Enzymes
| UniProtKB help_outline | 7,517 proteins |
| GO Molecular Function help_outline |
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Reaction participants Show >> << Hide
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Namehelp_outline
a 5'-end 2'-deoxyribose-2'-deoxyribonucleotide-DNA
Identifier
RHEA-COMP:18657
Reactive part
help_outline
- Name help_outline a 5'-end 2'-deoxyribose-deoxyribonucleotide residue Identifier CHEBI:195194 Charge -3 Formula C10H15O12P2R SMILEShelp_outline [O-]P(OC[C@H]1O[C@@H](O)C[C@@H]1OP(OC[C@H]2O[C@@H](*)C[C@@H]2O*)([O-])=O)([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 2 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline (2E,4S)-4-hydroxypenten-2-al-5-phosphate Identifier CHEBI:195195 Charge -2 Formula C5H7O6P InChIKeyhelp_outline XGGCBXHNTNZKEL-WYPBCBNTSA-L SMILEShelp_outline O=C/C=C/[C@@H](COP([O-])(=O)[O-])O 2D coordinates Mol file for the small molecule Search links Involved in 1 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
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Namehelp_outline
a 5'-end 5'-phospho-2'-deoxyribonucleoside-DNA
Identifier
RHEA-COMP:13180
Reactive part
help_outline
- Name help_outline 5'-phosphate 2'-deoxynucleoside residue Identifier CHEBI:136412 Charge -2 Formula C5H7O6PR SMILEShelp_outline *[C@@H]1O[C@H](COP(=O)([O-])[O-])[C@@H](O*)C1 2D coordinates Mol file for the small molecule Search links Involved in 9 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline H+ Identifier CHEBI:15378 Charge 1 Formula H InChIKeyhelp_outline GPRLSGONYQIRFK-UHFFFAOYSA-N SMILEShelp_outline [H+] 2D coordinates Mol file for the small molecule Search links Involved in 9,932 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Cross-references
| RHEA:76255 | RHEA:76256 | RHEA:76257 | RHEA:76258 | |
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| Reaction direction help_outline | undefined | left-to-right | right-to-left | bidirectional |
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Publications
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Human DNA polymerase beta deoxyribose phosphate lyase. Substrate specificity and catalytic mechanism.
Prasad R., Beard W.A., Strauss P.R., Wilson S.H.
DNA polymerase beta (beta-pol) cleaves the sugar-phosphate bond 3' to an intact apurinic/apyrimidinic (AP) site (i.e. AP lyase activity). The same bond is cleaved even if the AP site has been previously 5'-incised by AP endonuclease, resulting in a 5' 2-deoxyribose 5-phosphate (i.e. dRP lyase acti ... >> More
DNA polymerase beta (beta-pol) cleaves the sugar-phosphate bond 3' to an intact apurinic/apyrimidinic (AP) site (i.e. AP lyase activity). The same bond is cleaved even if the AP site has been previously 5'-incised by AP endonuclease, resulting in a 5' 2-deoxyribose 5-phosphate (i.e. dRP lyase activity). We characterized these lyase reactions by steady-state kinetics with the amino-terminal 8-kDa domain of beta-pol and with the entire 39-kDa polymerase. Steady-state kinetic analyses show that the Michaelis constants for both the dRP and AP lyase activities of beta-pol are similar. However, kcat is approximately 200-fold lower for the AP lyase activity on an intact AP site than for an AP endonuclease-preincised site. The 8-kDa domain was also less efficient with an intact AP site than on a preincised site. The full-length enzyme and the 8-kDa domain efficiently remove the 5' dRP from a preincised AP site in the absence of Mg2+, and the pH profiles of beta-pol and 8-kDa domain dRP lyase catalytic efficiency exhibit a broad alkaline pH optimum. An inhibitory effect of pyridoxal 5'-phosphate on the dRP lyase activity is consistent with involvement of a primary amine (Lys72) as the Schiff base nucleophile during lyase chemistry. << Less
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5'-deoxyribose phosphate lyase activity of human DNA polymerase iota in vitro.
Bebenek K., Tissier A., Frank E.G., McDonald J.P., Prasad R., Wilson S.H., Woodgate R., Kunkel T.A.
DNA polymerase iota (pol iota) is one of several recently discovered DNA polymerases in mammalian cells whose function is unknown. We report here that human pol iota has an intrinsic 5'-deoxyribose phosphate (dRP) lyase activity. In reactions reconstituted with uracil-DNA glycosylase (UDG), apurin ... >> More
DNA polymerase iota (pol iota) is one of several recently discovered DNA polymerases in mammalian cells whose function is unknown. We report here that human pol iota has an intrinsic 5'-deoxyribose phosphate (dRP) lyase activity. In reactions reconstituted with uracil-DNA glycosylase (UDG), apurinic/apyrimidinic (AP) endonuclease and DNA ligase I, pol iota can use its dRP lyase and polymerase activities to repair G*U and A*U pairs in DNA. These data and three distinct catalytic properties of pol iota implicate it in specialized forms of base excision repair (BER). << Less