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PR01839

Identifier
RAD23PROTEIN  [View Relations]  [View Alignment]  
Accession
PR01839
No. of Motifs
4
Creation Date
14-JAN-2003
Title
DNA repair protein Rad23 signature 
Database References

PRODOM; PD007144
INTERPRO; IPR004806
PDB; 1DV0; 1IFY
SCOP; 1DV0; 1IFY
CATH; 1DV0; 1IFY
MIM; 600062; 600061
Literature References
1. BERTOLAET, B.L., CLARKE, D.J., WOLFF, M., WATSON, M.H., HENZE, M., 
DIVITA, G. AND REED, S.I.
UBA domains of DNA damage-inducible proteins interact with ubiquitin.
NAT.STRUCT.BIOL. 8 417-422 (2001).
 
2. ELDER, R.T., SONG, X.Q., CHEN, M., HOPKINS, K.M., LIEBERMAN H.B.
AND ZHAO, Y.
Involvement of rhp23, a Schizosaccharomyces pombe homolog of the human 
HHR23A and Saccharomyces cerevisiae RAD23 nucleotide excision repair genes,
in cell cycle control and protein ubiquitination.
NUCLEIC ACIDS RES. 30 581-591 (2002).
 
3. NABIROCHKINA, E.N., GRISHCHUK, A.L. AND SOLDATOV, A.V.
Cloning and characterization of the homologue of the Saccharomyces cerevisiae 
gene in Drosophila melanogaster
GENETIKA 35 1012-1015 (1999). 
 
4. GUZDER, S.N., HABRAKEN, Y., SUNG, P., PRAKASH, L. AND PRAKASH, S.
Reconstitution of yeast nucleotide excision repair with purified Rad proteins,
replication protein A, and transcription factor TFIIH.
J.BIOL.CHEM. 270 12973-12976 (1995).
 
5. CHEN, L. AND MADURA, K.
Rad23 promotes the targeting of proteolytic substrates to the proteasome.
MOL.CELL BIOL. 22 4902-4913 (2002).
 
6. RAASI, S. AND PICKART, C.M.
Rad23 UBA domains inhibit 26S proteasome-catalyzed proteolysis by 
sequestering lysine 48-linked polyubiquitin chains.
J.BIOL.CHEM. 278(11) 8951-8959 (2003).
 
7.ELSASSER, S., GALI, R.R., SCHWICKART, M., LARSER, C.N., LEGGETT, D.S.,
MULLER, B., FENG, M.T., TUBING, F., DITTMAR, G.A. AND FINLEY, D.
Proteasome subunit Rpn1 binds ubiquitin-like protein domains.
NAT.CELL BIOL. 4 725-730 (2002).

Documentation
Rad23 is a highly conserved protein involved in nucleotide excision repair 
(NER) [1,2]. It is believed that Rad23 is present in all eukaryotic 
organisms from yeast to mammals [3], and the NER machinery has been 
conserved in structure and function from yeast to humans [4]. In humans,  
defective NER is the underlying cause of the cancer-related disease
xeroderma pigmentosum [4].
 
In order to facilitate assembly of the DNA repair complex on UV-damaged
DNA, Rad23 binds DNA repair factors that play essential roles in NER and 
specifically interacts with Rad4 [5].
 
Rad23 possesses an N-terminal ubiquitin-like domain (UBL(R23)) and a 
C-terminal ubiquitin-associated domain (UBA). UBLs interact with  
catalytically active 26S proteasomes, while UBAs bind to polyubiquitin  
chains [1,5,6]. A component of the base subcomplex of the regulatory 
particle of the proteasome, Rnp1, specifically recognises the UbL domain 
of Rad23 through its leucine-rich-repeat-like (LRR-like) domain. Thus, UBL  
mediates the binding of Rad23 to proteasomes, which in turn promotes DNA 
repair and modulates protein degradation, possibly by delivering 
ubiquitinylated cargo to proteasomes [7]. The UBA domain is less understood.
It has been shown that the synergistic action of its UBA domains, allows 
Rad23 to interact with ubiquitinated cellular proteins [1,5]. Recently, 
UBA domains have been shown to inhibit 26S proteasome-catalysed proteolysis
by sequestering lysine 48-linked polyubiquitin chains [6].
 
RAD23PROTEIN is a 4-element fingerprint that provides a signature for the
DNA repair Rad23 proteins. The fingerprint was derived from an initial
alignment of 19 sequences: the motifs were drawn from conserved regions
toward the C-terminal portion of the alignment - motifs 2-4 span the second
UBA domain. Two iterations on SPTR40_20f were required to reach convergence,
at which point a true set comprising 22 sequences was identified.
Summary Information
22 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
422222222
30000
20000
1234
True Positives
O03990        O03991        O74803        O97135        
Q23451 Q40742 Q8WUB0 Q94C35
Q94CE9 Q9FF16 Q9M887 Q9MA10
Q9SA20 Q9STA6 Q9V3W9 Q9VCD5
Q9XZE0 R23A_HUMAN R23A_MOUSE R23B_HUMAN
R23B_MOUSE RA23_YEAST
Sequence Titles
O03990      RAD23, ISOFORM I - Daucus carota (Carrot).    
O03991 RAD23 PROTEIN, ISOFORM II - Daucus carota (Carrot).
O74803 UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG - Schizosaccharomyces pombe (Fission yeast).
O97135 REPC-BINDING PROTEIN A - Dictyostelium discoideum (Slime mold).
Q23451 ZK20.3 PROTEIN - Caenorhabditis elegans.
Q40742 OSRAD23 - Oryza sativa (Rice).
Q8WUB0 RAD23 HOMOLOG B (S. CEREVISIAE) - Homo sapiens (Human).
Q94C35 HYPOTHETICAL 40.1 KDA PROTEIN - Arabidopsis thaliana (Mouse-ear cress).
Q94CE9 PUTATIVE RAD23 PROTEIN - Arabidopsis thaliana (Mouse-ear cress).
Q9FF16 DNA REPAIR PROTEIN RAD23 HOMOLOG (HYPOTHETICAL 40.1 KDA PROTEIN) - Arabidopsis thaliana (Mouse-ear cress).
Q9M887 PUTATIVE RAD23 (AT3G02540/F16B3_17) - Arabidopsis thaliana (Mouse-ear cress).
Q9MA10 F20B17.8 - Arabidopsis thaliana (Mouse-ear cress).
Q9SA20 F3O9.1 PROTEIN - Arabidopsis thaliana (Mouse-ear cress).
Q9STA6 RAD23 PROTEIN - Lycopersicon esculentum (Tomato).
Q9V3W9 RAD23 PROTEIN - Drosophila melanogaster (Fruit fly).
Q9VCD5 CG10694 PROTEIN - Drosophila melanogaster (Fruit fly).
Q9XZE0 DHR23 - Drosophila melanogaster (Fruit fly).
R23A_HUMAN UV excision repair protein RAD23 homolog A (HHR23A) - Homo sapiens (Human).
R23A_MOUSE UV excision repair protein RAD23 homolog A (MHR23A) - Mus musculus (Mouse).
R23B_HUMAN UV excision repair protein RAD23 homolog B (HHR23B) (XP-C repair complementing complex 58 kDa protein) (P58) - Homo sapiens (Human).
R23B_MOUSE UV excision repair protein RAD23 homolog B (MHR23B) (XP-C repair complementing complex 58 kDa protein) (P58) - Mus musculus (Mouse).
RA23_YEAST UV excision repair protein RAD23 - Saccharomyces cerevisiae (Baker's yeast).
Scan History
SPTR40_20f 2  300  NSINGLE    
Initial Motifs
Motif 1  width=23
Element Seqn Id St Int Rpt
MLQELGKQNPHLMRLIQEHQPDF Q9STA6 291 291 -
MLQELGKQNPQLLRLIQENQAEF Q9MA10 266 266 -
LLQQLGQENPQLLQQISRHQEQF R23A_HUMAN 258 258 -
LLQQLGQENPQLLQQISRHQEQF R23A_MOUSE 258 258 -
MLQELGKQNPHLMRLIQEHQADF O03990 289 289 -
MLQELGKQNPNLMRLIQDHQADF Q9M887 316 316 -
MLQELGKQNPQLVRLIQEHQADF Q9FF16 279 279 -
LLQQIGRENPQLLQQISQHQEHF R23B_MOUSE 302 302 -
LLQQIGRENPQLLQQISQHQEHF R23B_HUMAN 302 302 -
MLQELGKQNPQLLRLIQENQAEF Q9SA20 12 12 -
LLQELGKQNPQILQLIQENQAEF Q40742 288 288 -
MLLELGKQNPQLLRQIQEHHEEF O03991 280 280 -
VLQQIGQTNPALLQLISENQDAF Q9V3W9 267 267 -
VLQQIGQTNPALLQLISENQDAF Q9XZE0 267 267 -
ILQQIGQGDPALAQAITQNPEAF O74803 273 273 -
ILQQLAQTNPALVRQIQENPNEF O97135 251 251 -
LLENISARYPQLREHIMANPEVF RA23_YEAST 279 279 -
VLQQLAAVNPRLVQTIQNNQQAF Q23451 271 271 -
LMNRLAETDPATFEVFQRNQEEL Q9VCD5 198 198 -

Motif 2 width=17
Element Seqn Id St Int Rpt
VTVTPEEREAIERLEAM Q9STA6 339 25 -
INVTPAEQEAIQRLEAM Q9MA10 317 28 -
IQVTPQEKEAIERLKAL R23A_HUMAN 314 33 -
IQVTPQEKEAIERLKAL R23A_MOUSE 314 33 -
ISVTPEERDAIERLEAM O03990 333 21 -
IQVTHEEREAIERLEAM Q9M887 369 30 -
VTVTPEEREAIERLEGM Q9FF16 327 25 -
IQVTPQEKEAIERLKAL R23B_MOUSE 367 42 -
IQVTPQEKEAIERLKAL R23B_HUMAN 360 35 -
VNVTPEEQESIERLEAM Q9SA20 63 28 -
IAVTPEEDEAILRLEPM Q40742 338 27 -
ITVTAADQEAIERLEAM O03991 329 26 -
IRLNRQDKDAIERLKAL Q9V3W9 366 76 -
IRLNRQDKDAIERLKAL Q9XZE0 366 76 -
IQITQEESESIDRLCQL O74803 316 20 -
LQVTQEESEAIQRLQAL O97135 292 18 -
VDYTPEDDQAISRLCEL RA23_YEAST 351 49 -
IHLSPEEAAAIERIKAI Q23451 322 28 -
ITLTAEETAAVGRLEAL Q9VCD5 240 19 -

Motif 3 width=15
Element Seqn Id St Int Rpt
GFDRALVLEVYFACN Q9STA6 356 0 -
GFDRALVIEAFLACD Q9MA10 334 0 -
GFPESLVIQAYFACE R23A_HUMAN 331 0 -
GFPESLVIQAYFACE R23A_MOUSE 331 0 -
GFDRELVLEVFFACN O03990 350 0 -
GFERALVLEVFFACN Q9M887 386 0 -
GFDRAMVLEVFFACN Q9FF16 344 0 -
GFPEGLVIQAYFACE R23B_MOUSE 384 0 -
GFPEGLVIQAYFACE R23B_HUMAN 377 0 -
GFDRAIVIEAFLSCD Q9SA20 80 0 -
GFDRALVLDVFFACN Q40742 355 0 -
GFDRGLVIEAFLACD O03991 346 0 -
GFPEALVLQAYFACE Q9V3W9 383 0 -
GFPEALVLQAYFACE Q9XZE0 383 0 -
GFDRNIVIQAYLACD O74803 333 0 -
GMDKSTVIEAYFACD O97135 310 1 -
GFERDLVIQVYFACD RA23_YEAST 368 0 -
NAPEAVVVEAYFACD Q23451 341 2 -
GFERVMAVQAYLACD Q9VCD5 257 0 -

Motif 4 width=16
Element Seqn Id St Int Rpt
KNEELAANYLLDHLHE Q9STA6 371 0 -
RNEELAANYLLENSGD Q9MA10 349 0 -
KNENLAANFLLSQNFD R23A_HUMAN 346 0 -
KNENLAANFLLSQNFD R23A_MOUSE 346 0 -
KNEELAANYLLDHMHE O03990 365 0 -
KNEELAANYLLDHMHE Q9M887 401 0 -
KNEELAANYLLDHMHE Q9FF16 359 0 -
KNENLAANFLLQQNFD R23B_MOUSE 399 0 -
KNENLAANFLLQQNFD R23B_HUMAN 392 0 -
RNEELAANYLLEHSAD Q9SA20 95 0 -
KDEQLAANYLLDHMNE Q40742 370 0 -
RNEELAVNYLLENAGD O03991 361 0 -
KNEEQAANFLLSSSFD Q9V3W9 398 0 -
KNEEQAANFLLSSSFE Q9XZE0 398 0 -
KNEELAANYLFEHGHE O74803 348 0 -
KNEELTASYLFETADD O97135 325 0 -
KNEEAAANILFSDHAD RA23_YEAST 383 0 -
KNEEAAINFIFSNLDE Q23451 356 0 -
KDEQLAAEVLIRQSEE Q9VCD5 272 0 -
Final Motifs
Motif 1  width=23
Element Seqn Id St Int Rpt
MLQELGKQNPHLMRLIQEHQPDF Q9STA6 291 291 -
MLQELGKQNPQLLRLIQENQAEF Q94CE9 264 264 -
MLQELGKQNPQLLRLIQENQAEF Q9MA10 266 266 -
LLQQLGQENPQLLQQISRHQEQF R23A_HUMAN 258 258 -
LLQQLGQENPQLLQQISRHQEQF R23A_MOUSE 258 258 -
MLQELGKQNPHLMRLIQEHQADF O03990 289 289 -
MLQELGKQNPNLMRLIQDHQADF Q9M887 316 316 -
MLQELGKQNPQLVRLIQEHQADF Q94C35 279 279 -
MLQELGKQNPQLVRLIQEHQADF Q9FF16 279 279 -
LLQQIGRENPQLLQQISQHQEHF Q8WUB0 302 302 -
LLQQIGRENPQLLQQISQHQEHF R23B_MOUSE 302 302 -
LLQQIGRENPQLLQQISQHQEHF R23B_HUMAN 302 302 -
MLQELGKQNPQLLRLIQENQAEF Q9SA20 12 12 -
LLQELGKQNPQILQLIQENQAEF Q40742 288 288 -
MLLELGKQNPQLLRQIQEHHEEF O03991 280 280 -
VLQQIGQTNPALLQLISENQDAF Q9V3W9 267 267 -
VLQQIGQTNPALLQLISENQDAF Q9XZE0 267 267 -
ILQQIGQGDPALAQAITQNPEAF O74803 273 273 -
ILQQLAQTNPALVRQIQENPNEF O97135 251 251 -
LLENISARYPQLREHIMANPEVF RA23_YEAST 279 279 -
VLQQLAAVNPRLVQTIQNNQQAF Q23451 271 271 -
LMNRLAETDPATFEVFQRNQEEL Q9VCD5 198 198 -

Motif 2 width=17
Element Seqn Id St Int Rpt
VTVTPEEREAIERLEAM Q9STA6 339 25 -
INVTPAEQEAIQRLEAM Q94CE9 315 28 -
INVTPAEQEAIQRLEAM Q9MA10 317 28 -
IQVTPQEKEAIERLKAL R23A_HUMAN 314 33 -
IQVTPQEKEAIERLKAL R23A_MOUSE 314 33 -
ISVTPEERDAIERLEAM O03990 333 21 -
IQVTHEEREAIERLEAM Q9M887 369 30 -
VTVTPEEREAIERLEGM Q94C35 327 25 -
VTVTPEEREAIERLEGM Q9FF16 327 25 -
IQVTPQEKEAIERLKAL Q8WUB0 360 35 -
IQVTPQEKEAIERLKAL R23B_MOUSE 367 42 -
IQVTPQEKEAIERLKAL R23B_HUMAN 360 35 -
VNVTPEEQESIERLEAM Q9SA20 63 28 -
IAVTPEEDEAILRLEPM Q40742 338 27 -
ITVTAADQEAIERLEAM O03991 329 26 -
IRLNRQDKDAIERLKAL Q9V3W9 366 76 -
IRLNRQDKDAIERLKAL Q9XZE0 366 76 -
IQITQEESESIDRLCQL O74803 316 20 -
LQVTQEESEAIQRLQAL O97135 292 18 -
VDYTPEDDQAISRLCEL RA23_YEAST 351 49 -
IHLSPEEAAAIERIKAI Q23451 322 28 -
ITLTAEETAAVGRLEAL Q9VCD5 240 19 -

Motif 3 width=15
Element Seqn Id St Int Rpt
GFDRALVLEVYFACN Q9STA6 356 0 -
GFDRALVIEAFLACD Q94CE9 332 0 -
GFDRALVIEAFLACD Q9MA10 334 0 -
GFPESLVIQAYFACE R23A_HUMAN 331 0 -
GFPESLVIQAYFACE R23A_MOUSE 331 0 -
GFDRELVLEVFFACN O03990 350 0 -
GFERALVLEVFFACN Q9M887 386 0 -
GFDRAMVLEVFFACN Q94C35 344 0 -
GFDRAMVLEVFFACN Q9FF16 344 0 -
GFPEGLVIQAYFACE Q8WUB0 377 0 -
GFPEGLVIQAYFACE R23B_MOUSE 384 0 -
GFPEGLVIQAYFACE R23B_HUMAN 377 0 -
GFDRAIVIEAFLSCD Q9SA20 80 0 -
GFDRALVLDVFFACN Q40742 355 0 -
GFDRGLVIEAFLACD O03991 346 0 -
GFPEALVLQAYFACE Q9V3W9 383 0 -
GFPEALVLQAYFACE Q9XZE0 383 0 -
GFDRNIVIQAYLACD O74803 333 0 -
GMDKSTVIEAYFACD O97135 310 1 -
GFERDLVIQVYFACD RA23_YEAST 368 0 -
NAPEAVVVEAYFACD Q23451 341 2 -
GFERVMAVQAYLACD Q9VCD5 257 0 -

Motif 4 width=16
Element Seqn Id St Int Rpt
KNEELAANYLLDHLHE Q9STA6 371 0 -
RNEELAANYLLENSGD Q94CE9 347 0 -
RNEELAANYLLENSGD Q9MA10 349 0 -
KNENLAANFLLSQNFD R23A_HUMAN 346 0 -
KNENLAANFLLSQNFD R23A_MOUSE 346 0 -
KNEELAANYLLDHMHE O03990 365 0 -
KNEELAANYLLDHMHE Q9M887 401 0 -
KNEELAANYLLDHMHE Q94C35 359 0 -
KNEELAANYLLDHMHE Q9FF16 359 0 -
KNENLAANFLLQQNFD Q8WUB0 392 0 -
KNENLAANFLLQQNFD R23B_MOUSE 399 0 -
KNENLAANFLLQQNFD R23B_HUMAN 392 0 -
RNEELAANYLLEHSAD Q9SA20 95 0 -
KDEQLAANYLLDHMNE Q40742 370 0 -
RNEELAVNYLLENAGD O03991 361 0 -
KNEEQAANFLLSSSFD Q9V3W9 398 0 -
KNEEQAANFLLSSSFE Q9XZE0 398 0 -
KNEELAANYLFEHGHE O74803 348 0 -
KNEELTASYLFETADD O97135 325 0 -
KNEEAAANILFSDHAD RA23_YEAST 383 0 -
KNEEAAINFIFSNLDE Q23451 356 0 -
KDEQLAAEVLIRQSEE Q9VCD5 272 0 -