P04819
PR
Gene name |
CDC9 (YDL164C) |
Protein name |
DNA ligase 1 |
Names |
DNA ligase I, Polydeoxyribonucleotide synthase [ATP] 1 |
Species |
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
KEGG Pathway |
sce:YDL164C |
EC number |
6.5.1.1: Forming phosphoric ester bonds |
Protein Class |
|
Descriptions
The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.
Autoinhibitory domains (AIDs)
Target domain |
|
Relief mechanism |
|
Assay |
cis-regPred |
Accessory elements
No accessory elements
Autoinhibited structure
Activated structure
2 structures for P04819
| Entry ID | Method | Resolution | Chain | Position | Source |
|---|---|---|---|---|---|
| 2OD8 | X-ray | 280 A | B | 32-53 | PDB |
| AF-P04819-F1 | Predicted | AlphaFoldDB |
9 variants for P04819
| Variant ID(s) | Position | Change | Description | Diseaes Association | Provenance |
|---|---|---|---|---|---|
| s04-167227 | 10 | L>H | No | SGRP | |
| s04-167183 | 25 | S>P | No | SGRP | |
| s04-167140 | 39 | A>V | No | SGRP | |
| s04-167092 | 55 | G>D | No | SGRP | |
| s04-167049 | 69 | D>E | No | SGRP | |
| s04-167026 | 77 | E>G | No | SGRP | |
| s04-166775 | 161 | I>L | No | SGRP | |
| s04-165976 | 427 | V>A | No | SGRP | |
| s04-165033 | 741 | D>E | No | SGRP |
No associated diseases with P04819
5 regional properties for P04819
| Type | Name | Position | InterPro Accession |
|---|---|---|---|
| domain | DNA ligase, ATP-dependent, N-terminal | 147 - 323 | IPR012308 |
| domain | DNA ligase, ATP-dependent, C-terminal | 623 - 732 | IPR012309 |
| domain | DNA ligase, ATP-dependent, central | 393 - 636 | IPR012310 |
| conserved_site | DNA ligase, ATP-dependent, conserved site | 417 - 425 | IPR016059-1 |
| conserved_site | DNA ligase, ATP-dependent, conserved site | 571 - 598 | IPR016059-2 |
Functions
| Description | ||
|---|---|---|
| EC Number | 6.5.1.1 | Forming phosphoric ester bonds |
| Subcellular Localization |
|
|
| PANTHER Family | ||
| PANTHER Subfamily | ||
| PANTHER Protein Class | ||
| PANTHER Pathway Category | No pathway information available | |
3 GO annotations of cellular component
| Name | Definition |
|---|---|
| cytoplasm | The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. |
| mitochondrion | A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. |
| nucleus | A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. |
4 GO annotations of molecular function
| Name | Definition |
|---|---|
| ATP binding | Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. |
| DNA binding | Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). |
| DNA ligase (ATP) activity | Catalysis of the reaction: ATP + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + diphosphate + deoxyribonucleotide(n+m). |
| metal ion binding | Binding to a metal ion. |
10 GO annotations of biological process
| Name | Definition |
|---|---|
| base-excision repair | In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. |
| cell division | The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. |
| DNA biosynthetic process | The biosynthetic process resulting in the formation of DNA. |
| DNA ligation | The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase. |
| DNA recombination | Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction. |
| lagging strand elongation | The process in which an existing DNA strand is extended in a net 3' to 5' direction by activities including the addition of nucleotides to the 3' end of the strand, complementary to an existing template, as part of DNA replication. Lagging strand DNA elongation proceeds by discontinuous synthesis of short stretches of DNA, known as Okazaki fragments, from RNA primers; these fragments are then joined by DNA ligase. Although each segment of nascent DNA is synthesized in the 5' to 3' direction, the overall direction of lagging strand synthesis is 3' to 5', mirroring the progress of the replication fork. |
| maintenance of DNA trinucleotide repeats | Any process involved in sustaining the fidelity and copy number of DNA trinucleotide repeats. DNA trinucleotide repeats are naturally occurring runs of three base-pairs. |
| mitotic cell cycle | Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. |
| nucleotide-excision repair | A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts). |
| Okazaki fragment processing involved in mitotic DNA replication | Any DNA replication, Okazaki fragment processing that is involved in mitotic cell cycle DNA replication. |
4 homologous proteins in AiPD
| 10 | 20 | 30 | 40 | 50 | 60 |
| MRRLLTGCLL | SSARPLKSRL | PLLMSSSLPS | SAGKKPKQAT | LARFFTSMKN | KPTEGTPSPK |
| 70 | 80 | 90 | 100 | 110 | 120 |
| KSSKHMLEDR | MDNVSGEEEY | ATKKLKQTAV | THTVAAPSSM | GSNFSSIPSS | APSSGVADSP |
| 130 | 140 | 150 | 160 | 170 | 180 |
| QQSQRLVGEV | EDALSSNNND | HYSSNIPYSE | VCEVFNKIEA | ISSRLEIIRI | CSDFFIKIMK |
| 190 | 200 | 210 | 220 | 230 | 240 |
| QSSKNLIPTT | YLFINRLGPD | YEAGLELGLG | ENLLMKTISE | TCGKSMSQIK | LKYKDIGDLG |
| 250 | 260 | 270 | 280 | 290 | 300 |
| EIAMGARNVQ | PTMFKPKPLT | VGEVFKNLRA | IAKTQGKDSQ | LKKMKLIKRM | LTACKGIEAK |
| 310 | 320 | 330 | 340 | 350 | 360 |
| FLIRSLESKL | RIGLAEKTVL | ISLSKALLLH | DENREDSPDK | DVPMDVLESA | QQKIRDAFCQ |
| 370 | 380 | 390 | 400 | 410 | 420 |
| VPNYEIVINS | CLEHGIMNLD | KYCTLRPGIP | LKPMLAKPTK | AINEVLDRFQ | GETFTSEYKY |
| 430 | 440 | 450 | 460 | 470 | 480 |
| DGERAQVHLL | NDGTMRIYSR | NGENMTERYP | EINITDFIQD | LDTTKNLILD | CEAVAWDKDQ |
| 490 | 500 | 510 | 520 | 530 | 540 |
| GKILPFQVLS | TRKRKDVELN | DVKVKVCLFA | FDILCYNDER | LINKSLKERR | EYLTKVTKVV |
| 550 | 560 | 570 | 580 | 590 | 600 |
| PGEFQYATQI | TTNNLDELQK | FLDESVNHSC | EGLMVKMLEG | PESHYEPSKR | SRNWLKLKKD |
| 610 | 620 | 630 | 640 | 650 | 660 |
| YLEGVGDSLD | LCVLGAYYGR | GKRTGTYGGF | LLGCYNQDTG | EFETCCKIGT | GFSDEMLQLL |
| 670 | 680 | 690 | 700 | 710 | 720 |
| HDRLTPTIID | GPKATFVFDS | SAEPDVWFEP | TTLFEVLTAD | LSLSPIYKAG | SATFDKGVSL |
| 730 | 740 | 750 | |||
| RFPRFLRIRE | DKGVEDATSS | DQIVELYENQ | SHMQN |