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PDBsum entry 2o1p

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protein Protein-protein interface(s) links
Transferase PDB id
2o1p
Jmol
Contents
Protein chains
523 a.a. *
Waters ×183
* Residue conservation analysis
PDB id:
2o1p
Name: Transferase
Title: Structure of yeast poly(a) polymerase in a somewhat closed s
Structure: Poly(a) polymerase. Chain: a, b. Synonym: pap, polynucleotide adenylyltransferase. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: pap1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.70Å     R-factor:   0.199     R-free:   0.275
Authors: A.Bohm,P.Balbo,J.Toth
Key ref:
P.B.Balbo et al. (2007). X-ray crystallographic and steady state fluorescence characterization of the protein dynamics of yeast polyadenylate polymerase. J Mol Biol, 366, 1401-1415. PubMed id: 17223131 DOI: 10.1016/j.jmb.2006.12.030
Date:
29-Nov-06     Release date:   23-Jan-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P29468  (PAP_YEAST) -  Poly(A) polymerase
Seq:
Struc:
 
Seq:
Struc:
568 a.a.
523 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.19  - Polynucleotide adenylyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + RNA(n) = diphosphate + RNA(n+1)
ATP
+ RNA(n)
= diphosphate
+ RNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   3 terms 
  Biological process     snoRNA polyadenylation   5 terms 
  Biochemical function     nucleotide binding     9 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2006.12.030 J Mol Biol 366:1401-1415 (2007)
PubMed id: 17223131  
 
 
X-ray crystallographic and steady state fluorescence characterization of the protein dynamics of yeast polyadenylate polymerase.
P.B.Balbo, J.Toth, A.Bohm.
 
  ABSTRACT  
 
Polyadenylate polymerase (PAP) catalyzes the synthesis of poly(A) tails on the 3'-end of pre-mRNA. PAP is composed of three domains: an N-terminal nucleotide-binding domain (homologous to the palm domain of DNA and RNA polymerases), a middle domain (containing other conserved, catalytically important residues), and a unique C-terminal domain (involved in protein-protein interactions required for 3'-end formation). Previous X-ray crystallographic studies have shown that the domains are arranged in a V-shape such that they form a central cleft with the active site located at the base of the cleft at the interface between the N-terminal and middle domains. In the previous studies, the nucleotides were bound directly to the N-terminal domain and exhibited a conspicuous lack of adenine-specific interactions that would constitute nucleotide recognition. Furthermore, it was postulated that base-specific contacts with residues in the middle domain could occur either as a result of a change in the conformation of the nucleotide or domain movement. To address these issues and to better characterize the structural basis of substrate recognition and catalysis, we report two new crystal structures of yeast PAP. A comparison of these structures reveals that the N-terminal and C-terminal domains of PAP move independently as rigid bodies along two well defined axes of rotation. Modeling of the nucleotide into the most closed state allows us to deduce specific nucleotide interactions involving residues in the middle domain (K215, Y224 and N226) that are proposed to be involved in substrate binding and specificity. To further investigate the nature of PAP domain flexibility, 2-aminopurine labeled molecular probes were employed in steady state fluorescence and acrylamide quenching experiments. The results suggest that the closed domain conformation is stabilized upon recognition of the correct subtrate, MgATP, in an enzyme-substrate ternary complex. The implications of these results on the enzyme mechanism of PAP and the possible role for domain motion in an induced fit mechanism are discussed.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Summary difference distance matrix from ESCET. Error-weighted difference distance matrices were calculated for each of the ten unique pairs of different structures. The summary matrix shows the highest value at each matrix element among the ten matrices. Differences smaller than 4 are colored grey. Those larger than 4 σ are colored red (positive) or blue (negative), with the intensity of the color representing the magnitude of the shift. The most intense colors represent shifts of 15 sigma or larger. The large shifts near residue 270 are the result of a disordered loop at the surface of the protein.
Figure 2.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 366, 1401-1415) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21292163 Y.Bai, S.K.Srivastava, J.H.Chang, J.L.Manley, and L.Tong (2011).
Structural basis for dimerization and activity of human PAPD1, a noncanonical poly(A) polymerase.
  Mol Cell, 41, 311-320.
PDB code: 3pq1
19446524 C.Li, H.Li, S.Zhou, E.Sun, J.Yoshizawa, T.L.Poulos, and P.D.Gershon (2009).
Polymerase translocation with respect to single-stranded nucleic acid: looping or wrapping of primer around a poly(A) polymerase.
  Structure, 17, 680-689.
PDB codes: 3er8 3er9 3erc
19281452 P.B.Balbo, and A.Bohm (2009).
Proton transfer in the mechanism of polyadenylate polymerase.
  Biochem J, 420, 229-238.  
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.  
18177750 G.Martin, S.Doublié, and W.Keller (2008).
Determinants of substrate specificity in RNA-dependent nucleotidyl transferases.
  Biochim Biophys Acta, 1779, 206-216.  
18537269 G.Meinke, C.Ezeokonkwo, P.Balbo, W.Stafford, C.Moore, and A.Bohm (2008).
Structure of yeast poly(A) polymerase in complex with a peptide from Fip1, an intrinsically disordered protein.
  Biochemistry, 47, 6859-6869.
PDB code: 3c66
18543944 J.D.Ballin, J.P.Prevas, S.Bharill, I.Gryczynski, Z.Gryczynski, and G.M.Wilson (2008).
Local RNA conformational dynamics revealed by 2-aminopurine solvent accessibility.
  Biochemistry, 47, 7043-7052.  
17872511 G.Martin, and W.Keller (2007).
RNA-specific ribonucleotidyl transferases.
  RNA, 13, 1834-1849.  
17850751 P.B.Balbo, and A.Bohm (2007).
Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis.
  Structure, 15, 1117-1131.
PDB code: 2q66
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.