EzCatDB: T00202

DB codeT00202
RLCP classification3.103.70200.1160
CATH domainDomain 13.30.70.590
Domain 23.30.460.10Catalytic domain
Domain 31.10.1410.10
E.C.2.7.7.19
CSA1fa0

CATH domainRelated DB codes (homologues)
1.10.1410.10M00218
3.30.460.10M00218
3.30.70.590M00218

Enzyme Name
Swiss-protKEGG

P29468
Protein namePoly(A) polymerasepolynucleotide 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
SynonymsPAP
EC 2.7.7.19
Polynucleotide adenylyltransferase


Swiss-prot:Accession NumberP29468
Entry namePAP_YEAST
ActivityATP + RNA(n) = diphosphate + RNA(n+1).
SubunitComponent 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.
Subcellular locationNucleus.
Cofactor


CofactorsSubstratesProducts
KEGG-idC00305C00002C00046C00013C00046
CompoundMagnesiumATPRNA(n)PyrophosphateRNA(n+1)
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotidenucleic acidsphosphate group/phosphate ionnucleic acids
1fa0A01UnboundUnboundUnboundUnboundUnbound
1fa0B01UnboundUnboundUnboundUnboundUnbound
1fa0A02Analogue:2x_MNBound:3ATAnalogue:3ADUnboundUnbound
1fa0B02Analogue:2x_MNBound:3ATAnalogue:3ADUnboundUnbound
1fa0A03UnboundUnboundUnboundBound:POPUnbound
1fa0B03UnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot: P25500 & P29468
pdbCatalytic residuesCofactor-binding residues
1fa0A01

1fa0B01

1fa0A02ASP 102
ASP 100;ASP 102;ASP 154(Mg binding)
1fa0B02ASP 102
ASP 100;ASP 102;ASP 154(Mg binding)
1fa0A03

1fa0B03


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]p.2600
[4]p.4199

references
[1]
PubMed ID8665867
JournalEMBO J
Year1996
Volume15
Pages2593-603
AuthorsMartin G, Keller W
TitleMutational 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 Swiss-protP25500
[2]
PubMed ID9061026
JournalBiochim Biophys Acta
Year1997
Volume1350
Pages293-305
AuthorsWittmann T, Wahle E
TitlePurification and characterization of full-length mammalian poly(A) polymerase.
[3]
PubMed ID10595540
JournalProtein Sci
Year1999
Volume8
Pages2380-91
AuthorsMartin G, Jeno P, Keller W
TitleMapping of ATP binding regions in poly(A) polymerases by photoaffinity labeling and by mutational analysis identifies a domain conserved in many nucleotidyltransferases.
[4]
PubMed ID10944102
JournalEMBO J
Year2000
Volume19
Pages4193-203
AuthorsMartin G, Keller W, Doublie S
TitleCrystal structure of mammalian poly(A) polymerase in complex with an analog of ATP.
Related PDB1f5a
Related Swiss-protP25500
[5]
PubMed ID10958780
JournalScience
Year2000
Volume289
Pages1346-9
AuthorsBard J, Zhelkovsky AM, Helmling S, Earnest TN, Moore CL, Bohm A
TitleStructure of yeast poly(A) polymerase alone and in complex with 3'-dATP.
Related PDB1fa0

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.

createdupdated
2002-08-292009-03-09
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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