Selected proteins containing APIM
| Type/group of proteins | Proteins | Source |
| Proteins containing PIP box and APIM | DNA ligase I, MDN1 Midasin, ubiquitin thioesterase FAF-X, protein 18 homologue (hVPS18), cytokine signaling 6 (SOCS-6), Topo II β, IκB-related protein, UHRF2, PARP4 | Moldovan et al., 2007 |
| DNA polymerase | Pol ζ catalytic subunit (hREV3L) | Moldovan et al., 2007 |
| DNA ligases | DNA ligase I, DNA ligase IV | Moldovan et al., 2007 |
| Topo | Topo II α and β | This study; Niimi et al., 2001; Lou et al., 2005 |
| DNA repair proteins | hABH2, PARP-1, -2, and -4, RAD51B, FANCC, XPA | This study; Simbulan-Rosenthal et al., 1999; Jacquemont and Taniguchi, 2007 |
| DNA repair–associated/ interacting proteins | XPA-binding protein 2, BRCA1/BRCA2-containing complex subunit 45 (prot-BRE), x-ray radiation resistance-associated protein 1 | NA |
| Sister chromatid cohesion | N-acetyltransferase ESCO1/EFO1, hSMC5 | Potts et al., 2006; Moldovan et al., 2007 |
| Chromatin remodelling and DNA-binding proteins | Chromodomain helicase DNA-binding proteins 3–5, p325 subunit of remodeling and spacing factor chromatin–remodelling complex, telomeric repeat–binding protein 2 (TRF2) | Opresko et al., 2004 |
| E3 ubiquitin ligases | UHFR1, UHFR2, UBR1, UBR2, ring finger proteins 3, 17, and 151, probable E3 ubiquitin protein ligase MYCBP2 | Bronner et al., 2007 |
| Transcription factors | TFIIS-L, TFII-I, TFIIE-α, sterol regulatory element-binding transcription factor 2 (SREBF2), TFIIIC subunit α, TFIID 100 kD subunit (TAF5), TFIIIC 102 kD subunit (TF3C γ), transcription factor–like protein MRG15 and X (mortality factor 4–like proteins 1 and 2), E2 transcription factor 7 | This study |
| Cell cycle regulators | Cell division cycle-associated 2, Bcl2-interacting mediator of cell death, testis spermatocyte apoptosis-related gene 2 protein | NA |
| Protein kinases | Serine/threonine (S/T) protein kinases SRPK1 and -2, 33 and MST4, leucine-rich repeat S/T protein kinase 1, STK23 (S/T protein kinase 23), S/T protein kinase PLK3, microtubuli-associated S/T protein kinase, microtubuli-associated S/T protein kinase 1, MAPKAP kinase 2 (MK2) and 5 (MK5), mitogen-activated protein kinase 15 (MSK-15) | NA |
| Methyltransferase | H3 lysine 4–specific MLL3, H3-K9 methyltransferase 5, putative rRNA methyltransferase 3 | NA |
| Cancer-associated antigens | Melanoma-associated antigen E1 (MAGE E1), MAGE B18, MAGE-G1, natural killer tumor recognition protein (NK-TR), Myc-binding protein–associated protein, Myb-binding protein 1A, hepatoma-derived growth factor–related protein 2 isoform1, serologically defined colon cancer antigen 1 | NA |
| RNA polymerase and ribosome-associated proteins | RNA polymerase II, largest subunit (RPB1), RNA polymerase III subunit 5 (RPC5), RNA polymerase II 140 kD (RPB2), UTP14A U3 small nucleolar RNA-associated protein 14 homologue A, 60S ribosomal protein L18, 60S ribosomal protein L35, TAF5-like RNA polymerase II p300 (PAF65-beta), mediator of RNA polymerase II transcription subunit 12 homologue | NA |
| Type/group of proteins | Proteins | Source |
| Proteins containing PIP box and APIM | DNA ligase I, MDN1 Midasin, ubiquitin thioesterase FAF-X, protein 18 homologue (hVPS18), cytokine signaling 6 (SOCS-6), Topo II β, IκB-related protein, UHRF2, PARP4 | Moldovan et al., 2007 |
| DNA polymerase | Pol ζ catalytic subunit (hREV3L) | Moldovan et al., 2007 |
| DNA ligases | DNA ligase I, DNA ligase IV | Moldovan et al., 2007 |
| Topo | Topo II α and β | This study; Niimi et al., 2001; Lou et al., 2005 |
| DNA repair proteins | hABH2, PARP-1, -2, and -4, RAD51B, FANCC, XPA | This study; Simbulan-Rosenthal et al., 1999; Jacquemont and Taniguchi, 2007 |
| DNA repair–associated/ interacting proteins | XPA-binding protein 2, BRCA1/BRCA2-containing complex subunit 45 (prot-BRE), x-ray radiation resistance-associated protein 1 | NA |
| Sister chromatid cohesion | N-acetyltransferase ESCO1/EFO1, hSMC5 | Potts et al., 2006; Moldovan et al., 2007 |
| Chromatin remodelling and DNA-binding proteins | Chromodomain helicase DNA-binding proteins 3–5, p325 subunit of remodeling and spacing factor chromatin–remodelling complex, telomeric repeat–binding protein 2 (TRF2) | Opresko et al., 2004 |
| E3 ubiquitin ligases | UHFR1, UHFR2, UBR1, UBR2, ring finger proteins 3, 17, and 151, probable E3 ubiquitin protein ligase MYCBP2 | Bronner et al., 2007 |
| Transcription factors | TFIIS-L, TFII-I, TFIIE-α, sterol regulatory element-binding transcription factor 2 (SREBF2), TFIIIC subunit α, TFIID 100 kD subunit (TAF5), TFIIIC 102 kD subunit (TF3C γ), transcription factor–like protein MRG15 and X (mortality factor 4–like proteins 1 and 2), E2 transcription factor 7 | This study |
| Cell cycle regulators | Cell division cycle-associated 2, Bcl2-interacting mediator of cell death, testis spermatocyte apoptosis-related gene 2 protein | NA |
| Protein kinases | Serine/threonine (S/T) protein kinases SRPK1 and -2, 33 and MST4, leucine-rich repeat S/T protein kinase 1, STK23 (S/T protein kinase 23), S/T protein kinase PLK3, microtubuli-associated S/T protein kinase, microtubuli-associated S/T protein kinase 1, MAPKAP kinase 2 (MK2) and 5 (MK5), mitogen-activated protein kinase 15 (MSK-15) | NA |
| Methyltransferase | H3 lysine 4–specific MLL3, H3-K9 methyltransferase 5, putative rRNA methyltransferase 3 | NA |
| Cancer-associated antigens | Melanoma-associated antigen E1 (MAGE E1), MAGE B18, MAGE-G1, natural killer tumor recognition protein (NK-TR), Myc-binding protein–associated protein, Myb-binding protein 1A, hepatoma-derived growth factor–related protein 2 isoform1, serologically defined colon cancer antigen 1 | NA |
| RNA polymerase and ribosome-associated proteins | RNA polymerase II, largest subunit (RPB1), RNA polymerase III subunit 5 (RPC5), RNA polymerase II 140 kD (RPB2), UTP14A U3 small nucleolar RNA-associated protein 14 homologue A, 60S ribosomal protein L18, 60S ribosomal protein L35, TAF5-like RNA polymerase II p300 (PAF65-beta), mediator of RNA polymerase II transcription subunit 12 homologue | NA |
NA, not applicable. Bold indicates proteins localized in replication foci under normal conditions or after DNA damage. The full lists of hits for the APIM and PIP motifs are available at http://tare.medisin.ntnu.no/pcna/index.php.