DB code: M00218

RLCP classification 3.103.70200.1160 : Transfer
CATH domain 3.30.70.590 : Alpha-Beta Plaits
3.30.460.10 : Beta Polymerase; domain 2 Catalytic domain
1.10.1410.10 : Poly(a)-polymerase, middle domain
-.-.-.- :
E.C. 2.7.7.19
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
1.10.1410.10 : Poly(a)-polymerase, middle domain T00202
3.30.460.10 : Beta Polymerase; domain 2 T00202
3.30.70.590 : Alpha-Beta Plaits T00202

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P25500 Poly(A) polymerase alpha
PAP-alpha
EC 2.7.7.19
Polynucleotide adenylyltransferase alpha
NP_788820.1 (Protein)
NM_176647.2 (DNA/RNA sequence)
PF01909 (NTP_transf_2)
PF04928 (PAP_central)
PF04926 (PAP_RNA-bind)
[Graphical View]

KEGG enzyme name
polynucleotide adenylyltransferase
NTP polymerase
RNA adenylating enzyme
AMP polynucleotidylexotransferase
ATP-polynucleotide adenylyltransferase
ATP:polynucleotidylexotransferase
poly(A) polymerase
poly(A) synthetase
polyadenylate nucleotidyltransferase
polyadenylate polymerase
polyadenylate synthetase
polyadenylic acid polymerase
polyadenylic polymerase
terminal riboadenylate transferase
poly(A) hydrolase
RNA formation factors, PF1
adenosine triphosphate:ribonucleic acid adenylyltransferase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P25500 PAPOA_BOVIN ATP + RNA(n) = diphosphate + RNA(n+1). Monomer. Found in a complex with CPSF1, FIP1L1 and PAPOLA. Interacts with NUDT21/CPSF5 and FIP1L1 (By similarity). Nucleus.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00046 C00013 C00046
E.C.
Compound Magnesium ATP RNA(n) Pyrophosphate RNA(n+1)
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide nucleic acids phosphate group/phosphate ion nucleic acids
ChEBI 18420
15422
29888
PubChem 888
5957
1023
21961011
1f5aA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1f5aA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:3x_MN Bound:3AT Unbound Analogue:3PO Unbound
1f5aA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot: P25500 & P29468

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1f5aA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1f5aA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 115 ASP 113;ASP 115;ASP 167(Mg binding)
1f5aA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.2600
[4]
p.4199

References
[1]
Resource
Comments
Medline ID
PubMed ID 8665867
Journal EMBO J
Year 1996
Volume 15
Pages 2593-603
Authors Martin G, Keller W
Title Mutational analysis of mammalian poly(A) polymerase identifies a region for primer binding and catalytic domain, homologous to the family X polymerases, and to other nucleotidyltransferases.
Related PDB
Related UniProtKB P25500
[2]
Resource
Comments
Medline ID
PubMed ID 9061026
Journal Biochim Biophys Acta
Year 1997
Volume 1350
Pages 293-305
Authors Wittmann T, Wahle E
Title Purification and characterization of full-length mammalian poly(A) polymerase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 10595540
Journal Protein Sci
Year 1999
Volume 8
Pages 2380-91
Authors Martin G, Jeno P, Keller W
Title Mapping of ATP binding regions in poly(A) polymerases by photoaffinity labeling and by mutational analysis identifies a domain conserved in many nucleotidyltransferases.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 10944102
Journal EMBO J
Year 2000
Volume 19
Pages 4193-203
Authors Martin G, Keller W, Doublie S
Title Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP.
Related PDB 1f5a
Related UniProtKB P25500
[5]
Resource
Comments
Medline ID
PubMed ID 10958780
Journal Science
Year 2000
Volume 289
Pages 1346-9
Authors Bard J, Zhelkovsky AM, Helmling S, Earnest TN, Moore CL, Bohm A
Title Structure of yeast poly(A) polymerase alone and in complex with 3'-dATP.
Related PDB 1fa0
Related UniProtKB

Comments
This enzyme is homologous to the counterpart enzyme from yeast (T00202 in EzCatDB), showing the same reaction mechanism as that of the counterpart.
According to the literature [1], three acidic residues chelate two Mg2+ ions, which in turn coordinate the alpha-phosphorus of the incoming nucleotide and the 3'-hydroxyl group of the primer. The proton of the attacking hydroxyl group can be abstracted by the nearby acidic residue in the catalytic site. The activated hydroxyl acts as the nucleophile in the subsequent phosphoester bond formation. The reaction results in the inversion of the stereochemistry at the alpha-phosphorus of the now covalently linked nucleoside and ends with the release of Mg2+-pyrophosphate.
The paper [4] also suggests that the catalytic reaction involves an in-line attack of the 3'-hydroxyl group of the primer on the incoming ATP, without a covalent intermediate.
Considering the structure, Asp102 (PDB;1fa0 in T00202) acts as a general base, which activate the 3'-hydroxyl group.

Created Updated
2002-08-29 2009-03-09