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PR00852

Identifier
XRODRMPGMNTD  [View Relations]  [View Alignment]  
Accession
PR00852
No. of Motifs
9
Creation Date
05-MAR-1998  (UPDATE 07-JUN-1999)
Title
Xeroderma pigmentosum group D protein signature
Database References

PROSITE; PS00690 DEAH_ATP_HELICASE
BLOCKS; BL00690
INTERPRO; IPR001945
Literature References
1. TANAKA, K. AND WOOD, R.D.
Xeroderma pigmentosum and nucleotide excision-repair of DNA.
TRENDS BIOCHEM.SCI. 19 83-86 (1994).
 
2. SCHERLY, D., NOUSPIKEL, T., CORLET, J., UCLA, C., BAIROCH, A.
AND CLARKSON, S.G.
Complementation of the DNA repair defect in xeroderma pigmentosum
group G cells by a human cDNA related to yeast RAD2.
NATURE 363 182-185 (1993).
 
3. KOBAYASHI, T., KURAOKA, I., SAIJO, M., NAKATSU, Y., TANAKA, A.,
SOMEDA, Y., FUKURO, S. AND TANAKA, K.
Mutations in the XPD gene leading to xeroderma pigmentosum symptoms
HUM.MUTAT. 9 322-331 (1997).
 
4. BROUGHTON, B.C., STEINGRIMSDOTTIR, H., WEBER, C.A. AND LEHMANN, A.R.
Mutations in the xeroderma pigmentosum group D DNA repair/transcription
gene in patients with trichothiodystrophy. 
NAT.GENET. 7 189-194 (1994). 
 
5. HAROSH, I. AND DESCHAVANNE, P.
The RAD3 gene is a member of the deah family rna helicase-like protein.
NUCLEIC ACIDS RES. 19 6331-6331 (1991).

Documentation
Defects in DNA repair proteins can give rise, in humans, to the autosomal
recessive disorders xeroderma pigmentosum (XP) and Cockayne's syndrome [1,2].
XP is characterised by a high incidence of sunlight-induced skin cancer,
the effect of skin-cell hypersensitivity to UV resulting from defects in
the nucleotide excision pathway. Seven XP complementation groups have
been identified: XP-A to XP-G. 
 
The XP group D gene product (XPD) is a helicase that is required for
nucleotide excision repair, and is also one of the components of basal
transcription factor TFIIH [3,4]. DNA repair defects in the XPD group are
associated with the clinical features of XP and trichothiodystrophy (TTD),
which is characterised by sulphur-deficient brittle hair and a variety of
other associated abnormalities, but no skin cancer [4]. 
 
XPD belongs to a family of ATP-dependent helicases that are characterised
by a `D-E-A-H' motif [5]. This resembles the `D-E-A-D-box' of other known
helicases, which represents a special version of the B motif of ATP-binding
proteins. In XPD, His replaces the second Asp. 
 
XRODRMPGMNTD is a 9-element fingerprint that provides a signature for
xeroderma pigmentosum group D complementation proteins. The fingerprint 
was derived from an initial alignment of 7 sequences: the motifs were 
drawn from conserved regions spanning the full alignment length. A single
iteration on OWL30.0 was required to reach convergence, no further sequences
being identified beyond the starting set.
 
An update on SPTR37_9f identified a true set of 7 sequences.
Summary Information
7 codes involving  9 elements
0 codes involving 8 elements
0 codes involving 7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
9777777777
8000000000
7000000000
6000000000
5000000000
4000000000
3000000000
2000000000
123456789
True Positives
O00836        Q91941        RA15_SCHPO    RAD3_YEAST    
XPD_CRIGR XPD_HUMAN XPD_MOUSE
Sequence Titles
O00836      REPD - DICTYOSTELIUM DISCOIDEUM (SLIME MOLD). 
Q91941 ERCC2/XPD - XIPHOPHORUS MACULATUS (SOUTHERN PLATYFISH).
RA15_SCHPO DNA REPAIR HELICASE RAD15 (RHP3) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
RAD3_YEAST DNA REPAIR HELICASE RAD3 - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
XPD_CRIGR DNA-REPAIR PROTEIN COMPLEMENTING XP-D CELLS (XERODERMA PIGMENTOSUM GROUP D COMPLEMENTING PROTEIN) (DNA EXCISION REPAIR PROTEIN ERCC-2) - CRICETULUS GRISEUS (CHINESE HAMSTER).
XPD_HUMAN DNA-REPAIR PROTEIN COMPLEMENTING XP-D CELLS (XERODERMA PIGMENTOSUM GROUP D COMPLEMENTING PROTEIN) (DNA EXCISION REPAIR PROTEIN ERCC-2) - HOMO SAPIENS (HUMAN).
XPD_MOUSE DNA-REPAIR PROTEIN COMPLEMENTING XP-D CELLS (XERODERMA PIGMENTOSUM GROUP D COMPLEMENTING PROTEIN) (DNA EXCISION REPAIR PROTEIN ERCC-2) - MUS MUSCULUS (MOUSE).
Scan History
OWL30_0    1  50   NSINGLE    
SPTR37_9f 2 8 NSINGLE
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
LPILFPYPRIYPEQYQYM RA15_SCHPO 8 8 -
LPVLFPYPKIYPEQYNYM RAD3_YEAST 8 8 -
LLVYFPYSYIYPEQYSYM DDU77066 8 8 -
LLVYFPYDYIYPEQYSYM I51720 8 8 -
LLVYFPYDYIYPEQFSYM XPD_CRIGR 8 8 -
LLVYFPYDYIYPEQFSYM XPD_MOUSE 8 8 -
LLVYFPYDYIYPEQFSYM XPD_HUMAN 8 8 -

Motif 2 width=20
Element Seqn Id St Int Rpt
IKETDEQRLRDEYRRLVEGL XPD_MOUSE 273 247 -
VRKVDSQKLQDEYEKLVQGL RAD3_YEAST 274 248 -
VKQSDSKKLQDEYQKLVRGL RA15_SCHPO 272 246 -
IKETDEQRLRDEYRRLVEGL XPD_HUMAN 273 247 -
IKETDAAKLREEYRRLVEGL I51720 273 247 -
IKKVDEKRLKDEYQRLVNGL DDU77066 267 241 -
IKETDEQRLRDEYRRLVEGL XPD_CRIGR 273 247 -

Motif 3 width=19
Element Seqn Id St Int Rpt
PVLPDEVLQEAVPGSIRTA I51720 308 15 -
PVLPQDLLTEAIPGNIRRA RAD3_YEAST 310 16 -
PVLPEDVLKEAVPGNIRRA RA15_SCHPO 307 15 -
PVLPDEVLQEAVPGSIRTA XPD_HUMAN 308 15 -
PVLPDEVLQEAVPGSIRTA XPD_MOUSE 308 15 -
PVLPDEVLQEAVPGSIRTA XPD_CRIGR 308 15 -
PVLPNDVIQEAVPGNIRKP DDU77066 301 14 -

Motif 4 width=22
Element Seqn Id St Int Rpt
LRRVVDYLKSRLKSQMLLSESP DDU77066 326 6 -
LRRFLEYLKARLRVQHVVQESA I51720 333 6 -
LRRLLEYVKWRLRVQHVVQESP XPD_CRIGR 333 6 -
LRRLLEYVKWRLRVQHVVQESP XPD_MOUSE 333 6 -
LRRLLEYVKWRLRVQHVVQESP XPD_HUMAN 333 6 -
LKRFVEYLKTRMKVLHVIAETP RA15_SCHPO 332 6 -
LKRLIEYLKTRMKVLHVISETP RAD3_YEAST 335 6 -

Motif 5 width=23
Element Seqn Id St Int Rpt
LRFCSERLSLLVRTLEVTEVEDF RAD3_YEAST 374 17 -
LRFCSSRLSSLLRTLRINDVNQF DDU77066 365 17 -
LRFCAERLQCLLRTLEIADIADF I51720 372 17 -
LRFCAERLRSLLHTLEIADLADF XPD_CRIGR 372 17 -
LRFCAERLRSLLHTLEIADLADF XPD_MOUSE 372 17 -
LRFCAERLRSLLHTLEITDLADF XPD_HUMAN 372 17 -
LRFCAERLTSLVRALQISLVEDF RA15_SCHPO 371 17 -

Motif 6 width=19
Element Seqn Id St Int Rpt
FATLVSTYAKGFTIIIEPF XPD_HUMAN 403 8 -
FATLVGTYNNGFLIIIEPY DDU77066 396 8 -
FATLVSTYSQGFTIIIEPF I51720 403 8 -
FATLVSTYAKGFTIIIEPF XPD_MOUSE 403 8 -
FATLVSTYAKGFTIIIEPF XPD_CRIGR 403 8 -
FATLISTYEEGFLLIIEPY RAD3_YEAST 405 8 -
FATLVATYERGFILILEPF RA15_SCHPO 402 8 -

Motif 7 width=18
Element Seqn Id St Int Rpt
PCILTRGSDQISISTKFD DDU77066 485 70 -
PMIIGRGNDQVAISSKFE XPD_CRIGR 492 70 -
PMIIGRGNDQVAISSKFE XPD_MOUSE 492 70 -
PMIIGRGNDQVAISSKFE XPD_HUMAN 492 70 -
PMVVTRGSDQVAISSKFE RA15_SCHPO 491 70 -
PMIITKGSDQVAISSRFE RAD3_YEAST 494 70 -
PLIVGRGNDQVALSSKFE I51720 492 70 -

Motif 8 width=23
Element Seqn Id St Int Rpt
RLEFMRENYRIRENDFLSFDAMR RAD3_YEAST 638 126 -
RLEFLRDRYQIRENEFLTFDAMR DDU77066 629 126 -
RLEYLRDQFQIRENDFLTFDAMR I51720 636 126 -
RLEYLRDQFQIRENDFLTFDAMR XPD_CRIGR 636 126 -
RLEYLRDQFQIRENDFLTFDAMR XPD_MOUSE 636 126 -
RLEYLRDQFQIRENDFLTFDAMR XPD_HUMAN 636 126 -
RLEFLRDTYQIREADFLTFDAMR RA15_SCHPO 635 126 -

Motif 9 width=21
Element Seqn Id St Int Rpt
NLSTDMAISLSKTFLREMGQP DDU77066 700 48 -
NLTVDEAVQLSKHFLRQMAQP I51720 707 48 -
NLSTDMAISNTKQFLRTMAQP RAD3_YEAST 707 46 -
NLSTDMSLALAKKFLRTMAQP RA15_SCHPO 706 48 -
NLTVDEGVQVAKYFLRQMAQP XPD_HUMAN 707 48 -
NLTVDEGVQVAKYFLRQMAQP XPD_MOUSE 707 48 -
NLTVDEGVQVAKYFLRQMAQP XPD_CRIGR 707 48 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
LLVYFPYDYIYPEQFSYM XPD_CRIGR 8 8 -
LLVYFPYDYIYPEQFSYM XPD_MOUSE 8 8 -
LLVYFPYDYIYPEQFSYM XPD_HUMAN 8 8 -
LLVYFPYDYIYPEQYSYM Q91941 8 8 -
LPILFPYPRIYPEQYQYM RA15_SCHPO 8 8 -
LLVYFPYSYIYPEQYSYM O00836 8 8 -
LPVLFPYPKIYPEQYNYM RAD3_YEAST 8 8 -

Motif 2 width=20
Element Seqn Id St Int Rpt
IKETDEQRLRDEYRRLVEGL XPD_CRIGR 273 247 -
IKETDEQRLRDEYRRLVEGL XPD_MOUSE 273 247 -
IKETDEQRLRDEYRRLVEGL XPD_HUMAN 273 247 -
IKETDAAKLREEYRRLVEGL Q91941 273 247 -
VKQSDSKKLQDEYQKLVRGL RA15_SCHPO 272 246 -
IKKVDEKRLKDEYQRLVNGL O00836 267 241 -
VRKVDSQKLQDEYEKLVQGL RAD3_YEAST 274 248 -

Motif 3 width=19
Element Seqn Id St Int Rpt
PVLPDEVLQEAVPGSIRTA XPD_CRIGR 308 15 -
PVLPDEVLQEAVPGSIRTA XPD_MOUSE 308 15 -
PVLPDEVLQEAVPGSIRTA XPD_HUMAN 308 15 -
PVLPDEVLQEAVPGSIRTA Q91941 308 15 -
PVLPEDVLKEAVPGNIRRA RA15_SCHPO 307 15 -
PVLPNDVIQEAVPGNIRKP O00836 301 14 -
PVLPQDLLTEAIPGNIRRA RAD3_YEAST 310 16 -

Motif 4 width=22
Element Seqn Id St Int Rpt
LRRLLEYVKWRLRVQHVVQESP XPD_CRIGR 333 6 -
LRRLLEYVKWRLRVQHVVQESP XPD_MOUSE 333 6 -
LRRLLEYVKWRLRVQHVVQESP XPD_HUMAN 333 6 -
LRRFLEYLKARLRVQHVVQESA Q91941 333 6 -
LKRFVEYLKTRMKVLHVIAETP RA15_SCHPO 332 6 -
LRRVVDYLKSRLKSQMLLSESP O00836 326 6 -
LKRLIEYLKTRMKVLHVISETP RAD3_YEAST 335 6 -

Motif 5 width=23
Element Seqn Id St Int Rpt
LRFCAERLRSLLHTLEIADLADF XPD_CRIGR 372 17 -
LRFCAERLRSLLHTLEIADLADF XPD_MOUSE 372 17 -
LRFCAERLRSLLHTLEITDLADF XPD_HUMAN 372 17 -
LRFCAERLQCLLRTLEIADIADF Q91941 372 17 -
LRFCAERLTSLVRALQISLVEDF RA15_SCHPO 371 17 -
LRFCSSRLSSLLRTLRINDVNQF O00836 365 17 -
LRFCSERLSLLVRTLEVTEVEDF RAD3_YEAST 374 17 -

Motif 6 width=19
Element Seqn Id St Int Rpt
FATLVSTYAKGFTIIIEPF XPD_CRIGR 403 8 -
FATLVSTYAKGFTIIIEPF XPD_MOUSE 403 8 -
FATLVSTYAKGFTIIIEPF XPD_HUMAN 403 8 -
FATLVSTYSQGFTIIIEPF Q91941 403 8 -
FATLVATYERGFILILEPF RA15_SCHPO 402 8 -
FATLVGTYNNGFLIIIEPY O00836 396 8 -
FATLISTYEEGFLLIIEPY RAD3_YEAST 405 8 -

Motif 7 width=18
Element Seqn Id St Int Rpt
PMIIGRGNDQVAISSKFE XPD_CRIGR 492 70 -
PMIIGRGNDQVAISSKFE XPD_MOUSE 492 70 -
PMIIGRGNDQVAISSKFE XPD_HUMAN 492 70 -
PLIVGRGNDQVALSSKFE Q91941 492 70 -
PMVVTRGSDQVAISSKFE RA15_SCHPO 491 70 -
PCILTRGSDQISISTKFD O00836 485 70 -
PMIITKGSDQVAISSRFE RAD3_YEAST 494 70 -

Motif 8 width=23
Element Seqn Id St Int Rpt
RLEYLRDQFQIRENDFLTFDAMR XPD_CRIGR 636 126 -
RLEYLRDQFQIRENDFLTFDAMR XPD_MOUSE 636 126 -
RLEYLRDQFQIRENDFLTFDAMR XPD_HUMAN 636 126 -
RLEYLRDQFQIRENDFLTFDAMR Q91941 636 126 -
RLEFLRDTYQIREADFLTFDAMR RA15_SCHPO 635 126 -
RLEFLRDRYQIRENEFLTFDAMR O00836 629 126 -
RLEFMRENYRIRENDFLSFDAMR RAD3_YEAST 638 126 -

Motif 9 width=21
Element Seqn Id St Int Rpt
NLTVDEGVQVAKYFLRQMAQP XPD_CRIGR 707 48 -
NLTVDEGVQVAKYFLRQMAQP XPD_MOUSE 707 48 -
NLTVDEGVQVAKYFLRQMAQP XPD_HUMAN 707 48 -
NLTVDEAVQLSKHFLRQMAQP Q91941 707 48 -
NLSTDMSLALAKKFLRTMAQP RA15_SCHPO 706 48 -
NLSTDMAISLSKTFLREMGQP O00836 700 48 -
NLSTDMAISNTKQFLRTMAQP RAD3_YEAST 707 46 -