DB code: T00202

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 1fa0
M-CSA 1fa0
MACiE

CATH domain Related DB codes (homologues)
1.10.1410.10 : Poly(a)-polymerase, middle domain M00218
3.30.460.10 : Beta Polymerase; domain 2 M00218
3.30.70.590 : Alpha-Beta Plaits M00218

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P29468 Poly(A) polymerase
PAP
EC 2.7.7.19
Polynucleotide adenylyltransferase
NP_012927.3 (Protein)
NM_001179792.3 (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
P29468 PAP_YEAST ATP + RNA(n) = diphosphate + RNA(n+1). Component of the cleavage and polyadenylation factor (CPF) complex, which is composed of PTI1, SYC1, SSU72, GLC7, MPE1, REF2, PFS2, PTA1, YSH1/BRR5, SWD2, CFT2/YDH1, YTH1, CFT1/YHH1, FIP1 and PAP1. Interacts with FIR1. 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
1fa0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1fa0B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1fa0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_MN Bound:3AT Analogue:3AD Unbound Unbound
1fa0B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_MN Bound:3AT Analogue:3AD Unbound Unbound
1fa0A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:POP Unbound
1fa0B03 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
1fa0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1fa0B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1fa0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 102 ASP 100;ASP 102;ASP 154(Mg binding)
1fa0B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 102 ASP 100;ASP 102;ASP 154(Mg binding)
1fa0A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1fa0B03 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 bovine (M00218 in EzCatDB).
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) acts as a general base, which activate the 3'-hydroxyl group.

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