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PDBsum entry 1q79

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protein ligands metals links
Transferase PDB id
1q79
Jmol
Contents
Protein chain
470 a.a. *
Ligands
3AT
GOL ×5
Metals
_MN ×2
Waters ×375
* Residue conservation analysis
PDB id:
1q79
Name: Transferase
Title: Crystal structure of mammalian poly(a) polymerase
Structure: Poly(a) polymerase alpha. Chain: a. Fragment: residues 1-513. Synonym: pap, polynucleotide adenylyltransferase alpha. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Gene: papola or pap. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.15Å     R-factor:   0.205     R-free:   0.235
Authors: G.Martin,A.Moglich,W.Keller,S.Doublie
Key ref:
G.Martin et al. (2004). Biochemical and structural insights into substrate binding and catalytic mechanism of mammalian poly(A) polymerase. J Mol Biol, 341, 911-925. PubMed id: 15328606 DOI: 10.1016/j.jmb.2004.06.047
Date:
16-Aug-03     Release date:   07-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P25500  (PAPOA_BOVIN) -  Poly(A) polymerase alpha
Seq:
Struc:
 
Seq:
Struc:
739 a.a.
470 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 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
Bound ligand (Het Group name = 3AT)
matches with 96.77% similarity
+ 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   1 term 
  Biological process     RNA 3'-end processing   2 terms 
  Biochemical function     RNA binding     3 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2004.06.047 J Mol Biol 341:911-925 (2004)
PubMed id: 15328606  
 
 
Biochemical and structural insights into substrate binding and catalytic mechanism of mammalian poly(A) polymerase.
G.Martin, A.Möglich, W.Keller, S.Doublié.
 
  ABSTRACT  
 
Polyadenylation of messenger RNA precursors is an essential process in eukaryotes. Poly(A) polymerase (PAP), a member of the nucleotidyltransferase family that includes DNA polymerase beta, incorporates ATP at the 3' end of mRNAs in a template-independent manner. Although the structures of mammalian and yeast PAPs are known, their mechanism of ATP selection has remained elusive. In a recent bovine PAP structure complexed with an analog of ATP and Mn2+, strictly conserved residues interact selectively with the adenine base, but the nucleotide was found in a "non-productive" conformation. Here we report a second bovine crystal structure, obtained in the presence of Mg2+, where 3'-dATP adopts a "productive" conformation similar to that seen in yeast PAP or DNA polymerase beta. Mutational analysis and activity assays with ATP analogs suggest a role in catalysis for one of the two adenine-binding sites revealed by our structural data. The other site might function to prevent futile hydrolysis of ATP. In order to investigate the role of metals in catalysis we performed steady state kinetics experiments under distributive polymerization conditions. These tests suggest a sequential random mechanism in vitro in the presence of ATP and RNA, without preference for a particular order of binding of the two substrates. In vivo, however, where polyadenylation is processive and the primer does not dissociate from the enzyme, an ordered mechanism with the primer as the leading substrate is more likely.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. A, Cartoon of the interactions between PAP and 3'-dATP in site A. B, Cartoon of the interactions between PAP and 3'-dATP in site B. For clarity, only the interactions with the base and ribose are shown. Hydrophobic interactions are shown as spoked arcs, and hydrogen bonds as dotted lines.57
Figure 4.
Figure 4. Comparison of nucleotide conformation in Mg2+ (blue) and Mn2+-bound (pink) PAP structures superimposed with Pol b structure (grey; PDB No. 1BPY) including DNA primer and metals. The a-phosphates are indicated by circles (Mn2+-bound: hot pink; Mg2+-bound: dark blue; and Pol b: dark grey) and the modeled 3'-OH of the Pol b primer (3' deoxy in the crystal) by a grey sphere. The distances between the nucleophile and a-phosphate groups are shown as dotted lines. The proposed primer-binding motif is highlighted in yellow.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 341, 911-925) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22751018 L.A.Yates, S.Fleurdépine, O.S.Rissland, L.De Colibus, K.Harlos, C.J.Norbury, and R.J.Gilbert (2012).
Structural basis for the activity of a cytoplasmic RNA terminal uridylyl transferase.
  Nat Struct Mol Biol, 19, 782-787.
PDB codes: 4e7x 4e80 4e8f
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
19814999 L.S.Chen, L.Du-Cuny, V.Vethantham, D.H.Hawke, J.L.Manley, S.Zhang, and V.Gandhi (2010).
Chain termination and inhibition of mammalian poly(A) polymerase by modified ATP analogues.
  Biochem Pharmacol, 79, 669-677.  
20004168 M.Morar, K.Bhullar, D.W.Hughes, M.Junop, and G.D.Wright (2009).
Structure and mechanism of the lincosamide antibiotic adenylyltransferase LinB.
  Structure, 17, 1649-1659.
PDB codes: 3jyy 3jz0
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.  
18227433 F.R.Salsbury, S.T.Knutson, L.B.Poole, and J.S.Fetrow (2008).
Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid.
  Protein Sci, 17, 299-312.  
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
18439437 P.T.Nelson, W.X.Wang, B.R.Wilfred, and G.Tang (2008).
Technical variables in high-throughput miRNA expression profiling: much work remains to be done.
  Biochim Biophys Acta, 1779, 758-765.  
18191648 R.Aphasizhev, and I.Aphasizheva (2008).
Terminal RNA uridylyltransferases of trypanosomes.
  Biochim Biophys Acta, 1779, 270-280.  
18598057 S.Kumar, M.Bakhtina, and M.D.Tsai (2008).
Altered order of substrate binding by DNA polymerase X from African Swine Fever virus.
  Biochemistry, 47, 7875-7887.  
18281463 V.Vethantham, N.Rao, and J.L.Manley (2008).
Sumoylation regulates multiple aspects of mammalian poly(A) polymerase function.
  Genes Dev, 22, 499-511.  
17872511 G.Martin, and W.Keller (2007).
RNA-specific ribonucleotidyl transferases.
  RNA, 13, 1834-1849.  
17410550 I.Bougie, and M.Bisaillon (2007).
Characterization of the RNA binding energetics of the Candida albicans poly(A) polymerase.
  Yeast, 24, 431-446.  
17189640 J.Stagno, I.Aphasizheva, A.Rosengarth, H.Luecke, and R.Aphasizhev (2007).
UTP-bound and Apo structures of a minimal RNA uridylyltransferase.
  J Mol Biol, 366, 882-899.
PDB codes: 2ikf 2nom
17785418 J.Stagno, I.Aphasizheva, R.Aphasizhev, and H.Luecke (2007).
Dual role of the RNA substrate in selectivity and catalysis by terminal uridylyl transferases.
  Proc Natl Acad Sci U S A, 104, 14634-14639.
PDB codes: 2q0c 2q0d 2q0e 2q0f 2q0g
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
17223131 P.B.Balbo, J.Toth, and A.Bohm (2007).
X-ray crystallographic and steady state fluorescence characterization of the protein dynamics of yeast polyadenylate polymerase.
  J Mol Biol, 366, 1401-1415.
PDB codes: 2hhp 2o1p
16455498 S.West, N.Gromak, C.J.Norbury, and N.J.Proudfoot (2006).
Adenylation and exosome-mediated degradation of cotranscriptionally cleaved pre-messenger RNA in human cells.
  Mol Cell, 21, 437-443.  
16260630 L.Haracska, R.E.Johnson, L.Prakash, and S.Prakash (2005).
Trf4 and Trf5 proteins of Saccharomyces cerevisiae exhibit poly(A) RNA polymerase activity but no DNA polymerase activity.
  Mol Cell Biol, 25, 10183-10189.  
15987818 L.Rouhana, L.Wang, N.Buter, J.E.Kwak, C.A.Schiltz, T.Gonzalez, A.E.Kelley, C.F.Landry, and M.Wickens (2005).
Vertebrate GLD2 poly(A) polymerases in the germline and the brain.
  RNA, 11, 1117-1130.  
15828860 S.Vanácová, J.Wolf, G.Martin, D.Blank, S.Dettwiler, A.Friedlein, H.Langen, G.Keith, and W.Keller (2005).
A new yeast poly(A) polymerase complex involved in RNA quality control.
  PLoS Biol, 3, e189.  
16041059 T.E.Adamson, D.C.Shutt, and D.H.Price (2005).
Functional coupling of cleavage and polyadenylation with transcription of mRNA.
  J Biol Chem, 280, 32262-32271.  
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 codes are shown on the right.