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PR00869

Identifier
DNAPOLX  [View Relations]  [View Alignment]  
Accession
PR00869
No. of Motifs
6
Creation Date
29-JUN-1998  (UPDATE 14-JUN-1999)
Title
DNA-polymerase family X signature
Database References
PRINTS; PR90005 DNADNAPOL; PR00870 DNAPOLXBETA; PR00871 DNAPOLXTDT

PROSITE; PS00522 DNA_POLYMERASE_X
BLOCKS; BL00522
PFAM; PF00966 DNA_polymeraseX
INTERPRO; IPR002054
PDB; 1BPY; 1BPX
SCOP; 1BPY; 1BPX
CATH; 1BPY; 1BPX
Literature References
1. JUNG, G., LEAVITT, M.C.,	HSIEH, J-C. AND	ITO, J.
Bacteriophage PRD1 DNA polymerase: Evolution of DNA	polymerases.
PROC.NATL.ACAD.SCI.U.S.A. 84 8287-8291	(1987).
 
2. DELARUE,	M., POCH, O., TORDO, N., MORAS,	D. AND ARGOS, P.
An attempt to unify	the structure of polymerases.
PROTEIN ENG. 3(6) 461-467 (1990).

Documentation
DNA	carries the biological information that instructs cells how to exist
in an ordered fashion: accurate replication is thus one of the most
important events in the cell life cycle. This function is mediated by
DNA-directed DNA-polymerases, which add nucleotide triphosphate (dNTP)
residues to the 5'-end of the growing DNA chain, using a complementary 
DNA as template. Small RNA molecules are generally used as primers for
chain elongation, although terminal proteins may also be used.
 
DNA-dependent DNA-polymerases have been grouped into families, denoted A, B
and X, on the basis of sequence similarities [1,2].	Members of family X
encompass two distinct polymerase enzymes that have similar functionality:
vertebrate polymerase beta (yeast pol 4), and terminal deoxynucleotidyl-
transferase (TdT) (EC 2.7.7.31). The former functions in DNA repair, while
the latter terminally adds single nucleotides to polydeoxynucleotide chains.
Both enzymes catalyse addition of nucleotides in a distributive manner, 
i.e. they dissociate after the addition of a single nucleotide.
 
Three motifs, A, B and C, as defined by Delarue et al. [2], are seen to be 
conserved across all DNA-polymerases, with motifs A and C also seen in RNA- 
polymerases. They are centered on invariant residues, and their structural 
significance was implied from the Klenlow (E.coli) structure: motif A 
contains a strictly-conserved aspartate at the junction of a beta-strand 
and an alpha-helix; motif B contains an alpha-helix with positive charges; 
and motif C has a doublet of negative charges, located in a beta-turn-beta 
secondary structure [2]. 
 
DNAPOLX is a 6-element fingerprint that provides a signature for DNA-
polymerase family X. The fingerprint was derived from an initial alignment
of 8 sequences: the motifs were drawn from conserved regions spanning the
full alignment length - motif 1 includes helix 7 and a number of conserved
residues involved in metal and DNA binding; motif 2 straddles strands
2 and 3, and helix 12; motif 3 includes "motif C", which contains two of
the active site Asps; motif 4 spans strand 7 and helix 14, and corresponds
to "motif A", which includes an active site Asp; motif 5 spans the
C-terminus of helix 15 and the N-terminus of helix 16, and includes a
conserved aromatic residue involved in ligand binding; and motif 6, which
lies at the C-terminus, spans helices 17 and 18. Two iterations on OWL30.1
were required to reach convergence, at which point a true set comprising 16
sequences was identified. Several partial matches were also found, all of
which are non-vertebrate polymerase X family homologues.
 
An update on SPTR37_9f identified a true set of 13 sequences, and 6
partial matches.
Summary Information
  13 codes involving  6 elements
0 codes involving 5 elements
0 codes involving 4 elements
2 codes involving 3 elements
3 codes involving 2 elements
Composite Feature Index
6131313131313
5000000
4000000
3020022
2021111
123456
True Positives
DPO4_YEAST    DPOB_HUMAN    DPOB_RAT      DPOB_XENLA    
TDT_AMBME TDT_BOVIN TDT_CHICK TDT_HUMAN
TDT_MONDO TDT_MOUSE TDT_ONCMY TDT_XENLA
YA26_SCHPO
True Positive Partials
Codes involving 3 elements
O26650 Q23687
Codes involving 2 elements
O174_ASFB7 O67416 P77987
Sequence Titles
DPO4_YEAST  DNA POLYMERASE IV (EC 2.7.7.7) (POL IV) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). 
DPOB_HUMAN DNA POLYMERASE BETA (EC 2.7.7.7) - HOMO SAPIENS (HUMAN).
DPOB_RAT DNA POLYMERASE BETA (EC 2.7.7.7) - RATTUS NORVEGICUS (RAT).
DPOB_XENLA DNA POLYMERASE BETA (EC 2.7.7.7) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
TDT_AMBME DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TERMINAL TRANSFERASE) - AMBYSTOMA MEXICANUM (AXOLOTL).
TDT_BOVIN DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TDT) (TERMINAL TRANSFERASE) - BOS TAURUS (BOVINE).
TDT_CHICK DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TERMINAL TRANSFERASE) - GALLUS GALLUS (CHICKEN).
TDT_HUMAN DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TERMINAL TRANSFERASE) - HOMO SAPIENS (HUMAN).
TDT_MONDO DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TDT) (TERMINAL TRANSFERASE) - MONODELPHIS DOMESTICA (SHORT-TAILED GREY OPOSSUM).
TDT_MOUSE DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TDT) (TERMINAL TRANSFERASE) - MUS MUSCULUS (MOUSE).
TDT_ONCMY DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TERMINAL TRANSFERASE) - ONCORHYNCHUS MYKISS (RAINBOW TROUT) (SALMO GAIRDNERI).
TDT_XENLA DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITION ENZYME) (TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE) (TDT) (TERMINAL TRANSFERASE) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
YA26_SCHPO HYPOTHETICAL DNA POLYMERASE BETA-LIKE PROTEIN C2F7.06C - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).

O26650 DNA-DEPENDENT DNA POLYMERASE FAMILY X - METHANOBACTERIUM THERMOAUTOTROPHICUM.
Q23687 DNA POLYMERASE BETA - CRITHIDIA FASCICULATA.

O174_ASFB7 DNA POLYMERASE BETA-LIKE PROTEIN - AFRICAN SWINE FEVER VIRUS (STRAIN BA71V) (ASFV).
O67416 DNA POLYMERASE BETA FAMILY - AQUIFEX AEOLICUS.
P77987 DNA POLYMERASE FAMILY X (EC 2.7.7.7) (DNA-DIRECTED DNA POLYMERASE) (DNA NUCLEOTIDYLTRANSFERASE (DNA-DIRECTED)) - THERMUS AQUATICUS (SUBSP. THERMOPHILUS).
Scan History
OWL30_1    2  400  NSINGLE    
SPTR37_9f 2 200 NSINGLE
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
GVGLKTSEKWFRMGFRTL TDT_HUMAN 257 257 -
GVGVKTSEKWFRMGLRTV TDT_CHICK 257 257 -
GIGPSAARKFVDEGIKTL DPOB_HUMAN 104 104 -
GIGPSAARKLVDEGIKTL DPOB_RAT 104 104 -
GVGASHAAEWYQKGWRTI YA26_SCHPO 271 271 -
GIGPAAARKFFDEGIKTL XLY15732 105 105 -
GVGLKTAEKWFRMGFRTL TDT_MOUSE 257 257 -
GVGLKTSEKWFRMGFRSL TDT_BOVIN 268 268 -

Motif 2 width=15
Element Seqn Id St Int Rpt
TMTGGFRRGKKMGHD TDT_HUMAN 329 54 -
TVCGSFRRGAESSGD DPOB_HUMAN 175 53 -
TVCGSFRRGAESSGD XLY15732 176 53 -
CLVGGFRRGKPVGAD YA26_SCHPO 341 52 -
TVCGSFRRGAESSGD DPOB_RAT 175 53 -
TMTGGFRRGKMTGHD TDT_MOUSE 329 54 -
TMTGGFRRGKKIGHD TDT_BOVIN 340 54 -
TITGGFRRGKKIGHD TDT_CHICK 329 54 -

Motif 3 width=9
Element Seqn Id St Int Rpt
DMDVLLTHP DPOB_HUMAN 189 -1 -
DMDILLTHP XLY15732 190 -1 -
DVDFLITSP TDT_MOUSE 343 -1 -
DVDFLITSP TDT_BOVIN 354 -1 -
DVDFLITSP TDT_HUMAN 343 -1 -
DIDFLITSP TDT_CHICK 343 -1 -
DMDVLLTHP DPOB_RAT 189 -1 -
DVDMVLSPS YA26_SCHPO 355 -1 -

Motif 4 width=10
Element Seqn Id St Int Rpt
RIDIRLIPKD DPOB_RAT 253 55 -
RIDIRLIPKD XLY15732 253 54 -
RVDIIVVPPA YA26_SCHPO 417 53 -
RVDLVMCPYD TDT_MOUSE 432 80 -
RVDLVMCPYE TDT_BOVIN 442 79 -
RVDLVLCPYE TDT_HUMAN 431 79 -
RVDLVITPFE TDT_CHICK 428 76 -
RIDIRLIPKD DPOB_HUMAN 253 55 -

Motif 5 width=14
Element Seqn Id St Int Rpt
LGWTGSRFERDLRR TDT_HUMAN 447 6 -
LGWTGSRQFERDLR TDT_MOUSE 447 5 -
LGWTGSRQFERDIR TDT_BOVIN 458 6 -
LGWTGSRQFGRDLR TDT_CHICK 444 6 -
LYFTGSDIFNKNMR DPOB_HUMAN 269 6 -
LYFTGSDIFNKNMR DPOB_RAT 269 6 -
LGWSGGIFFLRDLK YA26_SCHPO 433 6 -
LYFTGSDIFNKNMR XLY15732 269 6 -

Motif 6 width=19
Element Seqn Id St Int Rpt
SEEEIFAHLGLDYVEPWER TDT_CHICK 486 28 -
AEKDIFRYFSLEYIEPKFR YA26_SCHPO 485 38 -
SEEEIFAHLGLDYIEPWER TDT_MOUSE 509 48 -
SEKDIFDYIQWKYREPKDR XLY15732 314 31 -
SEQDIFDYIQWRYREPKDR DPOB_RAT 314 31 -
SEKDIFDYIQWKYREPKDR DPOB_HUMAN 314 31 -
SEEEIFAHLGLDYIEPWER TDT_BOVIN 500 28 -
SEEEIFAHLGLDYIEPWER TDT_HUMAN 488 27 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
GVGLKTAEKWFRMGFRTL TDT_MOUSE 257 257 -
GVGLKTSEKWFRMGFRSL TDT_BOVIN 268 268 -
GVGLKTADKWYRMGFRTL TDT_MONDO 259 259 -
GVGLKTSEKWFRMGFRTL TDT_HUMAN 257 257 -
GVGVKTSEKWFRMGLRTV TDT_CHICK 257 257 -
GVGLRTAEKWHRLGIRTL TDT_AMBME 250 250 -
GVGLKTSDKWFRMGFRTL TDT_XENLA 253 253 -
GVGPKTAEKWYRRGLRSL TDT_ONCMY 248 248 -
GIGPAAARKFFDEGIKTL DPOB_XENLA 104 104 -
GIGPSAARKFVDEGIKTL DPOB_HUMAN 104 104 -
GIGPSAARKLVDEGIKTL DPOB_RAT 104 104 -
GVGASHAAEWYQKGWRTI YA26_SCHPO 271 271 -
GIGSEIAKRWNLLNFESF DPO4_YEAST 278 278 -

Motif 2 width=15
Element Seqn Id St Int Rpt
TMTGGFRRGKMTGHD TDT_MOUSE 329 54 -
TMTGGFRRGKKIGHD TDT_BOVIN 340 54 -
TITGGFRRGKEFGHD TDT_MONDO 331 54 -
TMTGGFRRGKKMGHD TDT_HUMAN 329 54 -
TITGGFRRGKKIGHD TDT_CHICK 329 54 -
TLTGGFRRGNKTGHD TDT_AMBME 322 54 -
TLTGGFRRGKKKGHD TDT_XENLA 325 54 -
ALTGGFRRGKEYGHD TDT_ONCMY 320 54 -
TVCGSFRRGAESSGD DPOB_XENLA 175 53 -
TVCGSFRRGAESSGD DPOB_HUMAN 175 53 -
TVCGSFRRGAESSGD DPOB_RAT 175 53 -
CLVGGFRRGKPVGAD YA26_SCHPO 341 52 -
ELQGSYNRGYSKCGD DPO4_YEAST 352 56 -

Motif 3 width=9
Element Seqn Id St Int Rpt
DVDFLITSP TDT_MOUSE 343 -1 -
DVDFLITSP TDT_BOVIN 354 -1 -
DVDFLITSP TDT_MONDO 345 -1 -
DVDFLITSP TDT_HUMAN 343 -1 -
DIDFLITSP TDT_CHICK 343 -1 -
DVDMLITSP TDT_AMBME 336 -1 -
DVDILITCA TDT_XENLA 339 -1 -
DVDFLLTMP TDT_ONCMY 334 -1 -
DMDILLTHP DPOB_XENLA 189 -1 -
DMDVLLTHP DPOB_HUMAN 189 -1 -
DMDVLLTHP DPOB_RAT 189 -1 -
DVDMVLSPS YA26_SCHPO 355 -1 -
DIDLLFFKP DPO4_YEAST 366 -1 -

Motif 4 width=10
Element Seqn Id St Int Rpt
RVDLVMCPYD TDT_MOUSE 432 80 -
RVDLVMCPYE TDT_BOVIN 442 79 -
RVDLVVCPYD TDT_MONDO 440 86 -
RVDLVLCPYE TDT_HUMAN 431 79 -
RVDLVITPFE TDT_CHICK 428 76 -
RVDLVFCPFE TDT_AMBME 429 84 -
RLDLVITPYE TDT_XENLA 429 81 -
RVDLVAPPVD TDT_ONCMY 424 81 -
RIDIRLIPKD DPOB_XENLA 252 54 -
RIDIRLIPKD DPOB_HUMAN 253 55 -
RIDIRLIPKD DPOB_RAT 253 55 -
RVDIIVVPPA YA26_SCHPO 417 53 -
RLDFFCCKWD DPO4_YEAST 499 124 -

Motif 5 width=14
Element Seqn Id St Int Rpt
LGWTGSRQFERDLR TDT_MOUSE 447 5 -
LGWTGSRQFERDIR TDT_BOVIN 458 6 -
LGWSGSRQFERDLR TDT_MONDO 456 6 -
LGWTGSRFERDLRR TDT_HUMAN 447 6 -
LGWTGSRQFGRDLR TDT_CHICK 444 6 -
LGWTGSRQFERDLR TDT_AMBME 445 6 -
LGWTGSRQFERDLR TDT_XENLA 445 6 -
LGWTGSRFGRDLRT TDT_ONCMY 440 6 -
LYFTGSDIFNKNMR DPOB_XENLA 268 6 -
LYFTGSDIFNKNMR DPOB_HUMAN 269 6 -
LYFTGSDIFNKNMR DPOB_RAT 269 6 -
LGWSGGIFFLRDLK YA26_SCHPO 433 6 -
IHYTGSKEYNRWIR DPO4_YEAST 515 6 -

Motif 6 width=19
Element Seqn Id St Int Rpt
SEEEIFAHLGLDYIEPWER TDT_MOUSE 509 48 -
SEEEIFAHLGLDYIEPWER TDT_BOVIN 500 28 -
SEEEIFAHLGLEYIQPSER TDT_MONDO 498 28 -
SEEEIFAHLGLDYIEPWER TDT_HUMAN 488 27 -
SEEEIFAHLGLDYVEPWER TDT_CHICK 486 28 -
SGEEIFGHLGLEYIDPVER TDT_AMBME 487 28 -
NEEDIFKQLGLDYLEPWER TDT_XENLA 487 28 -
TEEDIFTHLGLEYVEPWQR TDT_ONCMY 481 27 -
SEKDIFDYIQWKYREPKDR DPOB_XENLA 313 31 -
SEKDIFDYIQWKYREPKDR DPOB_HUMAN 314 31 -
SEQDIFDYIQWRYREPKDR DPOB_RAT 314 31 -
AEKDIFRYFSLEYIEPKFR YA26_SCHPO 485 38 -
NERRIFELLNLKYAEPEHR DPO4_YEAST 554 25 -