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

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 18420	15422 15422		29888 29888
PubChem	888 888	5957 5957		1023 21961011 1023 21961011

1f5aA01	Unbound	Unbound	Unbound	Unbound	Unbound
1f5aA02	Analogue:3x_MN	Bound:3AT	Unbound	Analogue:3PO	Unbound
1f5aA03	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
1f5aA02	ASP 115	ASP 113;ASP 115;ASP 167(Mg binding)
1f5aA03

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.

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