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2.7.7.19: polynucleotide adenylyltransferase

This is an abbreviated version!
For detailed information about polynucleotide adenylyltransferase, go to the full flat file.

Word Map on EC 2.7.7.19

Reaction

ATP
+
RNAn
=
diphosphate
 +
RNAn+3'-A

Synonyms

AAS, adenosine triphosphate:ribonucleic acid adenylyltransferase, AMP polynucleotidylexotransferase, ATP-polynucleotide adenylyltransferase, ATP:polynucleotidylexotransferase, CC-adding enzyme, Cid1, Cid14, FAM46A, FAM46B, FAM46C, FAM46D, germline development 2, GLD-2, GLD2, GLD4, Hs2, MTPAP, neo-PAP, non-canonical poly(A) RNA polymerase PAPD7, NTP polymerase, nuclear poly(A) polymerase 1, nuclear speckle targeted PIPKIalpha regulated-poly(A) polymerase, nucleotidyltransferase, polyadenylate, PAP, PAP I, Pap II, PAP1, Pap1p, PAPalpha, PAPbeta, PapD1, PapD5, PAPD7, PAPgamma, PAPOLA, PAPOLB/TPAP, PAPOLG, PAPS1, PAPS2, PAPS4, PcnB, pcnB2, pcnB2 aq_2158, poly A polymerase, poly(A) hydrolase, poly(A) polymerase, poly(A) polymerase gamma, poly(A) polymerase I, poly(A) polymerase II, poly(A) RNA polymerase protein 1, poly(A) synthetase, poly(A)-polymerase, poly(A)polymerase I, polyA polymerase, polyadenylate nucleotidyltransferase, polyadenylate polymerase, polyadenylate synthetase, polyadenylic acid polymerase, polyadenylic polymerase, poly[A] polymerase beta, RNA adenylating enzyme, RNA formation factors, PF1, RNA poly(A) polymerase, Star-PAP, Tb927.3.3160, Tb927.7.3780, terminal riboadenylate transferase, Tpap, Trf5, Trf5p, TUT1, TUTase1, VP55, Wisp, yPAP, ZCCHC6

ECTree

     2 Transferases
         2.7 Transferring phosphorus-containing groups
             2.7.7 Nucleotidyltransferases
                2.7.7.19 polynucleotide adenylyltransferase

Crystallization

Crystallization on EC 2.7.7.19 - polynucleotide adenylyltransferase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Crystals of PAP complexed to 3'-dATP and Mn2+ are grown from a solution made of 22% (w/v) polyethylene glycol 8000, 100 mM Mes (pH 6), 120 mM ammonium sulfate, 5 mM CaCl2, 2 mM MnCl2, and 2 mM beta-mercaptoethanol. Cocrystallization of PAP with 3'-dATP and MgCl2 is performed under conditions similar to those reported, with the exception that 5 mM MgCl2 is used instead of 2 mM MnCl2. Crystals are of the space group p212121, with one monomer per asymmetric unit and a solvent content of ~55%.
-
in complex with an ATP analog
mutant C36S/C118V/A152C/C160S/C197S/C257S/C293S/C204V in complex with a chemically modified RNA, to 2.25 A resolution
core complex of isoform GLD-2 and RRM RNA binding domain protein RNP-8, to 2.5 A resolution. RNP-8 embraces the poly(A)-polymerase, docking onto several conserved hydrophobic hotspots present on the GLD-2 surface. RNP-8 stabilizes GLD-2 and indirectly stimulates polyadenylation. RNP-8 differs in amino-acid sequence and structure from GLD-2 binding partner GLD-3 but binds the same surfaces of GLD-2 by forming alternative interactions
germ-line development defective GLD-2–GLD-3 complex up-regulates the expression of genes required for meiotic progression. The structure of a minimal polyadenylation complex that includes the conserved nucleotidyl-transferase core of GLD-2 and the N-terminal domain of GLD-3, to 2.3 A resolution, shows that the N-terminal domain of GLD-3 does not fold into the predicted multi-K homology domain but wraps around the catalytic domain of GLD-2. GLD-3 activates GLD-2 both indirectly by stabilizing the enzyme and directly by contributing positively charged residues near the RNA-binding cleft. Due to distinct structural features, GLD-2 displays unusual specificity in vitro for single-stranded RNAs with at least one adenosine at the 3'-end
mature enzyme, to 1.82 A resolution. Enzyme crystallizes as a dimer and consists of a N-terminal domain (NTD: 52-194 aa) and of palm (195-341 aa) and fingers (342-527 aa). The palm domain harbors the catalytic triad, residue D237, located at the base of sheet beta6, D239 on strand beta6 and D319, which belongs to beta10. Structures of mtPAP in complex with cosubstrates UTP, CTP and GTP indicate that initial nucleotide selection occurs in the absence of a template
isoform PAPgamma bound to cordycepin triphosphate (3?dATP) and Ca2+, to 2.8 A resolution. One 3'-dATP and one Ca2+ are present in the active site of each PAP molecule. Strictly conserved catalytic residues Asp112 and Asp114 interact with Ca2+, which also ligates three non-bridging oxygens of the alpha, beta and gamma phosphates of 3'-dATP. PAPgamma closely resembles its PAPalpha ortholog
mutant D325A, to 3.1 A resolution. The overall structure of the palm and fingers domains is similar to that in the canonical poly(A) polymerases. The active site is located at the interface between the two domains, with a large pocket that can accommodate the substrates. The structure reveals a domain in the N-terminal region of PAPD1, with a backbone-fold that is similar to that of RNP-type RNA binding domains. This domain, together with a beta-arm insertion in the palm domain, contributes to dimerization of PAPD1. The crystal structure reveals a dimer, formed by the two molecules in the asymmetric unit
alone and in complex with 3’-dATP
-
hanging drop vapour diffusion method, using 20% (w/v) PEG 8000, 100 mM magnesium acetate, 100 mM imidazole (pH 6.2), 3% ethylene glycol
mutant D154A in complex with MgATP-RNA, hanging drop vapour diffusion method, in 0.1 M bis-Tris propane, pH 6.4, 0.2 M Li-acetate, and 16% PEG 3350
mutant D154A, trapped in complex with ATP and a five residue poly(A). Enzyme has undergone significant domain movement and shows a closed conformation with extensive interactions between substrates and all three polymerase domains
tethered to the 3'-end processing complex via Fip1 peptide, hanging drop vapour diffusion method, with 100 mM MES, pH 6.5, 8-10% PEG 20000
ATP-gamma-S bound and unbound structures. Subunit VP55 residues of the active site make specific interactions with ATP-gamma-S. Concave surface of subunit VP55 docks the globular subunit VP39. Model of RNA primer binding shows that subunit VP39 functions as a processivity factor by partially enclosing the RNA primer at the heterodimer interface
-
hanging drop vapor diffusion method, using 2% (w/v) tacsimate pH 5.0, 0.15 M sodium citrate tribasic dehydrate pH 5.6 and 10% (w/v) PEG 3350 at 10°C