EzCatDB: T00202
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DB codeT00202
RLCP classification3.103.70200.1160 : Transfer
CATH domainDomain 13.30.70.590 : Alpha-Beta Plaits
Domain 23.30.460.10 : Beta Polymerase; domain 2Catalytic domain
Domain 31.10.1410.10 : Poly(a)-polymerase, middle domain
E.C.2.7.7.19
CSA1fa0

CATH domainRelated DB codes (homologues)
1.10.1410.10 : Poly(a)-polymerase, middle domainM00218
3.30.460.10 : Beta Polymerase; domain 2M00218
3.30.70.590 : Alpha-Beta PlaitsM00218

Enzyme Name
UniProtKBKEGG

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
RefSeqNP_012927.3 (Protein)
NM_001179792.3 (DNA/RNA sequence)
PfamPF01909 (NTP_transf_2)
PF04928 (PAP_central)
PF04926 (PAP_RNA-bind)
[Graphical view]


UniProtKB: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

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00002C00046C00013C00046
CompoundMagnesiumATPRNA(n)PyrophosphateRNA(n+1)
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotidenucleic acidsphosphate group/phosphate ionnucleic acids
ChEBI18420
15422

29888

PubChem888
5957

21961011
1023

             
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 UniProtKBP25500
[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 UniProtKBP25500
[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


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Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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