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Information on EC 3.6.1.71 - adenosine-5'-diphospho-5'-[DNA] diphosphatase and Organism(s) Homo sapiens and UniProt Accession Q7Z2E3
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3.6.1.71 adenosine-5'-diphospho-5'-[DNA] diphosphataseIUBMB Comments
Aprataxin is a DNA-binding protein involved in different types of DNA break repair. The enzyme acts (among other activities) on abortive DNA ligation intermediates that contain an adenylate covalently linked to the 5'-phosphate DNA terminus. It also acts when the adenylate is covalently linked to the 5'-phosphate of a ribonucleotide linked to a DNA strand, which is the result of abortive ligase activty on products of EC 3.1.26.4, ribonuclease H, an enzyme that cleaves RNA-DNA hybrids on the 5' side of the ribonucleotide found in the 5'-RNA-DNA-3' junction. Aprataxin binds the adenylate group to a histidine residue within the active site, followed by its hydrolysis from the nucleic acid and eventual release, leaving a 5'-phosphate terminus that can be efficiently rejoined. The enzyme also possesses the activities of EC 3.6.1.70, guanosine-5'-diphospho-5'-[DNA] diphosphatase, and EC 3.6.1.72, DNA-3'-diphospho-5'-guanosine diphosphatase.
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Word Map
- 3.6.1.71
- apraxia
-
oculomotor
-
early-onset
- xrcc1
- hypoalbuminemia
- polynucleotide
-
5'-adenylated
- friedreich
- ataxia-telangiectasia
-
ataxia-oculomotor
- medicine
-
cross-complementing
-
forkhead-associated
-
deadenylation
- fen1
The taxonomic range for the selected organisms is: Homo sapiens
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
adenosine-5'-diphospho-5'-[DNA]
+
=
+
phospho-5'-[DNA]
adenosine-5'-diphospho-5'-(ribonucleotide)-[DNA]
+
=
+
5'-phospho-(ribonucleotide)-[DNA]
Synonyms
aprataxin, dna-adenylate hydrolase, rna-dna deadenylase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
5'-App5'-DNA adenylate hydrolase
-
-
-
-
aprataxin
-
-
-
-
APTX
-
-
-
-
HNT3
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
adenosine-5'-diphospho-5'-(ribonucleotide)-[DNA] + H2O = AMP + 5'-phospho-(ribonucleotide)-[DNA]
adenosine-5'-diphospho-5'-[DNA] + H2O = AMP + phospho-5'-[DNA]
a two-step mechanism for hydrolysis of 5'-AMP from RNA-DNA and DNA, APTX catalytic mechanism, overview. In the first step, the active site nucleophile (His260 of the HIT loop in APTX) attacks the 5'-adenylate phosphoanhydride forming a transient enzyme-AMP intermediate and releasing a DNA 5'-phosphate product. Several hydrogen bonds with active-site residues and peptide backbone amides stabilize the negative charge on the transition-state of step 1. The nucleophile (His260) is activated by a hydrogen bond to the carbonyl of His258, while His251 is proposed to protonate the 5'-phosphate leaving group. The second step involves hydrolysis of the His260-AMP-RNA/DNA intermediate, using chemistry that is essentially the reverse of the first step with water replacing the 5'-phosphate, and with His251 proposed to act as a general base to deprotonate a water nucleophile
adenosine-5'-diphospho-5'-[DNA] + H2O = AMP + phospho-5'-[DNA]
the catalytic reaction proceeds in three steps: substrate protonation, DNA deadenylation and histidine-AMP intermediate hydrolysis. The calculated activation energies for the second and third reactions are 19.0 and 10.5 kcal/mol, which can be attributed to a penta-coordinated AMP-phosphoryl formation and closing of a water molecule, respectively. A histidine-AMP intermediate is hydrolyzed easily in the third step when a water molecule closes within 3 A to the phosphorus nucleus
adenosine-5'-diphospho-5'-(ribonucleotide)-[DNA] + H2O = AMP + 5'-phospho-(ribonucleotide)-[DNA]
a two-step mechanism for hydrolysis of 5'-AMP from RNA-DNA and DNA, APTX catalytic mechanism, overview. In the first step, the active site nucleophile (His260 of the HIT loop in APTX) attacks the 5'-adenylate phosphoanhydride forming a transient enzyme-AMP intermediate and releasing a DNA vphosphate product. Several hydrogen bonds with active-site residues and peptide backbone amides stabilize the negative charge on the transitin-state of step 1. The nucleophile (His260) is activated by a hydrogen bond to the carbonyl of His258, while His251 is proposed to protonate the 5'-phosphate leaving group. The second step involves hydrolysis of the His260-AMP-RNA/DNA intermediate, using chemistry that is essentially the reverse of the first step with water replacing the 5'-phosphate, and with His251 proposed to act as a general base to deprotonate a water nucleophile
adenosine-5'-diphospho-5'-(ribonucleotide)-[DNA] + H2O = AMP + 5'-phospho-(ribonucleotide)-[DNA]
the catalytic reaction proceeds in three steps: substrate protonation, DNA deadenylation and histidine-AMP intermediate hydrolysis. The calculated activation energies for the second and third reactions are 19.0 and 10.5 kcal/mol, which can be attributed to a penta-coordinated AMP-phosphoryl formation and closing of a water molecule, respectively. A histidine-AMP intermediate is hydrolyzed easily in the third step when a water molecule closes within 3 A to the phosphorus nucleus
SYSTEMATIC NAME
IUBMB Comments
adenosine-5'-diphospho-5'-[DNA] hydrolase (adenosine 5'-phosphate-forming)
Aprataxin is a DNA-binding protein involved in different types of DNA break repair. The enzyme acts (among other activities) on abortive DNA ligation intermediates that contain an adenylate covalently linked to the 5'-phosphate DNA terminus. It also acts when the adenylate is covalently linked to the 5'-phosphate of a ribonucleotide linked to a DNA strand, which is the result of abortive ligase activty on products of EC 3.1.26.4, ribonuclease H, an enzyme that cleaves RNA-DNA hybrids on the 5' side of the ribonucleotide found in the 5'-RNA-DNA-3' junction. Aprataxin binds the adenylate group to a histidine residue within the active site, followed by its hydrolysis from the nucleic acid and eventual release, leaving a 5'-phosphate terminus that can be efficiently rejoined. The enzyme also possesses the activities of EC 3.6.1.70, guanosine-5'-diphospho-5'-[DNA] diphosphatase, and EC 3.6.1.72, DNA-3'-diphospho-5'-guanosine diphosphatase.
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
adenosine-5'-diphospho-5'-(ribonucleotide)-[DNA] + H2O
AMP + 5'-phospho-(ribonucleotide)-[DNA]
adenosine-5'-diphospho-5'-[5'-AGATTATCTTCGAGCTAC-3'] + H2O
AMP + phospho-5'-[5'-AGATTATCTTCGAGCTAC-3']
-
-
-
?
adenosine-5'-diphospho-5'-[5'-ATTCCGATAGTGACTACA-3'] + H2O
AMP + phospho-5'-[5'-ATTCCGATAGTGACTACA-3']
-
-
-
?
adenosine-5'-diphospho-5'-[5'-CATATCCGTGTCGCCCTCATTCCGATAGTGACTACA-3'] + H2O
AMP + phospho-5'-[5'-CATATCCGTGTCGCCCTCATTCCGATAGTGACTACA-3']
-
-
-
?
adenosine-5'-diphospho-5'-[5'-GTAGCTCGAAGATAATCTGAGGGCGACACGGATATG-3'] + H2O
AMP + phospho-5'-[5'-GTAGCTCGAAGATAATCTGAGGGCGACACGGATATG-3']
-
-
-
?
adenosine-5'-diphospho-5'-[5'-TGTAGTCACTATCGGAATGAGGGCGACACGGATATG-3'] + H2O
AMP + phospho-5'-[5'-TGTAGTCACTATCGGAATGAGGGCGACACGGATATG-3']
-
-
-
?
adenosine-5'-diphospho-5'-(ribonucleotide)-[DNA] + H2O
AMP + 5'-phospho-(ribonucleotide)-[DNA]
-
-
-
?
adenosine-5'-diphospho-5'-(ribonucleotide)-[DNA] + H2O
AMP + 5'-phospho-(ribonucleotide)-[DNA]
-
-
-
-
?
adenosine-5'-diphospho-5'-[DNA] + H2O
AMP + phospho-5'-[DNA]
-
-
-
?
adenosine-5'-diphospho-5'-[DNA] + H2O
AMP + phospho-5'-[DNA]
-
-
-
?
adenosine-5'-diphospho-5'-[DNA] + H2O
AMP + phospho-5'-[DNA]
substrate with single strand DNA
-
-
?
adenosine-5'-diphospho-5'-[DNA] + H2O
AMP + phospho-5'-[DNA]
the enzyme can use nicked and blunt substrates
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-
?
additional information
?
-
aprataxin hydrolyzes with similar efficiency the model histidine triad nucleotide-binding protein substrate : adenosine-5'-monophosphoramidate, AMPNH2, and the Fragile histidine triad protein substrate, Ap4A. No substrate: dATP
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-
?
additional information
?
-
aprataxin possesses an active-site-dependent AMP-lysine and GMP-lysine hydrolase activity that depends additionally on the zinc finger for protein stability and on the forkhead associated domain for enzymatic activity. Aprataxin also shows guanosine-5'-diphospho-5'-[DNA] diphosphatase activity, reaction of EC 3.1.11.8
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-
?
additional information
?
-
aprataxin hydrolyses abnormal 5'-AMP DNA termini formed in abortive DNA ligations
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-
?
additional information
?
-
APTX-mediated DNA deadenylation activity (i.e. 5'-AMP removal) is measured in extracts of cells expressing wild-type XRCC1 or the XRCC1 phosphorylation mutant, and compared with activity in APTX-deficient and APTX-complemented human cells. APTX activity is lower in extracts from Xrcc1-/- and XRCC1 phosphorylation mutant cells compared to the robust activity in extract from wild-type XRCC1 expressing cells. And APTX-mediated DNA deadenylation activity (i.e. 5'-AMP removal) is measured in cell extracts of the XRCC1 variants, and compared with activity in patient AOA1 human fibroblasts and APTX-complemented cells
-
-
?
additional information
?
-
APTX-mediated DNA deadenylation activity (i.e. 5'-AMP removal) is measured
-
-
?
additional information
?
-
aprataxin acts preferentially on adenylated nicks and double-strand breaks rather than on single-stranded DNA
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-
?
additional information
?
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the target of APTX ares 5'-adenylates at DNA nicks or breaks that result from abortive DNA ligation reactions
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-
?
additional information
?
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-
the target of APTX ares 5'-adenylates at DNA nicks or breaks that result from abortive DNA ligation reactions
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
adenosine-5'-diphospho-5'-(ribonucleotide)-[DNA] + H2O
AMP + 5'-phospho-(ribonucleotide)-[DNA]
-
-
-
?
adenosine-5'-diphospho-5'-[DNA] + H2O
AMP + phospho-5'-[DNA]
-
-
-
?
adenosine-5'-diphospho-5'-[DNA] + H2O
AMP + phospho-5'-[DNA]
-
-
-
?
additional information
?
-
aprataxin hydrolyses abnormal 5'-AMP DNA termini formed in abortive DNA ligations
-
-
?
additional information
?
-
APTX-mediated DNA deadenylation activity (i.e. 5'-AMP removal) is measured in extracts of cells expressing wild-type XRCC1 or the XRCC1 phosphorylation mutant, and compared with activity in APTX-deficient and APTX-complemented human cells. APTX activity is lower in extracts from Xrcc1-/- and XRCC1 phosphorylation mutant cells compared to the robust activity in extract from wild-type XRCC1 expressing cells. And APTX-mediated DNA deadenylation activity (i.e. 5'-AMP removal) is measured in cell extracts of the XRCC1 variants, and compared with activity in patient AOA1 human fibroblasts and APTX-complemented cells
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-
?
additional information
?
-
aprataxin acts preferentially on adenylated nicks and double-strand breaks rather than on single-stranded DNA
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
interaction with phosphorylated XRCC1 is a requirement for significant APTX recruitment to cellular DNA damage and enzymatic activity in cell extracts. XRCC1 is a multi-domain protein without catalytic activity
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Zn2+
additional information
Zn2+
required, the APTX Zn2+-binding betabetaalpha core is structurally related to the ubiquitous family of DNA binding C2H2 transcription factors including the prototypical Zif268
Zn2+
binding of Aptx to duplex DNA is mediated by the C-terminal zinc finger domain, and efficient deadenylation requires the zinc finger
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Duplex DNA
significantly reduces catalytic catalytic activity on the model histidine triad nucleotide-binding protein substrate, AMPNH2, and the Fragile histidine triad protein substrate, Ap4A
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single-strand DNA
reduces catalytic catalytic activity on the model histidine triad nucleotide-binding protein substrate, AMPNH2, and the Fragile histidine triad protein substrate, Ap4A
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0000166
adenosine-5'-diphospho-5'-(ribonucleotide)-[DNA]
pH 8.0, 20°C
-
0.0000171
adenosine-5'-diphospho-5'-[DNA]
nicked DNA substrate, pH 7.5, 25-37°C, recombinant His-tagged wild-type enzyme
-
0.0000371
adenosine-5'-diphospho-5'-[DNA]
blunt DNA substrate, pH 7.5, 25-37°C, recombinant His-tagged wild-type enzyme
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.38
adenosine-5'-diphospho-5'-[DNA]
nicked DNA substrate, pH 7.5, 25-37°C, recombinant His-tagged wild-type enzyme
-
0.51
adenosine-5'-diphospho-5'-[DNA]
blunt DNA substrate, pH 7.5, 25-37°C, recombinant His-tagged wild-type enzyme
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
13747
adenosine-5'-diphospho-5'-[DNA]
blunt DNA substrate, pH 7.5, 25-37°C, recombinant His-tagged wild-type enzyme
-
22222
adenosine-5'-diphospho-5'-[DNA]
nicked DNA substrate, pH 7.5, 25-37°C, recombinant His-tagged wild-type enzyme
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
isoforms carrying a 42-nt N-terminal mitochondrial targeting sequence are localized to mitochondria
aprataxin localizes at sites of DNA damage induced by high low linear energy transfer radiation
GFP-aprataxin fusion protein colocalizes with nucleolin, nucleophosmin and UBF-1 in nucleoli. Inhibition of ribosomal DNA transcription alters the distribution of aprataxin in the nucleolus. Down-regulation of nucleolin by RNA interference does not affect aprataxin protein levels but abolishes its nucleolar localization
the first nuclear localization signal located near the amino terminus of the long-form aprataxin is essential for its nuclear localization
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
aprataxin (APTX) belongs to a family of histidine triad (HIT) enzymes. Mutation of His138 to alanine does not completely abolish the catalytic activity; the residual activity is 25% of the wild-type enzyme activity. The DNA deadenylation reaction catalyzed by the H138A mutant can proceed by the protonated substrate
malfunction
physiological function
physiological function
additional information
malfunction
APTX human mutations cause the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1). AOA1 mutagenic effects on APTX solubility, stability, and catalytic activity, and molecular basis for APTX inactivation in AOA1, APTX mutations variably impact protein folding and activity, overview
malfunction
ataxia oculomotor apraxia-1 (AOA1) is a recessive human neurodegenerative disorder linked to more than 20 distinct mutations in the gene encoding APTX. Although reminiscent of ataxia-telangiectasia, primary AOA1 fibroblasts exhibit only mild hypersensitivity to ionizing radiation
malfunction
lack of aprataxin impairs mitochondrial functions, independent of its role in mitochondrial DNA repair, via downregulation of the APE1/NRF1/NRF2 pathway. Ataxia oculomotor apraxia type 1 (AOA1) is an autosomal recessive disease caused by mutations in APTX, which encodes the DNA strand-break repair protein aprataxin (APTX). CoQ10 deficiency is identified in fibroblasts and muscle of AOA1 patients carrying the common W279X mutation, and aprataxin has been localized to mitochondria in neuroblastoma cells, where it enhances preservation of mitochondrial function. The bioenergetics defect in AOA1-mutant fibroblasts and APTX-depleted Hela cells is caused by decreased expression of SDHA and genes encoding CoQ biosynthetic enzymes, in association with reductions of APE1, NRF1 and NRF2. APE1 depletion impairs NRF1 expression in Hela cells and resembles APTX knockdown clones, mitochondrial genes are downregulated in APE1-deficient cells owing to the regulatory role of APE1 on DNA-binding and transcriptional activity of NRF1
malfunction
mutation of aprataxin (APTX) is causing the heritable neurological disorder ataxia with oculomotor apraxia 1 (AOA1)
malfunction
mutations of the APTX gene cause neurological diseases such as ataxia oculomotor aparaxia type 1 (AOA1)
physiological function
aprataxin has dual DNA binding and nucleotide hydrolase activities. The protein binds to double-stranded DNA with high affinity but is also capable of binding double-stranded RNA and single-strand DNA, with increased affinity for hairpin structures. The DNA binding is not dependent on zinc
physiological function
aprataxin interacts with the repair proteins XRCC1, PARP-1 and p53 and colocalizes with XRCC1 along charged particle tracks on chromatin
physiological function
aprataxin localizes at sites of DNA damage induced by high low linear energy transfer radiation and binds to mediator of DNA-damage checkpoint protein MDC1/NFBD1 through a phosphorylation-dependent interaction. This interaction is mediated via the aprataxin forkhead-associated domain and multiple casein kinase 2 diphosphorylated S-D-T-D motifs in MDC1
physiological function
APTX interacts with X-ray repair cross-complementing group XRCC1, which has an essential role in single-strand DNA break repair. The 20 N-terminal amino acids of the forkhead-associated FHA-domain of APTX are important for its interaction with the C-terminal region (residues 492574) of XRCC1. Poly(ADPribose) polymerase PARP-1 is also co-immunoprecipitated with APTX
physiological function
during repair of non-canonical ribonucleotides introduced into DNA during replication of the nuclear genome, DNA ligases generate 5'-adenylated RNA-DNA junctions repaired by Aptx deadenylase. In the proposed reaction scheme, step 1 generates an enzyme-AMP intermediate, which is then resolved via hydrolysis
physiological function
interaction between aprataxin and nucleolin occurs through their respective N-terminal regions. In cells from patients with ataxia with oculomotor apraxia type 1, AOA1, lacking aprataxin, the stability of nucleolin is significantly reduced. Down-regulation of nucleolin by RNA interference does not affect aprataxin protein levels but abolishes its nucleolar localization
physiological function
poly-ADP ribose polymerase PARP-1 is required in the recruitment of aprataxin to sites of DNA breaks. Inhibition of PARP activity does not affect aprataxin activity in vitro, it retards its recruitment to sites of DNA damage in vivo
physiological function
the long-form but not the short-form aprataxin interacts with x-ray repair cross-complementing group XRCC1. Aprataxin and XRCC1 may constitute a multiprotein complex and are involved in single-strand DNA break repair
physiological function
the protein is composed of three domains that share distant homology with the amino-terminal domain of polynucleotide kinase 3'-phosphatase, with histidine-triad proteins and with DNA-binding C2H2 zinc-finger proteins, respectively
physiological function
5'-AMP DNA hydrolysis of aprataxin, energy profile of the APTX catalytic reaction and the protonate states, by quantum mechanical/molecular mechanical (QM/MM) calculations and modeling, overview. Aprataxin hydrolyses abnormal 5'-AMP DNA termini formed in abortive DNA ligations, it is an important DNA repair enzyme
physiological function
aprataxin (APTX) is a DNA-adenylate hydrolase that removes 5'-AMP blocking groups from abortive ligation repair intermediates. Primary role of aprataxin is processing of adenylated 5' ends. XRCC1, a multi-domain protein without catalytic activity, interacts with a number of known repair proteins including APTX, modulating and coordinating the various steps of DNA repair. CK2- phosphorylation of XRCC1 is thought to be crucial for its interaction with the FHA domain of APTX. A phosphorylated XRCC1 is required for APTX recruitment.No interaction of APTX with a phosphorylation mutant of XRCC1
physiological function
critical role of APTX in transcription regulation of mitochondrial function and the pathogenesis of AOA1 via a novel pathomechanistic pathway, which may be relevant to other neurodegenerative diseases
physiological function
eukaryotic DNA ligases seal DNA breaks in the final step of DNA replication and repair transactions via a three-step reaction mechanism that can abort if DNA ligases encounter modified DNA termini, such as the products and repair intermediates of DNA oxidation, alkylation, or the aberrant incorporation of ribonucleotides into genomic DNA. Such abortive DNA ligation reactions create 5'-adenylated nucleic acid termini in the context of DNA and RNA-DNA substrates in DNA base excision repair (BER), double strand break repair (DSBR) and ribonucleotide excision repair (RER). Aprataxin (APTX), a protein altered in the heritable neurological disorder ataxia with oculomotor apraxia 1 (AOA1), acts as a DNA ligase proofreader to directly reverse AMP-modified nucleic acid termini in DNA- and RNA-DNA damage response, molecular mechanism, overview. Elongation of the wedge helix enables dynamic interactions with both the AMP lesion and the exposed base stack on the 5'-end of the damaged DNA strand. The second major DNA binding interface involves undamaged DNA strand binding by the Znf domain
physiological function
the APTX RNA-DNA deadenylase protects genome integrity and corrects abortive DNA ligation arising during ribonucleotide excision repair and base excision DNA repair, APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease, mechanism
physiological function
APTX acts as a nick sensor. When an adenylated nick is encountered by APTX, base pairing at the 5' terminus of the nick is disrupted as the adenylate is accepted into the active site of the enzyme. Adenylate removal occurs by a two-step process that proceeds through a transient AMP-APTX covalent intermediate
physiological function
depletion of aprataxin in human SHSY5Y neuroblastoma cells and primary skeletal muscle myoblasts results in mitochondrial dysfunction, revealed by reduced citrate synthase activity and mtDNA copy number. mtDNA, not nuclear DNA, has higher levels of background DNA damage on aprataxin knockdown
physiological function
FD105 cells, lacking aprataxin, show a 5.7-fold increase in diadenosine 5', 5'''-P(1),P(4)-tetraphosphate (Ap4A) level
physiological function
the catalytic activity of Aptx resides within the HIT domain, the C-terminal zinc finger domain provides stabilizing contacts that lock the enzyme onto its high affinity AMP-DNA target site. Both domains are required for efficient AMP-DNA hydrolase activity. Aprataxin plays a role in base excision repair, specifically in the removal of adenylates that arise from abortive ligation reactions that take place at incised abasic sites in DNA
physiological function
FLJ20157
aprataxin is directly involved in DNA single-strand-break repair
physiological function
-
APTX suppresses DNA-ligase 11-catalyzed ligation of 8oxoG-containing DNA. In presence of APTX, the catalytic commitment of DNA ligase 1 to erroneous ligation is reduced by 70 and 90%, respectively, for the 8oxoG:A and 8oxoG:C substrates
additional information
active site structure of APTX, and molecular reaction mechanism, modeling, overview. General acid-base catalysis of APTX with and important role of His138 as a general acid. The second step, the histidine-AMP intermediate hydrolysis, can proceed with the aid of the product DNA phosphate without a general base residue
additional information
two highly conserved amino acid sequence motifs typify the HIT-Znf region of APTX. The first is the histidine triad motif HXHXHXX (X = hydrophobic residue) of the HIT domain, and the second is a C-terminal Zn-binding (Znf) domain with a sequence motif C(x2)C(x11-12)H(x3)H/E (x = any amino acid). This core HIT-Znf architecture is conserved in APTX orthologs with bona-fide polynucleotide adenylate hydrolase activity including plant, yeast and vertebrate homologues, suggesting that the Znf domain imparts critical substrate specificity to the aprataxins. The APTX Zn2+-binding betabetaalpha core is structurally related to the ubiquitous family of DNA binding C2H2 transcription factors including the prototypical Zif268. APTX Zn2+ ligands can be of either the C2H2 (Cys2-His2 in vertebrate APTX) or C2HE (Cys2-His-Glu in fungal Aptx), which both fold into very similar DNA damage recognition elements
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). APTX_HUMAN
356
0
40740
Swiss-Prot
Mitochondrion (Reliability: 3), other Location (Reliability: 2)
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
aprataxin forkhead-associated domain and modeling of the pSDpTD peptide into the apo structure. pT recognition is provided by residues Arg29 and Ser41
purified wild-type enzyme in complex with RNA/DNA, hAPTX-nicked-RNA-DNA-AMP-Zn2+ complex is grown by mixing 300 nl of 10 mg/ml hAptx (165-342) protein and 1 mM AMP, 1.5:1 DNA:protein molar ratio, in 150 mM NaCl, 20 mM Tris-HCl, pH 7.5, and 0.1% 2-mercaptoethanol, with an equal volume of precipitant solution containing 100 mM MES, pH 6.5, 16% w/v PEG 3350 at 4°C, methods for mutant product complexes hAPTX-R199H/RNA-DNA/AMP-Zn2+, hAPTXH201Q/RNA-DNA/AMP-Zn2+, hAPTX-S242N/RNA-DNA/AMPZn2+, hAPTX-L248M/DNA/AMP-Zn2+, and hAPTX-V263G/RNA-DNA/AMP-Zn2+, differ, overview. X-ray diffraction structure determination and analysis, molecular replacement using PDB ID 4NDG as a search model
structure-function studies of human Aptx in complex with RNA-DNA, AMP and Zn2+
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
689insT
recessive mutation associated with ataxia and oculomotor apraxia, huge loss in protein stability
840delT
recessive mutation associated with ataxia and oculomotor apraxia, huge loss in protein stability
A198V
A198V/P206L
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
D185E
D267G
D267G/W279X
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
G231E
G231E/689insT
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
H138A
site-directed mutagenesis, mutation of His138 to alanine does not completely abolish the catalytic activity, the residual activity is 25% of the wild-type enzyme activity. The DNA deadenylation reaction catalyzed by the H138A mutant can proceed by the protonated substrate
H201Q
H201R
H260A
K197Q
K197Q/W279X
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
L223P
L248M
P206L
R199H
R247X
R29A
mutation of forkhead-associated domain residue, prevents its interaction with mediator of DNA-damage checkpoint protein MDC1 and recruitment to sites of DNA damage
R306X
R306X/W279X
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
S242N
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
V263G
V263G/P206L
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
W279R
W279R/IVS5
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
W279X
W279X/I159fs
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
W279X/Q181X
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
W279X/R306X
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
T739C
FLJ20157
homozygous mutation idientified in a patient with ataxia-oculomotor apraxia type 1
additional information
A198V
recessive mutation associated with ataxia and oculomotor apraxia, huge loss in protein stability
A198V
naturally occuring mutation predicted to affect protein stability by destabilizing or truncating the folded core of APTX, catalytically inactive mutant
A198V
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
D185E
naturally occuring mutation predicted to affect protein stability by destabilizing or truncating the folded core of APTX
D185E
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
D267G
recessive mutation associated with ataxia and oculomotor apraxia, huge loss in protein stability
D267G
naturally occuring mutation predicted to affect protein stability by destabilizing or truncating the folded core of APTX, catalytically inactive mutant
D267G
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
G231E
naturally occuring mutation predicted to affect protein stability by destabilizing or truncating the folded core of APTX, catalytically inactive mutant
G231E
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
H201Q
naturally occuring active site mutation, the mutant displays impaired AMP-lysine hydrolase activity
H201Q
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
H201R
naturally occuring active site mutation, the mutant displays impaired AMP-lysine hydrolase activity
H201R
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
H260A
recessive mutation associated with ataxia and oculomotor apraxia, huge loss in protein stability
K197Q
mutation identified in patient with AOA1. The mutant protein harbors a distorted active site pocket
K197Q
recessive mutation associated with ataxia but not oculomotor apraxia, mild presentation allele
K197Q
naturally occuring mutation, the mutant displays impaired AMP-lysine hydrolase activity, confers a late onset neurological disease AOA1
K197Q
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
L223P
naturally occuring mutation predicted to affect protein stability by destabilizing or truncating the folded core of APTX, catalytically inactive mutant
L223P
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
L248M
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
P206L
recessive mutation associated with ataxia and oculomotor apraxia, huge loss in protein stability
P206L
naturally occuring mutation predicted to affect protein stability by destabilizing or truncating the folded core of APTX, catalytically inactive mutant
R199H
recessive mutation associated with ataxia and oculomotor apraxia, protein retains substantial function, consistent with altered activity
R199H
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
R247X
naturally occuring mutation predicted to affect protein stability by destabilizing or truncating the folded core of APTX, catalytically inactive mutant
R306X
naturally occuring mutation predicted to affect protein stability by destabilizing or truncating the folded core of APTX, catalytically inactive mutant
R306X
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
V263G
mutation identified in a AOA1 patient, mutant protein is unable to bind DNA
V263G
recessive mutation associated with ataxia and oculomotor apraxia, huge loss in protein stability
V263G
naturally occuring mutation predicted to affect protein stability by destabilizing or truncating the folded core of APTX, catalytically inactive mutant
V263G
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
W279R
recessive mutation associated with ataxia and oculomotor apraxia, huge loss in protein stability
W279R
naturally occuring mutation, the mutant displays impaired AMP-lysine hydrolase activity, confers a late onset neurological disease AOA1
W279R
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
W279X
recessive mutation associated with ataxia and oculomotor apraxia, huge loss in protein stability
W279X
naturally occuring mutation causing Ataxia oculomotor apraxia type 1 (AOA1) autosomal recessive disease
W279X
naturally occuring mutation predicted to affect protein stability by destabilizing or truncating the folded core of APTX, catalytically inactive mutant, confers a late onset neurological disease AOA1
W279X
site-directed mutagenesis, a mutation causing the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1)
additional information
removal of the N-terminal forkhead associated domain does not alter activity with substrates AMPNH2 and Ap4A
additional information
the biochemical and molecular abnormalities in APTX-depleted cells are recapitulated by knockdown of APE1 in Hela cells and are rescued by overexpression of NRF1/2. Importantly, pharmacological upregulation of NRF1 alone by 5-aminoimidazone-4-carboxamide ribonucleotide does not rescue the phenotype, which, in contrast, is reversed by the upregulation of NRF2 by rosiglitazone. The lack of aprataxin causes reduction of the pathway APE1/NRF1/NRF2 and their target genes. APTX-mutant fibroblasts show reduced succinate dehydrogenase. APTX-mutant fibroblasts show reduced levels and biosynthesis of CoQ10. Levels of APE1 are reduced in APTX-mutant and APTX-depleted cells. Phenotype, overview
additional information
-
the biochemical and molecular abnormalities in APTX-depleted cells are recapitulated by knockdown of APE1 in Hela cells and are rescued by overexpression of NRF1/2. Importantly, pharmacological upregulation of NRF1 alone by 5-aminoimidazone-4-carboxamide ribonucleotide does not rescue the phenotype, which, in contrast, is reversed by the upregulation of NRF2 by rosiglitazone. The lack of aprataxin causes reduction of the pathway APE1/NRF1/NRF2 and their target genes. APTX-mutant fibroblasts show reduced succinate dehydrogenase. APTX-mutant fibroblasts show reduced levels and biosynthesis of CoQ10. Levels of APE1 are reduced in APTX-mutant and APTX-depleted cells. Phenotype, overview
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged human APTX from Escherichia coli strain Rosetta 2 (DE3) cells by nickel affinity chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant expression of His-tagged human APTX in Escherichia coli strain Rosetta 2 (DE3) cells
transient transfection of XRCC1 wild-type, XPK4, and Xrcc1-/- cells with GFP-tagged APTX. Expression of Myc-NLS-tagged human aprataxin from a plasmid complements HNT3 deletion in Saccharomyces cerevisiae
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
of the two splicing variants of APTX mRNA, the short and the long forms, long-form APTX mRNA is the major isoform
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
medicine
FLJ20157
cells of an ataxia-oculomotor apraxia type 1 patient, homozygous for aprataxin mutation T739C, treated with camptothecin, inhibitor of DNA topoisomerase I which induces DNA single-strand breaks, show marked and dose-related increases in induced chromosomal aberrations compared to the intrafamilial wild-type control
medicine
ataxia-oculomotor apraxia, AOA1, is a neurological disorder with symptoms that overlap those of ataxiatelangiectasia, characterized by abnormal responses to double-strand DNA breaks and genome instability. The gene mutated in AOA1, APTX, codes for aprataxin which contains domains of homology with proteins involved in DNA damage signalling and repair. Cells from AOA1 show enhanced sensitivity to agents that cause single-strand breaks in DNA but there is no evidence for a gross defect in single-strand break repair
medicine
cells from patients with ataxia oculomotor apraxia AOA1 show reduced expression of poly-ADP ribose polymerase PARP-1, apurinic endonuclease APE1 and N-glycosylase/DNA lyase OGG1. AOA1 cells exhibit elevated levels of oxidative DNA damage coupled with reduced base excision and gap filling repair efficiencies
medicine
in cells from patients with ataxia with oculomotor apraxia type 1, AOA1, lacking aprataxin, the stability of nucleolin is significantly reduced
medicine
mutations in aprataxin cause ataxia-ocular apraxia 1, leading to early onset ataxia, oculomotor apraxia and cerebellar atrophy as well as axonal motor neuropathy and the later decrease of serum albumin levels and elevation of total cholesterol
medicine
in bone marrow of patients from a phase 2 study of the farnesyltransferase inhibitor tipifarnib in older adults with previously untreated acute myeloid leukemia, the RASGRP1/APTX gene expression ratio predicts response to tipifarnib with the greatest accuracy. RASGRP1 is a guanine nucleotide exchange factor that activates RAS, while APTX (aprataxin) is involved in DNA excision repair
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Harris, J.L.; Jakob, B.; Taucher-Scholz, G.; Dianov, G.L.; Becherel, O.J.; Lavin, M.F.
Aprataxin, poly-ADP ribose polymerase 1 (PARP-1) and apurinic endonuclease 1 (APE1) function together to protect the genome against oxidative damage
Hum. Mol. Genet.
18
4102-4117
2009
Homo sapiens (Q7Z2E3)
Sano, Y.; Date, H.; Igarashi, S.; Onodera, O.; Oyake, M.; Takahashi, T.; Hayashi, S.; Morimatsu, M.; Takahashi, H.; Makifuchi, T.; Fukuhara, N.; Tsuji, S.
Aprataxin, the causative protein for EAOH is a nuclear protein with a potential role as a DNA repair protein
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2004
Homo sapiens (Q7Z2E3)
Date, H.; Igarashi, S.; Sano, Y.; Takahashi, T.; Takahashi, T.; Takano, H.; Tsuji, S.; Nishizawa, M.; Onodera, O.
The FHA domain of aprataxin interacts with the C-terminal region of XRCC1
Biochem. Biophys. Res. Commun.
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2004
Homo sapiens (Q7Z2E3)
Mosesso, P.; Piane, M.; Palitti, F.; Pepe, G.; Penna, S.; Chessa, L.
The novel human gene aprataxin is directly involved in DNA single-strand-break repair
Cell. Mol. Life Sci.
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2005
Homo sapiens (FLJ20157), Homo sapiens
Gueven, N.; Becherel, O.J.; Kijas, A.W.; Chen, P.; Howe, O.; Rudolph, J.H.; Gatti, R.; Date, H.; Onodera, O.; Taucher-Scholz, G.; Lavin, M.F.
Aprataxin, a novel protein that protects against genotoxic stress
Hum. Mol. Genet.
13
1081-1093
2004
Homo sapiens (Q7Z2E3), Homo sapiens
Becherel, O.J.; Gueven, N.; Birrell, G.W.; Schreiber, V.; Suraweera, A.; Jakob, B.; Taucher-Scholz, G.; Lavin, M.F.
Nucleolar localization of aprataxin is dependent on interaction with nucleolin and on active ribosomal DNA transcription
Hum. Mol. Genet.
15
2239-2249
2006
Homo sapiens (Q7Z2E3), Homo sapiens
Seidle, H.F.; Bieganowski, P.; Brenner, C.
Disease-associated mutations inactivate AMP-lysine hydrolase activity of aprataxin
J. Biol. Chem.
280
20927-20931
2005
Homo sapiens (Q7Z2E3)
Kijas, A.W.; Harris, J.L.; Harris, J.M.; Lavin, M.F.
Aprataxin forms a discrete branch in the HIT (histidine triad) superfamily of proteins with both DNA/RNA binding and nucleotide hydrolase activities
J. Biol. Chem.
281
13939-13948
2006
Homo sapiens (Q7Z2E3)
Moreira, M.C.; Barbot, C.; Tachi, N.; Kozuka, N.; Uchida, E.; Gibson, T.; Mendonca, P.; Costa, M.; Barros, J.; Yanagisawa, T.; Watanabe, M.; Ikeda, Y.; Aoki, M.; Nagata, T.; Coutinho, P.; Sequeiros, J.; Koenig, M.
The gene mutated in ataxia-ocular apraxia 1 encodes the new HIT/Zn-finger protein aprataxin
Nat. Genet.
29
189-193
2001
Homo sapiens (Q7Z2E3)
Tumbale, P.; Williams, J.S.; Schellenberg, M.J.; Kunkel, T.A.; Williams, R.S.
Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity
Nature
506
111-115
2014
Saccharomyces cerevisiae (Q08702), Saccharomyces cerevisiae, Homo sapiens (Q7Z2E3), Homo sapiens, Saccharomyces cerevisiae ATCC 204508 (Q08702)
Becherel, O.J.; Jakob, B.; Cherry, A.L.; Gueven, N.; Fusser, M.; Kijas, A.W.; Peng, C.; Katyal, S.; McKinnon, P.J.; Chen, J.; Epe, B.; Smerdon, S.J.; Taucher-Scholz, G.; Lavin, M.F.
CK2 phosphorylation-dependent interaction between aprataxin and MDC1 in the DNA damage response
Nucleic Acids Res.
38
1489-1503
2010
Homo sapiens (Q7Z2E3)
Hanaoka, K.; Tanaka, W.; Kayanuma, M.; Shoji, M.
A QM/MM study of the 5'-AMP DNA hydrolysis of aprataxin
Chem. Phys. Lett.
631-632
16-20
2015
Homo sapiens (Q7Z2E3)
-
Horton, J.K.; Stefanick, D.F.; Caglayan, M.; Zhao, M.L.; Janoshazi, A.K.; Prasad, R.; Gassman, N.R.; Wilson, S.H.
XRCC1 phosphorylation affects aprataxin recruitment and DNA deadenylation activity
DNA Repair
64
26-33
2018
Saccharomyces cerevisiae (Q08702), Homo sapiens (Q7Z2E3)
Tumbale, P.; Schellenberg, M.; Mueller, G.; Fairweather, E.; Watson, M.; Little, J.; Krahn, J.; Waddell, I.; London, R.; Williams, R.
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Homo sapiens (Q7Z2E3), Homo sapiens
Garcia-Diaz, B.; Barca, E.; Balreira, A.; Lopez, L.C.; Tadesse, S.; Krishna, S.; Naini, A.; Mariotti, C.; Castellotti, B.; Quinzii, C.M.
Lack of aprataxin impairs mitochondrial functions via downregulation of the APE1/NRF1/NRF2 pathway
Hum. Mol. Genet.
24
4516-4529
2015
Homo sapiens (Q7Z2E3), Homo sapiens
Schellenberg, M.J.; Tumbale, P.P.; Williams, R.S.
Molecular underpinnings of Aprataxin RNA/DNA deadenylase function and dysfunction in neurological disease
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117
157-165
2015
Homo sapiens (Q7Z2E3)
Raponi, M.; Lancet, J.E.; Fan, H.; Dossey, L.; Lee, G.; Gojo, I.; Feldman, E.J.; Gotlib, J.; Morris, L.E.; Greenberg, P.L.; Wright, J.J.; Harousseau, J.L.; Loewenberg, B.; Stone, R.M.; De Porre, P.; Wang, Y.; Karp, J.E.
A 2-gene classifier for predicting response to the farnesyltransferase inhibitor tipifarnib in acute myeloid leukemia
Blood
111
2589-2596
2008
Homo sapiens (Q7Z2E3)
Marriott, A.S.; Copeland, N.A.; Cunningham, R.; Wilkinson, M.C.; McLennan, A.G.; Jones, N.J.
Diadenosine 5', 5'''-P(1),P(4)-tetraphosphate (Ap4A) is synthesized in response to DNA damage and inhibits the initiation of DNA replication
DNA Repair
33
90-100
2015
Cricetulus griseus (G3I8V7), Homo sapiens (Q7Z2E3)
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Actions of aprataxin in multiple DNA repair pathways
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282
9469-9474
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Homo sapiens (Q7Z2E3)
Rass, U.; Ahel, I.; West, S.C.
Molecular mechanism of DNA deadenylation by the neurological disease protein aprataxin
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283
33994-34001
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Homo sapiens (Q7Z2E3), Homo sapiens
Tumbale, P.; Jurkiw, T.; Schellenberg, M.; Riccio, A.; O'Brien, P.; Williams, R.
Two-tiered enforcement of high-fidelity DNA ligation
Nat. Commun.
10
5431
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Homo sapiens
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