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PDBsum entry 1ckm

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protein ligands Protein-protein interface(s) links
Capping enzyme PDB id
1ckm
Jmol
Contents
Protein chains
317 a.a. *
Ligands
GTP ×2
Waters ×360
* Residue conservation analysis
PDB id:
1ckm
Name: Capping enzyme
Title: Structure of two different conformations of mRNA capping enzyme in complex with gtp
Structure: mRNA capping enzyme. Chain: a, b. Synonym: RNA guanylyltransferase. Engineered: yes
Source: Paramecium bursaria chlorella virus 1. Organism_taxid: 10506. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.50Å     R-factor:   0.218     R-free:   0.299
Authors: K.Hakansson,A.J.Doherty,D.B.Wigley
Key ref:
K.Håkansson et al. (1997). X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes. Cell, 89, 545-553. PubMed id: 9160746 DOI: 10.1016/S0092-8674(00)80236-6
Date:
20-Apr-97     Release date:   07-Jul-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q84424  (MCE_PBCV1) -  mRNA-capping enzyme
Seq:
Struc:
330 a.a.
317 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: 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
+ G(5')ppp-Pur-mRNA
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     mRNA processing   2 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0092-8674(00)80236-6 Cell 89:545-553 (1997)
PubMed id: 9160746  
 
 
X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes.
K.Håkansson, A.J.Doherty, S.Shuman, D.B.Wigley.
 
  ABSTRACT  
 
We have solved the crystal structure of an mRNA capping enzyme at 2.5 A resolution. The enzyme comprises two domains with a deep, but narrow, cleft between them. The two molecules in the crystallographic asymmetric unit adopt very different conformations; both contain a bound GTP, but one protein molecule is in an open conformation while the other is in a closed conformation. Only in the closed conformation is the enzyme able to bind manganese ions and undergo catalysis within the crystals to yield the covalent guanylated enzyme intermediate. These structures provide direct evidence for a mechanism that involves a significant conformational change in the enzyme during catalysis.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. The GTP-Binding Sites in Each MoleculeResidues from domain 1 are labeled in yellow and those from domain 2 in white.(A) Electron density at the active site of the open molecule. Lys-82 and Lys-234 are the only residues in hydrogen-bonding contact with the triphosphate chain of the GTP.(B) Electron density at the active site of the closed molecule. In this complex, additional hydrogen-bonded interactions are formed between the GTP and residues from domain 2 as well as Arg-106, Arg-228, and Lys-236 from domain 1, which are not present in the open form.(C) Electron density at the active site of the closed molecule after treatment with Mn^2+ ions. In this complex, the α phosphate is interacting with Lys-234, Lys-236, and the manganese ion. In A–C, the difference electron density (Fo-Fc) was calculated at a stage in the refinement prior to inclusion of GTP in the model and is contoured at 3σ.(D) Comparison of the bound nucleotide in all three forms of the enzyme. Superposition was performed as described in Figure 3.
Figure 7.
Figure 7. A Schematic Diagram for Nucleotidyl Transfer by Capping Enzymes and LigasesThe reaction pathway is the same as in Figure 6, but the roles of some of the most important residues for catalysis are shown.
 
  The above figures are reprinted by permission from Cell Press: Cell (1997, 89, 545-553) copyright 1997.  
  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
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.  
19633819 S.Rasheedi, M.Suragani, S.K.Haq, S.Ghosh, N.Z.Ehtesham, and S.E.Hasnain (2010).
Characterization of LEF4 ligand binding property and its role as part of baculoviral transcription machinery.
  Mol Cell Biochem, 333, 83-89.  
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.  
19690099 N.Tanaka, and S.Shuman (2009).
Structure-activity relationships in human RNA 3'-phosphate cyclase.
  RNA, 15, 1865-1874.  
19301911 R.V.Swift, and J.A.McCammon (2009).
Substrate induced population shifts and stochastic gating in the PBCV-1 mRNA capping enzyme.
  J Am Chem Soc, 131, 5126-5133.  
19133737 R.V.Swift, J.Durrant, R.E.Amaro, and J.A.McCammon (2009).
Toward understanding the conformational dynamics of RNA ligation.
  Biochemistry, 48, 709-719.  
20354588 R.V.Swift, and R.E.Amaro (2009).
Discovery and design of DNA and RNA ligase inhibitors in infectious microorganisms.
  Expert Opin Drug Discov, 4, 1281-1294.  
19329793 S.Shuman (2009).
DNA ligases: progress and prospects.
  J Biol Chem, 284, 17365-17369.  
20636060 T.Conze, A.Shetye, Y.Tanaka, J.Gu, C.Larsson, J.Göransson, G.Tavoosidana, O.Söderberg, M.Nilsson, and U.Landegren (2009).
Analysis of genes, transcripts, and proteins via DNA ligation.
  Annu Rev Anal Chem (Palo Alto Calif), 2, 215-239.  
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
18238776 E.Cotner-Gohara, I.K.Kim, A.E.Tomkinson, and T.Ellenberger (2008).
Two DNA-binding and nick recognition modules in human DNA ligase III.
  J Biol Chem, 283, 10764-10772.  
18003731 J.Li, A.Rahmeh, M.Morelli, and S.P.Whelan (2008).
A conserved motif in region v of the large polymerase proteins of nonsegmented negative-sense RNA viruses that is essential for mRNA capping.
  J Virol, 82, 775-784.  
18262407 J.M.Pascal (2008).
DNA and RNA ligases: structural variations and shared mechanisms.
  Curr Opin Struct Biol, 18, 96.  
18511537 M.A.Brooks, L.Meslet-Cladiére, M.Graille, J.Kuhn, K.Blondeau, H.Myllykallio, and H.van Tilbeurgh (2008).
The structure of an archaeal homodimeric ligase which has RNA circularization activity.
  Protein Sci, 17, 1336-1345.
PDB code: 2vug
18632949 P.Roy (2008).
Bluetongue virus: dissection of the polymerase complex.
  J Gen Virol, 89, 1789-1804.  
18518823 T.Ellenberger, and A.E.Tomkinson (2008).
Eukaryotic DNA ligases: structural and functional insights.
  Annu Rev Biochem, 77, 313-338.  
18449192 X.Yu, L.Jin, and Z.H.Zhou (2008).
3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy.
  Nature, 453, 415-419.
PDB code: 3cnf
18403197 Z.H.Zhou (2008).
Towards atomic resolution structural determination by single-particle cryo-electron microscopy.
  Curr Opin Struct Biol, 18, 218-228.  
17204483 A.Raymond, and S.Shuman (2007).
Deinococcus radiodurans RNA ligase exemplifies a novel ligase clade with a distinctive N-terminal module that is important for 5'-PO4 nick sealing and ligase adenylylation but dispensable for phosphodiester formation at an adenylylated nick.
  Nucleic Acids Res, 35, 839-849.  
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.  
17618295 P.A.Nair, J.Nandakumar, P.Smith, M.Odell, C.D.Lima, and S.Shuman (2007).
Structural basis for nick recognition by a minimal pluripotent DNA ligase.
  Nat Struct Mol Biol, 14, 770-778.
PDB codes: 2q2t 2q2u
17978174 S.Kaneko, C.Chu, A.J.Shatkin, and J.L.Manley (2007).
Human capping enzyme promotes formation of transcriptional R loops in vitro.
  Proc Natl Acad Sci U S A, 104, 17620-17625.  
17416901 Y.Takagi, S.Sindkar, D.Ekonomidis, M.P.Hall, and C.K.Ho (2007).
Trypanosoma brucei encodes a bifunctional capping enzyme essential for cap 4 formation on the spliced leader RNA.
  J Biol Chem, 282, 15995-16005.  
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
16516998 D.D.Dunigan, L.A.Fitzgerald, and J.L.Van Etten (2006).
Phycodnaviruses: a peek at genetic diversity.
  Virus Res, 117, 119-132.  
17052461 J.M.Pascal, O.V.Tsodikov, G.L.Hura, W.Song, E.A.Cotner, S.Classen, A.E.Tomkinson, J.A.Tainer, and T.Ellenberger (2006).
A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA.
  Mol Cell, 24, 279-291.
PDB codes: 2hii 2hik 2hiv 2hix
17068206 L.K.Wang, B.Schwer, and S.Shuman (2006).
Structure-guided mutational analysis of T4 RNA ligase 1.
  RNA, 12, 2126-2134.  
16342145 L.Liu (2006).
Functional characterization of the C-terminal domain of mouse capping enzyme.
  Cell Biochem Funct, 24, 95.  
16481318 M.E.Fraser, K.Hayakawa, M.S.Hume, D.G.Ryan, and E.R.Brownie (2006).
Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase.
  J Biol Chem, 281, 11058-11065.
PDB codes: 2fp4 2fpg 2fpi 2fpp
16431985 M.P.Hall, and C.K.Ho (2006).
Characterization of a Trypanosoma brucei RNA cap (guanine N-7) methyltransferase.
  RNA, 12, 488-497.  
15920472 A.Strasser, A.Dickmanns, R.Lührmann, and R.Ficner (2005).
Structural basis for m3G-cap-mediated nuclear import of spliceosomal UsnRNPs by snurportin1.
  EMBO J, 24, 2235-2243.
PDB code: 1xk5
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.  
16199559 N.Keppetipola, and S.Shuman (2005).
Characterization of a thermophilic ATP-dependent DNA ligase from the euryarchaeon Pyrococcus horikoshii.
  J Bacteriol, 187, 6902-6908.  
15611301 R.Sawaya, B.Schwer, and S.Shuman (2005).
Structure-function analysis of the yeast NAD+-dependent tRNA 2'-phosphotransferase Tpt1.
  RNA, 11, 107-113.  
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.  
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
14747344 D.Georlette, V.Blaise, F.Bouillenne, B.Damien, S.H.Thorbjarnardóttir, E.Depiereux, C.Gerday, V.N.Uversky, and G.Feller (2004).
Adenylation-dependent conformation and unfolding pathways of the NAD+-dependent DNA ligase from the thermophile Thermus scotoductus.
  Biophys J, 86, 1089-1104.  
15226422 H.J.Kim, S.H.Jeong, J.H.Heo, S.J.Jeong, S.T.Kim, H.D.Youn, J.W.Han, H.W.Lee, and E.J.Cho (2004).
mRNA capping enzyme activity is coupled to an early transcription elongation.
  Mol Cell Biol, 24, 6184-6193.  
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.  
15565146 J.M.Pascal, P.J.O'Brien, A.E.Tomkinson, and T.Ellenberger (2004).
Human DNA ligase I completely encircles and partially unwinds nicked DNA.
  Nature, 432, 473-478.
PDB code: 1x9n
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.  
15296738 K.S.Gajiwala, and C.Pinko (2004).
Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal.
  Structure, 12, 1449-1459.
PDB codes: 1ta8 1tae
14722282 Y.L.Huang, Y.T.Han, Y.T.Chang, Y.H.Hsu, and M.Meng (2004).
Critical residues for GTP methylation and formation of the covalent m7GMP-enzyme intermediate in the capping enzyme domain of bamboo mosaic virus.
  J Virol, 78, 1271-1280.  
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
14523019 D.Georlette, V.Blaise, C.Dohmen, F.Bouillenne, B.Damien, E.Depiereux, C.Gerday, V.N.Uversky, and G.Feller (2003).
Cofactor binding modulates the conformational stabilities and unfolding patterns of NAD(+)-dependent DNA ligases from Escherichia coli and Thermus scotoductus.
  J Biol Chem, 278, 49945-49953.  
14616059 J.L.Van Etten (2003).
Unusual life style of giant chlorella viruses.
  Annu Rev Genet, 37, 153-195.  
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.  
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.  
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
12646557 P.Fechter, L.Mingay, J.Sharps, A.Chambers, E.Fodor, and G.G.Brownlee (2003).
Two aromatic residues in the PB2 subunit of influenza A RNA polymerase are crucial for cap binding.
  J Biol Chem, 278, 20381-20388.  
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.  
12611899 S.Yin, C.K.Ho, and S.Shuman (2003).
Structure-function analysis of T4 RNA ligase 2.
  J Biol Chem, 278, 17601-17608.  
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.  
12473094 A.V.Cherepanov, and S.de Vries (2002).
Dynamic mechanism of nick recognition by DNA ligase.
  Eur J Biochem, 269, 5993-5999.  
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.  
12228725 C.K.Ho, and S.Shuman (2002).
Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains.
  Proc Natl Acad Sci U S A, 99, 12709-12714.  
12244300 H.Naitow, J.Tang, M.Canady, R.B.Wickner, and J.E.Johnson (2002).
L-A virus at 3.4 A resolution reveals particle architecture and mRNA decapping mechanism.
  Nat Struct Biol, 9, 725-728.
PDB code: 1m1c
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.  
12455993 T.Takagi, E.J.Cho, R.T.Janoo, V.Polodny, Y.Takase, M.C.Keogh, S.A.Woo, L.D.Fresco-Cohen, C.S.Hoffman, and S.Buratowski (2002).
Divergent subunit interactions among fungal mRNA 5'-capping machineries.
  Eukaryot Cell, 1, 448-457.  
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.  
11751916 V.Sriskanda, and S.Shuman (2002).
Role of nucleotidyl transferase motif V in strand joining by chlorella virus DNA ligase.
  J Biol Chem, 277, 9661-9667.  
11781321 V.Sriskanda, and S.Shuman (2002).
Conserved residues in domain Ia are required for the reaction of Escherichia coli DNA ligase with NAD+.
  J Biol Chem, 277, 9695-9700.  
11842101 V.Sriskanda, and S.Shuman (2002).
Role of nucleotidyltransferase motifs I, III and IV in the catalysis of phosphodiester bond formation by Chlorella virus DNA ligase.
  Nucleic Acids Res, 30, 903-911.  
11893740 Y.Pei, and S.Shuman (2002).
Interactions between fission yeast mRNA capping enzymes and elongation factor Spt5.
  J Biol Chem, 277, 19639-19648.  
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.  
11721015 A.V.Cherepanov, and S.de Vries (2001).
Binding of nucleotides by T4 DNA ligase and T4 RNA ligase: optical absorbance and fluorescence studies.
  Biophys J, 81, 3545-3559.  
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.  
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.  
11167066 J.Banér, M.Nilsson, A.Isaksson, M.Mendel-Hartvig, D.O.Antson, and U.Landegren (2001).
More keys to padlock probes: mechanisms for high-throughput nucleic acid analysis.
  Curr Opin Biotechnol, 12, 11-15.  
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.  
11134291 Y.I.Li, Y.J.Chen, Y.H.Hsu, and M.Meng (2001).
Characterization of the AdoMet-dependent guanylyltransferase activity that is associated with the N terminus of bamboo mosaic virus replicase.
  J Virol, 75, 782-788.  
11058099 A.J.Doherty, and S.W.Suh (2000).
Structural and mechanistic conservation in DNA ligases.
  Nucleic Acids Res, 28, 4051-4058.  
  10924457 B.Schwer, N.Saha, X.Mao, H.W.Chen, and S.Shuman (2000).
Structure-function analysis of yeast mRNA cap methyltransferase and high-copy suppression of conditional mutants by AdoMet synthase and the ubiquitin conjugating enzyme Cdc34p.
  Genetics, 155, 1561-1576.  
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.  
10644745 C.L.Luongo, K.M.Reinisch, S.C.Harrison, and M.L.Nibert (2000).
Identification of the guanylyltransferase region and active site in reovirus mRNA capping protein lambda2.
  J Biol Chem, 275, 2804-2810.  
10679461 F.A.Quiocho, G.Hu, and P.D.Gershon (2000).
Structural basis of mRNA cap recognition by proteins.
  Curr Opin Struct Biol, 10, 78-86.  
10944393 H.Ponstingl, K.Henrick, and J.M.Thornton (2000).
Discriminating between homodimeric and monomeric proteins in the crystalline state.
  Proteins, 41, 47-57.  
10698952 J.Y.Lee, C.Chang, H.K.Song, J.Moon, J.K.Yang, H.K.Kim, S.T.Kwon, and S.W.Suh (2000).
Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.
  EMBO J, 19, 1119-1129.
PDB codes: 1dgs 1dgt 1v9p
11106756 M.Odell, V.Sriskanda, S.Shuman, and D.B.Nikolov (2000).
Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining.
  Mol Cell, 6, 1183-1193.
PDB code: 1fvi
10871342 V.Sriskanda, Z.Kelman, J.Hurwitz, and S.Shuman (2000).
Characterization of an ATP-dependent DNA ligase from the thermophilic archaeon Methanobacterium thermoautotrophicum.
  Nucleic Acids Res, 28, 2221-2228.  
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.  
10589681 C.D.Lima, L.K.Wang, and S.Shuman (1999).
Structure and mechanism of yeast RNA triphosphatase: an essential component of the mRNA capping apparatus.
  Cell, 99, 533-543.
PDB codes: 1d8h 1d8i
10198643 C.K.Ho, and S.Shuman (1999).
Distinct roles for CTD Ser-2 and Ser-5 phosphorylation in the recruitment and allosteric activation of mammalian mRNA capping enzyme.
  Mol Cell, 3, 405-411.  
  10482634 C.Lin, and J.L.Kim (1999).
Structure-based mutagenesis study of hepatitis C virus NS3 helicase.
  J Virol, 73, 8798-8807.  
10395545 E.Riballo, S.E.Critchlow, S.H.Teo, A.J.Doherty, A.Priestley, B.Broughton, B.Kysela, H.Beamish, N.Plowman, C.F.Arlett, A.R.Lehmann, S.P.Jackson, and P.A.Jeggo (1999).
Identification of a defect in DNA ligase IV in a radiosensitive leukaemia patient.
  Curr Biol, 9, 699-702.  
10364504 F.Kong, K.Sivakumaran, and C.Kao (1999).
The N-terminal half of the brome mosaic virus 1a protein has RNA capping-associated activities: specificity for GTP and S-adenosylmethionine.
  Virology, 259, 200-210.  
  10543760 G.Ciarrocchi, D.G.MacPhee, L.W.Deady, and L.Tilley (1999).
Specific inhibition of the eubacterial DNA ligase by arylamino compounds.
  Antimicrob Agents Chemother, 43, 2766-2772.  
10547698 J.L.Van Etten, and R.H.Meints (1999).
Giant viruses infecting algae.
  Annu Rev Microbiol, 53, 447-494.  
10318816 M.Odell, and S.Shuman (1999).
Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA.
  J Biol Chem, 274, 14032-14039.  
10368271 M.R.Singleton, K.Håkansson, D.J.Timson, and D.B.Wigley (1999).
Structure of the adenylation domain of an NAD+-dependent DNA ligase.
  Structure, 7, 35-42.
PDB code: 1b04
10419478 Z.B.Mackey, C.Niedergang, J.M.Murcia, J.Leppard, K.Au, J.Chen, G.de Murcia, and A.E.Tomkinson (1999).
DNA ligase III is recruited to DNA strand breaks by a zinc finger motif homologous to that of poly(ADP-ribose) polymerase. Identification of two functionally distinct DNA binding regions within DNA ligase III.
  J Biol Chem, 274, 21679-21687.  
  9811740 C.H.Gross, and S.Shuman (1998).
RNA 5'-triphosphatase, nucleoside triphosphatase, and guanylyltransferase activities of baculovirus LEF-4 protein.
  J Virol, 72, 10020-10028.  
  9710603 C.K.Ho, B.Schwer, and S.Shuman (1998).
Genetic, physical, and functional interactions between the triphosphatase and guanylyltransferase components of the yeast mRNA capping apparatus.
  Mol Cell Biol, 18, 5189-5198.  
9545288 C.K.Ho, V.Sriskanda, S.McCracken, D.Bentley, B.Schwer, and S.Shuman (1998).
The guanylyltransferase domain of mammalian mRNA capping enzyme binds to the phosphorylated carboxyl-terminal domain of RNA polymerase II.
  J Biol Chem, 273, 9577-9585.  
  9832501 E.J.Cho, C.R.Rodriguez, T.Takagi, and S.Buratowski (1998).
Allosteric interactions between capping enzyme subunits and the RNA polymerase II carboxy-terminal domain.
  Genes Dev, 12, 3482-3487.  
  9671471 E.Silva, E.Ullu, R.Kobayashi, and C.Tschudi (1998).
Trypanosome capping enzymes display a novel two-domain structure.
  Mol Cell Biol, 18, 4612-4619.  
9493270 J.L.Kim, K.A.Morgenstern, J.P.Griffith, M.D.Dwyer, J.A.Thomson, M.A.Murcko, C.Lin, and P.R.Caron (1998).
Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding.
  Structure, 6, 89.
PDB code: 1a1v
9421505 J.Wittschieben, B.O.Petersen, and S.Shuman (1998).
Replacement of the active site tyrosine of vaccinia DNA topoisomerase by glutamate, cysteine or histidine converts the enzyme into a site-specific endonuclease.
  Nucleic Acids Res, 26, 490-496.  
9465045 K.Hâkansson, and D.B.Wigley (1998).
Structure of a complex between a cap analogue and mRNA guanylyl transferase demonstrates the structural chemistry of RNA capping.
  Proc Natl Acad Sci U S A, 95, 1505-1510.
PDB code: 1cko
9512541 T.Yamada-Okabe, R.Doi, O.Shimmi, M.Arisawa, and H.Yamada-Okabe (1998).
Isolation and characterization of a human cDNA for mRNA 5'-capping enzyme.
  Nucleic Acids Res, 26, 1700-1706.  
9421510 V.Sriskanda, and S.Shuman (1998).
Chlorella virus DNA ligase: nick recognition and mutational analysis.
  Nucleic Acids Res, 26, 525-531.  
9770468 Y.Wen, Z.Yue, and A.J.Shatkin (1998).
Mammalian capping enzyme binds RNA and uses protein tyrosine phosphatase mechanism.
  Proc Natl Acad Sci U S A, 95, 12226-12231.  
9334736 A.Liljas, and S.al-Karadaghi (1997).
Structural aspects of protein synthesis.
  Nat Struct Biol, 4, 767-771.  
9261078 G.Varani (1997).
A cap for all occasions.
  Structure, 5, 855-858.  
  9371657 L.Yu, A.Martins, L.Deng, and S.Shuman (1997).
Structure-function analysis of the triphosphatase component of vaccinia virus mRNA capping enzyme.
  J Virol, 71, 9837-9843.  
  9407024 S.McCracken, N.Fong, E.Rosonina, K.Yankulov, G.Brothers, D.Siderovski, A.Hessel, S.Foster, S.Shuman, and D.L.Bentley (1997).
5'-Capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II.
  Genes Dev, 11, 3306-3318.  
9275164 S.P.Wang, L.Deng, C.K.Ho, and S.Shuman (1997).
Phylogeny of mRNA capping enzymes.
  Proc Natl Acad Sci U S A, 94, 9573-9578.  
9398072 S.Shuman (1997).
Origins of mRNA identity: capping enzymes bind to the phosphorylated C-terminal domain of RNA polymerase II.
  Proc Natl Acad Sci U S A, 94, 12758-12760.  
9371772 Z.Yue, E.Maldonado, R.Pillutla, H.Cho, D.Reinberg, and A.J.Shatkin (1997).
Mammalian capping enzyme complements mutant Saccharomyces cerevisiae lacking mRNA guanylyltransferase and selectively binds the elongating form of RNA polymerase II.
  Proc Natl Acad Sci U S A, 94, 12898-12903.  
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