin as a substrate for a viral RNA capping enzyme.
  J Biol Chem, 279, 22124-22130.  
15084599 J.Nandakumar, C.K.Ho, C.D.Lima, and S.Shuman (2004).
RNA substrate specificity and structure-guided mutational analysis of bacteriophage T4 RNA ligase 2.
  J Biol Chem, 279, 31337-31347.  
15494308 J.Nandakumar, and S.Shuman (2004).
How an RNA ligase discriminates RNA versus DNA damage.
  Mol Cell, 16, 211-221.  
15189994 J.W.Stiller, and M.S.Cook (2004).
Functional unit of the RNA polymerase II C-terminal domain lies within heptapeptide pairs.
  Eukaryot Cell, 3, 735-740.  
15114340 S.Hahn (2004).
Structure and mechanism of the RNA polymerase II transcription machinery.
  Nat Struct Mol Biol, 11, 394-403.  
14701811 S.Hausmann, H.Erdjument-Bromage, and S.Shuman (2004).
Schizosaccharomyces pombe carboxyl-terminal domain (CTD) phosphatase Fcp1: distributive mechanism, minimal CTD substrate, and active site mapping.
  J Biol Chem, 279, 10892-10900.  
15136722 S.S.Mandal, C.Chu, T.Wada, H.Handa, A.J.Shatkin, and D.Reinberg (2004).
Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II.
  Proc Natl Acad Sci U S A, 101, 7572-7577.  
12906819 A.Greenleaf (2003).
Getting a grip on the CTD of Pol II.
  Structure, 11, 900-902.  
12766156 L.K.Wang, C.K.Ho, Y.Pei, and S.Shuman (2003).
Mutational analysis of bacteriophage T4 RNA ligase 1. Different functional groups are required for the nucleotidyl transfer and phosphodiester bond formation steps of the ligation reaction.
  J Biol Chem, 278, 29454-29462.  
12930960 M.Odell, L.Malinina, V.Sriskanda, M.Teplova, and S.Shuman (2003).
Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase-adenylate intermediate.
  Nucleic Acids Res, 31, 5090-5100.
PDB code: 1p8l
12933796 R.Sawaya, B.Schwer, and S.Shuman (2003).
Genetic and biochemical analysis of the functional domains of yeast tRNA ligase.
  J Biol Chem, 278, 43928-43938.  
12942140 S.Buratowski (2003).
The CTD code.
  Nat Struct Biol, 10, 679-680.  
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.  
12904290 Y.Pei, and S.Shuman (2003).
Characterization of the Schizosaccharomyces pombe Cdk9/Pch1 protein kinase: Spt5 phosphorylation, autophosphorylation, and mutational analysis.
  J Biol Chem, 278, 43346-43356.  
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.