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Sep. 10, 2014:
A total of 174 experimentally verified S-nitrosylation sites on 94 S-nitrosylated proteins from individualized human colorectal cancer tissues using a label-free quantitation strategy.

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Protein Name: DNA-dependent protein kinase catalytic subunit

UniprotKB/SwissProt ID: P78527 (P78527)

Gene Name: PRKDC

Organism: Homo sapiens (Human)

Function: Serine/threonine-protein kinase that acts as a molecular sensor for DNA damage (PubMed:11955432, PubMed:12649176, PubMed:14734805, PubMed:33854234). Involved in DNA non-homologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination (PubMed:11955432, PubMed:12649176, PubMed:14734805, PubMed:33854234, PubMed:34352203). Must be bound to DNA to express its catalytic properties (PubMed:11955432). Promotes processing of hairpin DNA structures in V(D)J recombination by activation of the hairpin endonuclease artemis (DCLRE1C) (PubMed:11955432). Recruited by XRCC5 and XRCC6 to DNA ends and is required to (1) protect and align broken ends of DNA, thereby preventing their degradation, (2) and sequester the DSB for repair by NHEJ (PubMed:11955432, PubMed:12649176, PubMed:14734805, PubMed:15574326, PubMed:33854234). Acts as a scaffold protein to aid the localization of DNA repair proteins to the site of damage (PubMed:11955432, PubMed:12649176, PubMed:14734805, PubMed:15574326). The assembly of the DNA-PK complex at DNA ends is also required for the NHEJ ligation step (PubMed:11955432, PubMed:12649176, PubMed:14734805, PubMed:15574326). Found at the ends of chromosomes, suggesting a further role in the maintenance of telomeric stability and the prevention of chromosomal end fusion (By similarity). Also involved in modulation of transcription (PubMed:11955432, PubMed:12649176, PubMed:14734805, PubMed:15574326). As part of the DNA-PK complex, involved in the early steps of ribosome assembly by promoting the processing of precursor rRNA into mature 18S rRNA in the small-subunit processome (PubMed:32103174). Binding to U3 small nucleolar RNA, recruits PRKDC and XRCC5/Ku86 to the small-subunit processome (PubMed:32103174). Recognizes the substrate consensus sequence [ST]-Q (PubMed:11955432, PubMed:12649176, PubMed:14734805, PubMed:15574326). Phosphorylates 'Ser-139' of histone variant H2AX, thereby regulating DNA damage response mechanism (PubMed:14627815, PubMed:16046194). Phosphorylates ASF1A, DCLRE1C, c-Abl/ABL1, histone H1, HSPCA, c-jun/JUN, p53/TP53, PARP1, POU2F1, DHX9, FH, SRF, NHEJ1/XLF, XRCC1, XRCC4, XRCC5, XRCC6, WRN, MYC and RFA2 (PubMed:10026262, PubMed:10467406, PubMed:11889123, PubMed:12509254, PubMed:14599745, PubMed:14612514, PubMed:14704337, PubMed:15177042, PubMed:1597196, PubMed:16397295, PubMed:18644470, PubMed:2247066, PubMed:2507541, PubMed:26237645, PubMed:26666690, PubMed:28712728, PubMed:29478807, PubMed:30247612, PubMed:8407951, PubMed:8464713, PubMed:9139719, PubMed:9362500). Can phosphorylate C1D not only in the presence of linear DNA but also in the presence of supercoiled DNA (PubMed:9679063). Ability to phosphorylate p53/TP53 in the presence of supercoiled DNA is dependent on C1D (PubMed:9363941). Acts as a regulator of the phosphatidylinositol 3-kinase/protein kinase B signal transduction by mediating phosphorylation of 'Ser-473' of protein kinase B (PKB/AKT1, PKB/AKT2, PKB/AKT3), promoting their activation (PubMed:15262962). Contributes to the determination of the circadian period length by antagonizing phosphorylation of CRY1 'Ser-588' and increasing CRY1 protein stability, most likely through an indirect mechanism (By similarity). Plays a role in the regulation of DNA virus-mediated innate immune response by assembling into the HDP-RNP complex, a complex that serves as a platform for IRF3 phosphorylation and subsequent innate immune response activation through the cGAS-STING pathway (PubMed:28712728). Also regulates the cGAS-STING pathway by catalyzing phosphorylation of CGAS, thereby impairing CGAS oligomerization and activation (PubMed:33273464). Also regulates the cGAS-STING pathway by mediating phosphorylation of PARP1 (PubMed:35460603)

Other Modifications: View all modification sites in dbPTM

Protein Subcellular Localization: Nucleus. Nucleus, nucleolus. Cytoplasm, cytosol

Graphical Visualization of S-nitrosylation Sites:
InterPro ID Domain Name
IPR011989 ARM-like
IPR016024 ARM-type_fold
IPR050517 DDR_Repair_Kinase
IPR037706 DNA-PK_dom
IPR046804 DNA-PKcs_N
IPR046803 DNAPKcs_CC1-2
IPR012582 DNAPKcs_CC3
IPR045581 DNAPKcs_CC5
IPR003152 FATC_dom
IPR011009 Kinase-like_dom_sf
IPR000403 PI3/4_kinase_cat_dom
IPR036940 PI3/4_kinase_cat_sf
IPR018936 PI3/4_kinase_CS
IPR003151 PIK-rel_kinase_FAT
IPR014009 PIK_FAT

The S-nitrosylation sites of P78527

No. Position S-nitrosylated Peptide Secondary Structure of S-nitrosylated Peptide Solvent Accessibility of nitrosylated Site PubMed ID
1 111 APYSVEIKNT C TSVYTKDRAA  CCCCCHHHHH H HHHHHHHHCH  3.59%
2 1135 QQCCDAIDHL C RIIEKKHVSL  CCCCCHHHHH H HHHHHHHHCH  2.35%
3 1229 FLINTFEGGG C GQPSGILAQP  CCCCCHHHHH H HHHHHHHHCH  5.31%
4 1312 AMHDIIAAEK C FGTGAAGNRT  CCCCCHHHHH H HHHHHHHHCH  2.6%
5 1335 QEGERYNYSK C TVVVRIMEFT  CCCCCHHHHH H HHHHHHHHCH  2.61%
6 1364 EGWKLLKKDL C NTHLMRVLVQ  CCCCCHHHHH H HHHHHHHHCH  8.72%
7 1432 KITAQSIEEL C AVNLYGPDAQ  CCCCCHHHHH H HHHHHHHHCH  4.49%
8 1455 RSRLAAVVSA C KQLHRAGLLH  CCCCCHHHHH H HHHHHHHHCH  1.94%
9 1499 KGIAPGDERQ C LPSLDLSCKQ  CCCCCHHHHH H HHHHHHHHCH  8.27% 19483679
10 1507 RQCLPSLDLS C KQLASGLLEL  CCCCCHHHHH H HHHHHHHHCH  4.18% 19483679
11 1629 ATTILQHWKK C DSWWAKDSPL  CCCCCHHHHH H HHHHHHHHCH  4.44%
12 1742 GTPRFNNYVD C MKKFLDALEL  CCCCCHHHHH H HHHHHHHHCH  2.84%
13 1767 MLLELMTEVL C REQQHVMEEL  CCCCCHHHHH H HHHHHHHHCH  5.63%
14 1791 SFRRIARRGS C VTQVGLLESV  CCCCCHHHHH H HHHHHHHHCH  4.23%
15 1904 SKINQVFHGS C ITEGNELTKT  CCCCCHHHHH H HHHHHHHHCH  5.44%
16 1919 NELTKTLIKL C YDAFTENMAG  CCCCCHHHHH H HHHHHHHHCH  2.16%
17 2093 LEMDELNRHE C MAPLTALVKH  CCCCCHHHHH H HHHHHHHHCH  2%
18 223 REPKLPVLAG C LKGLSSLLCN  CCCCCHHHHH H HHHHHHHHCH  2.7%
19 2244 NLEIIKTLVE C WKDCLSIPYR  CCCCCHHHHH H HHHHHHHHCH  4.22%
20 2248 IKTLVECWKD C LSIPYRLIFE  CCCCCHHHHH H HHHHHHHHCH  2.59%
21 232 GCLKGLSSLL C NFTKSMEEDP  CCCCCHHHHH H HHHHHHHHCH  4.83%
22 2342 ERKNILEESL C ELVAKQLKQH  CCCCCHHHHH H HHHHHHHHCH  5.45% 19483679
23 2435 RHRDDERQKV C LDIIYKMMPK  CCCCCHHHHH H HHHHHHHHCH  3.49%
24 2469 VEFVSHPSTT C REQMYNILMW  CCCCCHHHHH H HHHHHHHHCH  4.58%
25 25 LQETLSAADR C GAALAGHQLI  CCCCCHHHHH H HHHHHHHHCH  4.47% 19483679
37478858
26 3014 HLAEWKSLEY C STASIDSENP  CCCCCHHHHH H HHHHHHHHCH  1.81%
27 3187 NIWDDIITNR C FFLSKIEEKL  CCCCCHHHHH H HHHHHHHHCH  2.83% 19483679
28 3281 DWLVSWVQSY C RLSHCRSRSQ  CCCCCHHHHH H HHHHHHHHCH  4.23%
29 3286 WVQSYCRLSH C RSRSQGCSEQ  CCCCCHHHHH H HHHHHHHHCH  3.67%
30 3293 LSHCRSRSQG C SEQVLTVLKT  CCCCCHHHHH H HHHHHHHHCH  2.91% 2212679
31 3347 IANALSSEPA C LAEIEEDKAR  CCCCCHHHHH H HHHHHHHHCH  5.6% 19483679
32 3683 DSKPPGNLKE C SPWMSDFKVE  CCCCCHHHHH H HHHHHHHHCH  5.91%
33 373 IRGYGLFAGP C KVINAKDVDF  CCCCCHHHHH H HHHHHHHHCH  5.56%
34 3781 MNGILAQDSA C SQRALQLRTY  CCCCCHHHHH H HHHHHHHHCH  4.05%
35 3837 AYLSDPRAPP C EYKDWLTKMS  CCCCCHHHHH H HHHHHHHHCH  9.69%
36 4045 EKNWYPRQKI C YAKRKLAGAN  CCCCCHHHHH H HHHHHHHHCH  3.3% 19483679
37 4061 LAGANPAVIT C DELLLGHEKA  CCCCCHHHHH H HHHHHHHHCH  2.35%
38 4106 SGLSEETQVK C LMDQATDPNI  CCCCCHHHHH H HHHHHHHHCH  3.9% 37478858
39 42 HQLIRGLGQE C VLSSSPAVLA  CCCCCHHHHH H HHHHHHHHCH  2.61%
40 458 QYSPKMQLVC C RAIVKVFLAL  CCCCCHHHHH H HHHHHHHHCH  2.28%
41 478 LAAKGPVLRN C ISTVVHQGLI  CCCCCHHHHH H HHHHHHHHCH  1.78% 19483679
42 491 TVVHQGLIRI C SKPVVLPKGP  CCCCCHHHHH H HHHHHHHHCH  2.84%
43 630 FSAFINLVEF C REILPEKQAE  CCCCCHHHHH H HHHHHHHHCH  2.12%
44 795 MQPYYKDILP C LDGYLKTSAL  CCCCCHHHHH H HHHHHHHHCH  4.92% 19483679
45 90 ECREEILKFL C IFLEKMGQKI  CCCCCHHHHH H HHHHHHHHCH  2.02%
46 974 RTFPVLLRLA C DVDQVTRQLY  CCCCCHHHHH H HHHHHHHHCH  6.57%