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PR00147

Identifier
DNAPHOTLYASE  [View Relations]  [View Alignment]  
Accession
PR00147
No. of Motifs
4
Creation Date
25-FEB-1994  (UPDATE 07-JUN-1999)
Title
DNA photolyase signature
Database References

PROSITE; PS00394 DNA_PHOTOLYASES_1_1; PS00691 DNA_PHOTOLYASES_1_2
BLOCKS; BL00394
PFAM; PF00875 DNA_photolyase
INTERPRO; IPR000474
Literature References
1. SANCAR, G.B., SMITH, F.W., LORENCE, M.C., RUPERT, C.S. AND SANCAR, A.
Sequences of the Escherichia coli photolyase gene and protein.
J.BIOL.CHEM. 259(9) 6028-6038 (1984).
 
2. YASUI, A. AND LANGEVELD, S.A.
Homology between the photoreactivation genes of Saccharomyces cerevisiae
and Escherichia coli.
GENE 36(3) 349-355 (1985).
 
3. EKER, A.P.M., KOOIMAN, P., HESSELS, J.K.C. AND YASUI, A.
DNA Photoreactivating enzyme from the cyanobacterium Anacystis nidulans.
J.BIOL.CHEM. 265(14) 8009-8015 (1990).

Documentation
DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers:
on absorption of visible light, they catalyse dimer splitting into the
constituent monomers, a process called photoreactivation [1]. This is a DNA
repair mechanism, repairing mismatched pyrimidine dimers induced by
exposure to ultra-violet light [2]. The precise mechanisms involved in
substrate binding, conversion of light energy to the mechanical energy
needed to rupture the cyclobutane ring, and subsequent release of the
product are uncertain [1]. Analysis of DNA lyases has revealed the presence
of an intrinsic chromophore, all monomers containing a reduced FAD moiety,
and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a
second chromophore [2,3]. Either chromophore may act as the primary photon
acceptor, peak absorptions occurring in the blue region of the spectrum
and in the UV-B region, at a wavelength around 290nm [3].
 
DNAPHOTLYASE is a 4-element fingerprint that provides a signature for the 
DNA photolyases. The fingerprint was derived from an initial alignment of
5 sequences: the motifs were drawn from conserved regions spanning
virtually the full alignment length, motifs 2 and 3 including the regions
encoded by PROSITE patterns DNA_PHOTOLYASE_1 (PS00394) and DNA_PHOTOLYASE_2
(PS00691). Two iterations on OWL22.1 were required to reach convergence, at
which point a true set comprising 8 sequences was identified. A single
partial match was also found, SAPHR1, a DNA lyase from Sinapis alba, which
only matches motifs 2 and 3.
 
An update on SPTR37_9f identified a true set of 8 sequences, and 9
partial matches.
Summary Information
   8 codes involving  4 elements
2 codes involving 3 elements
6 codes involving 2 elements
Composite Feature Index
48888
30222
20660
1234
True Positives
PHR_ANANI     PHR_ECOLI     PHR_HALHA     PHR_NEUCR     
PHR_SALTY PHR_STRGR PHR_SYNY3 PHR_YEAST
True Positive Partials
Codes involving 3 elements
P77967 Q42696
Codes involving 2 elements
CRY1_ARATH CRY2_ARATH O82769 O82779
O82786 PHR1_SINAL
Sequence Titles
PHR_ANANI   DEOXYRIBODIPYRIMIDINE PHOTOLYASE (EC 4.1.99.3) (DNA PHOTOLYASE) (PHOTOREACTIVATING ENZYME) - ANACYSTIS NIDULANS. 
PHR_ECOLI DEOXYRIBODIPYRIMIDINE PHOTOLYASE (EC 4.1.99.3) (DNA PHOTOLYASE) (PHOTOREACTIVATING ENZYME) - ESCHERICHIA COLI.
PHR_HALHA DEOXYRIBODIPYRIMIDINE PHOTOLYASE (EC 4.1.99.3) (DNA PHOTOLYASE) (PHOTOREACTIVATING ENZYME) - HALOBACTERIUM HALOBIUM.
PHR_NEUCR DEOXYRIBODIPYRIMIDINE PHOTOLYASE (EC 4.1.99.3) (DNA PHOTOLYASE) (PHOTOREACTIVATING ENZYME) - NEUROSPORA CRASSA.
PHR_SALTY DEOXYRIBODIPYRIMIDINE PHOTOLYASE (EC 4.1.99.3) (DNA PHOTOLYASE) (PHOTOREACTIVATING ENZYME) - SALMONELLA TYPHIMURIUM.
PHR_STRGR DEOXYRIBODIPYRIMIDINE PHOTOLYASE (EC 4.1.99.3) (DNA PHOTOLYASE) (PHOTOREACTIVATING ENZYME) - STREPTOMYCES GRISEUS.
PHR_SYNY3 DEOXYRIBODIPYRIMIDINE PHOTOLYASE (EC 4.1.99.3) (DNA PHOTOLYASE) (PHOTOREACTIVATING ENZYME) - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
PHR_YEAST DEOXYRIBODIPYRIMIDINE PHOTOLYASE PRECURSOR (EC 4.1.99.3) (DNA PHOTOLYASE) (PHOTOREACTIVATING ENZYME) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).

P77967 DNA PHOTOLYASE - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
Q42696 DEOXYRIBODIPYRIMIDINE PHOTOLYASE (EC 4.1.99.3) (DNA PHOTOLYASE) (PHOTOREACTIVATING ENZYME) - CHLAMYDOMONAS REINHARDTII.

CRY1_ARATH CRYPTOCHROME 1 APOPROTEIN (BLUE LIGHT PHOTORECEPTOR) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
CRY2_ARATH CRYPTOCHROME 2 APOPROTEIN (BLUE LIGHT PHOTORECEPTOR) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O82769 BLUE-LIGHT PHOTORECEPTOR - ADIANTUM CAPILLUS-VENERIS (FERN).
O82779 BLUE-LIGHT PHOTORECEPTOR - ADIANTUM CAPILLUS-VENERIS (FERN).
O82786 DEOXYRIBODIPYRIMIDINE PHOTOLYASE (EC 4.1.99.3) (DNA PHOTOLYASE) (PHOTOREACTIVATING ENZYME) - ADIANTUM CAPILLUS-VENERIS (FERN).
PHR1_SINAL DEOXYRIBODIPYRIMIDINE PHOTOLYASE (EC 4.1.99.3) (DNA PHOTOLYASE) (PHOTOREACTIVATING ENZYME) - SINAPIS ALBA (WHITE MUSTARD) (BRASSICA HIRTA).
Scan History
OWL22_1    2  100  NSINGLE    
OWL26_0 1 100 NSINGLE
SPTR37_9f 2 139 NSINGLE
Initial Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
GNHEMYKVFTPFKNAWL PHR_ECOLI 143 143 -
GNHEMYKVFTPFKNAWL PHR_SALTY 136 136 -
GSGNPYSVYGPFWKNWQ PHR_ANANI 140 140 -
GSGGQYAVYSPWFRAWI PHR_NEUCR 285 285 -
DRGTNYSVFTPWYKKWV PHR_YEAST 235 235 -

Motif 2 width=17
Element Seqn Id St Int Rpt
TGYPIVDAAMRQLNSTG PHR_ECOLI 322 162 -
TGYPIVDAAMRQLNATG PHR_SALTY 307 154 -
TGYPIVDAAMRQLTETG PHR_ANANI 328 171 -
TGFPIIDAAMRQVLSTG PHR_NEUCR 481 179 -
TGIPIVDAIMRKLLYTG PHR_YEAST 431 179 -

Motif 3 width=19
Element Seqn Id St Int Rpt
NRLRMITASFLVKDLLIDW PHR_ECOLI 342 3 -
NRLRMITASFLVKDLLIWR PHR_SALTY 326 2 -
NRCRMIVASFLTKDLIIDW PHR_ANANI 348 3 -
NRLRMIVASFLAKDLLVDW PHR_NEUCR 501 3 -
NRSRMITASFLSKNLLIDW PHR_YEAST 451 3 -

Motif 4 width=15
Element Seqn Id St Int Rpt
GGWQWAASTGTDAAP PHR_ECOLI 381 20 -
GGWQWAASTGTDAAP PHR_SALTY 363 18 -
GGWQWSASSGMDPKP PHR_ANANI 387 20 -
GGWGFAASVGVDPQP PHR_NEUCR 540 20 -
GGWGFCSSTGIDAQP PHR_YEAST 490 20 -
Final Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
GNHEMYKVFTPFKNAWL PHR_ECOLI 143 143 -
GNHEMYKVFTPFKNAWL PHR_SALTY 136 136 -
GSGNPYSVYGPFWKNWQ PHR_ANANI 140 140 -
NAGDPYSVYTYFWRKWQ PHR_HALHA 145 145 -
QAGSPYTVYTPFWKNWS PHR_SYNY3 155 155 -
GSGGQYAVYSPWFRAWI PHR_NEUCR 285 285 -
DRGTNYSVFTPWYKKWV PHR_YEAST 235 235 -
GGKDHFAVFTPYFRRWE PHR_STRGR 142 142 -

Motif 2 width=17
Element Seqn Id St Int Rpt
TGYPIVDAAMRQLNSTG PHR_ECOLI 322 162 -
TGYPIVDAAMRQLNATG PHR_SALTY 307 154 -
TGYPIVDAAMRQLTETG PHR_ANANI 328 171 -
TGYPIVDAGMRQLRAEA PHR_HALHA 329 167 -
TGYPIIDAAMAQLNQTG PHR_SYNY3 343 171 -
TGFPIIDAAMRQVLSTG PHR_NEUCR 481 179 -
TGIPIVDAIMRKLLYTG PHR_YEAST 431 179 -
TGYPLVDAAMRQLAHEG PHR_STRGR 310 151 -

Motif 3 width=19
Element Seqn Id St Int Rpt
NRLRMITASFLVKDLLIDW PHR_ECOLI 342 3 -
NRLRMITASFLVKDLLIWR PHR_SALTY 326 2 -
NRCRMIVASFLTKDLIIDW PHR_ANANI 348 3 -
NRVRMIVAAFLTKDLLVDW PHR_HALHA 349 3 -
NRCRMIVASFLIKDLILNW PHR_SYNY3 363 3 -
NRLRMIVASFLAKDLLVDW PHR_NEUCR 501 3 -
NRSRMITASFLSKNLLIDW PHR_YEAST 451 3 -
NRARMLAASFLTKTLYVDW PHR_STRGR 330 3 -

Motif 4 width=15
Element Seqn Id St Int Rpt
GGWQWAASTGTDAAP PHR_ECOLI 381 20 -
GGWQWAASTGTDAAP PHR_SALTY 363 18 -
GGWQWSASSGMDPKP PHR_ANANI 387 20 -
GGWQWAASTGTDAQP PHR_HALHA 388 20 -
GGWQWSASSGMDPKP PHR_SYNY3 402 20 -
GGWGFAASVGVDPQP PHR_NEUCR 540 20 -
GGWGFCSSTGIDAQP PHR_YEAST 490 20 -
LNWQWVAGTGTDTRP PHR_STRGR 369 20 -